Starting phenix.real_space_refine on Mon Mar 25 04:02:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj6_20089/03_2024/6oj6_20089.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj6_20089/03_2024/6oj6_20089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj6_20089/03_2024/6oj6_20089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj6_20089/03_2024/6oj6_20089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj6_20089/03_2024/6oj6_20089.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oj6_20089/03_2024/6oj6_20089.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.025 sd= 0.677 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 22 5.49 5 S 398 5.16 5 C 47141 2.51 5 N 12740 2.21 5 O 13964 1.98 5 H 74396 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 822": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148661 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 12787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 12787 Classifications: {'peptide': 781} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 751} Chain: "B" Number of atoms: 12787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 12787 Classifications: {'peptide': 781} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 752} Chain: "C" Number of atoms: 12772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 12772 Classifications: {'peptide': 780} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 751} Chain: "D" Number of atoms: 13574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 13574 Classifications: {'peptide': 827} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 796} Chain: "E" Number of atoms: 12584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 12584 Classifications: {'peptide': 767} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 736} Chain breaks: 1 Chain: "F" Number of atoms: 13151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 13151 Classifications: {'peptide': 802} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 771} Chain: "G" Number of atoms: 13151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 13151 Classifications: {'peptide': 802} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 771} Chain: "H" Number of atoms: 13151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 13151 Classifications: {'peptide': 802} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 771} Chain: "I" Number of atoms: 13114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 13114 Classifications: {'peptide': 800} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 769} Chain: "J" Number of atoms: 13391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 13391 Classifications: {'peptide': 816} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 785} Chain: "P" Number of atoms: 17429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 17429 Classifications: {'peptide': 1072} Link IDs: {'PTRANS': 33, 'TRANS': 1038} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 458 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "U" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 312 Classifications: {'RNA': 10} Modifications used: {'3*END': 1, '5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna3p': 9} Time building chain proxies: 45.99, per 1000 atoms: 0.31 Number of scatterers: 148661 At special positions: 0 Unit cell: (285.36, 325.95, 194.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 398 16.00 P 22 15.00 O 13964 8.00 N 12740 7.00 C 47141 6.00 H 74396 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 89.15 Conformation dependent library (CDL) restraints added in 10.4 seconds 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17624 Finding SS restraints... Secondary structure from input PDB file: 381 helices and 111 sheets defined 50.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.62 Creating SS restraints... Processing helix chain 'A' and resid 107 through 117 removed outlier: 3.512A pdb=" N ILE A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.904A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 274 through 280 removed outlier: 3.973A pdb=" N PHE A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 288 Processing helix chain 'A' and resid 321 through 338 removed outlier: 3.641A pdb=" N THR A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 360 Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.617A pdb=" N ALA A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.758A pdb=" N LEU A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 442 removed outlier: 3.614A pdb=" N LEU A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.708A pdb=" N GLY A 448 " --> pdb=" O PRO A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 468 removed outlier: 4.096A pdb=" N GLN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.588A pdb=" N GLN A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 545 removed outlier: 3.789A pdb=" N LYS A 533 " --> pdb=" O PRO A 529 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 566 Processing helix chain 'A' and resid 585 through 594 removed outlier: 3.759A pdb=" N LEU A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 638 Processing helix chain 'A' and resid 646 through 656 removed outlier: 3.538A pdb=" N LEU A 656 " --> pdb=" O PHE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.524A pdb=" N VAL A 664 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 677 removed outlier: 3.893A pdb=" N MET A 669 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 694 removed outlier: 3.806A pdb=" N MET A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 742 through 748 Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 778 through 783 Processing helix chain 'A' and resid 785 through 789 removed outlier: 3.925A pdb=" N VAL A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 Processing helix chain 'A' and resid 810 through 814 removed outlier: 4.413A pdb=" N ASN A 814 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 823 removed outlier: 4.051A pdb=" N ASP A 823 " --> pdb=" O VAL A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 removed outlier: 3.522A pdb=" N ALA A 875 " --> pdb=" O PRO A 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 118 removed outlier: 4.411A pdb=" N LEU B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 184 removed outlier: 3.874A pdb=" N VAL B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.801A pdb=" N GLN B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 235 removed outlier: 3.873A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 273 through 281 Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 321 through 338 removed outlier: 3.748A pdb=" N THR B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 361 Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.661A pdb=" N THR B 375 " --> pdb=" O GLN B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 3.791A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 421 removed outlier: 3.936A pdb=" N TRP B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 427 through 442 Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'B' and resid 461 through 468 removed outlier: 3.688A pdb=" N ILE B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 468 " --> pdb=" O GLN B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 508 through 523 removed outlier: 3.663A pdb=" N GLN B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 545 removed outlier: 3.698A pdb=" N LYS B 533 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 567 removed outlier: 3.755A pdb=" N CYS B 567 " --> pdb=" O THR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 594 removed outlier: 3.738A pdb=" N LEU B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 637 removed outlier: 3.569A pdb=" N ASN B 614 " --> pdb=" O TYR B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 655 Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 665 through 678 removed outlier: 4.016A pdb=" N MET B 669 " --> pdb=" O PRO B 665 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 701 removed outlier: 4.950A pdb=" N GLU B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLN B 698 " --> pdb=" O MET B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 748 Processing helix chain 'B' and resid 750 through 760 removed outlier: 4.761A pdb=" N ILE B 754 " --> pdb=" O ASP B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 784 Processing helix chain 'B' and resid 785 through 790 removed outlier: 3.990A pdb=" N VAL B 789 " --> pdb=" O ASP B 786 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE B 790 " --> pdb=" O ALA B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 796 removed outlier: 3.789A pdb=" N LYS B 795 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 814 removed outlier: 3.627A pdb=" N SER B 813 " --> pdb=" O ASN B 810 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN B 814 " --> pdb=" O SER B 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 814' Processing helix chain 'B' and resid 815 through 822 removed outlier: 4.217A pdb=" N VAL B 819 " --> pdb=" O ASP B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 875 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 165 through 184 Processing helix chain 'C' and resid 189 through 194 removed outlier: 4.456A pdb=" N MET C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.908A pdb=" N ARG C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 Processing helix chain 'C' and resid 273 through 280 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.640A pdb=" N ARG C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 337 Processing helix chain 'C' and resid 348 through 361 Processing helix chain 'C' and resid 371 through 375 Processing helix chain 'C' and resid 381 through 396 removed outlier: 3.868A pdb=" N ILE C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 421 removed outlier: 3.502A pdb=" N LEU C 411 " --> pdb=" O ASN C 407 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TRP C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 426 Processing helix chain 'C' and resid 427 through 442 removed outlier: 3.547A pdb=" N LEU C 431 " --> pdb=" O ILE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 448 Processing helix chain 'C' and resid 461 through 468 removed outlier: 3.588A pdb=" N ILE C 465 " --> pdb=" O THR C 461 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN C 468 " --> pdb=" O GLN C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 508 through 522 removed outlier: 3.617A pdb=" N GLN C 512 " --> pdb=" O HIS C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 545 removed outlier: 3.627A pdb=" N LYS C 533 " --> pdb=" O PRO C 529 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 566 Processing helix chain 'C' and resid 585 through 594 Processing helix chain 'C' and resid 603 through 638 Processing helix chain 'C' and resid 646 through 655 removed outlier: 3.767A pdb=" N ARG C 655 " --> pdb=" O ASP C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 679 removed outlier: 3.880A pdb=" N TYR C 670 " --> pdb=" O ASP C 666 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU C 678 " --> pdb=" O ASP C 674 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 679 " --> pdb=" O ARG C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 702 removed outlier: 3.514A pdb=" N MET C 694 " --> pdb=" O ASN C 690 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 695 " --> pdb=" O LEU C 691 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU C 697 " --> pdb=" O LEU C 693 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLN C 698 " --> pdb=" O MET C 694 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA C 702 " --> pdb=" O GLN C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 748 Processing helix chain 'C' and resid 751 through 760 Processing helix chain 'C' and resid 777 through 783 removed outlier: 3.570A pdb=" N LEU C 781 " --> pdb=" O SER C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 796 removed outlier: 4.174A pdb=" N VAL C 794 " --> pdb=" O PHE C 790 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 795 " --> pdb=" O ALA C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 4.048A pdb=" N ALA C 820 " --> pdb=" O PHE C 816 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP C 823 " --> pdb=" O VAL C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 875 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 73 through 99 Processing helix chain 'D' and resid 108 through 117 removed outlier: 4.142A pdb=" N LEU D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 184 Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 208 through 220 Processing helix chain 'D' and resid 225 through 234 removed outlier: 3.844A pdb=" N ARG D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 274 through 280 removed outlier: 3.875A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 321 through 340 removed outlier: 3.826A pdb=" N SER D 338 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 360 removed outlier: 3.576A pdb=" N GLN D 352 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 375 removed outlier: 3.895A pdb=" N THR D 371 " --> pdb=" O GLN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 396 removed outlier: 3.768A pdb=" N ILE D 390 " --> pdb=" O PHE D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 421 removed outlier: 3.955A pdb=" N LEU D 411 " --> pdb=" O ASN D 407 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 443 removed outlier: 3.684A pdb=" N LEU D 431 " --> pdb=" O ILE D 427 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 443 " --> pdb=" O ILE D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 447 Processing helix chain 'D' and resid 461 through 467 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 508 through 523 removed outlier: 3.638A pdb=" N GLN D 512 " --> pdb=" O HIS D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 545 removed outlier: 3.531A pdb=" N LYS D 533 " --> pdb=" O PRO D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 566 Processing helix chain 'D' and resid 585 through 592 Processing helix chain 'D' and resid 603 through 638 removed outlier: 3.658A pdb=" N ASN D 614 " --> pdb=" O TYR D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 656 Processing helix chain 'D' and resid 660 through 664 removed outlier: 3.873A pdb=" N ARG D 663 " --> pdb=" O ASP D 660 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 664 " --> pdb=" O ILE D 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 660 through 664' Processing helix chain 'D' and resid 667 through 678 removed outlier: 4.164A pdb=" N LEU D 678 " --> pdb=" O ASP D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 701 removed outlier: 3.717A pdb=" N MET D 694 " --> pdb=" O ASN D 690 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU D 697 " --> pdb=" O LEU D 693 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLN D 698 " --> pdb=" O MET D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 748 Processing helix chain 'D' and resid 751 through 760 Processing helix chain 'D' and resid 778 through 783 Processing helix chain 'D' and resid 784 through 788 removed outlier: 3.903A pdb=" N ALA D 787 " --> pdb=" O LYS D 784 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 788 " --> pdb=" O LEU D 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 784 through 788' Processing helix chain 'D' and resid 791 through 796 removed outlier: 3.570A pdb=" N LYS D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 822 removed outlier: 3.522A pdb=" N ALA D 820 " --> pdb=" O PHE D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 845 Processing helix chain 'D' and resid 871 through 875 Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 165 through 184 Processing helix chain 'E' and resid 189 through 194 removed outlier: 4.333A pdb=" N MET E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 225 through 235 removed outlier: 3.884A pdb=" N ARG E 229 " --> pdb=" O GLU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 266 Processing helix chain 'E' and resid 273 through 280 Processing helix chain 'E' and resid 282 through 287 removed outlier: 3.516A pdb=" N ARG E 286 " --> pdb=" O PRO E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 340 removed outlier: 3.812A pdb=" N LEU E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 396 removed outlier: 3.721A pdb=" N ILE E 390 " --> pdb=" O PHE E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 421 removed outlier: 4.091A pdb=" N LEU E 411 " --> pdb=" O ASN E 407 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TRP E 416 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 443 removed outlier: 3.709A pdb=" N LEU E 431 " --> pdb=" O ILE E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 470 removed outlier: 3.649A pdb=" N ILE E 465 " --> pdb=" O THR E 461 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN E 468 " --> pdb=" O GLN E 464 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE E 470 " --> pdb=" O ALA E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 508 through 522 removed outlier: 3.601A pdb=" N GLN E 512 " --> pdb=" O HIS E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 545 Processing helix chain 'E' and resid 546 through 566 Processing helix chain 'E' and resid 585 through 594 Processing helix chain 'E' and resid 603 through 637 Processing helix chain 'E' and resid 646 through 656 removed outlier: 3.529A pdb=" N LEU E 656 " --> pdb=" O PHE E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 664 removed outlier: 3.558A pdb=" N VAL E 664 " --> pdb=" O ILE E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 678 removed outlier: 3.820A pdb=" N MET E 669 " --> pdb=" O PRO E 665 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU E 678 " --> pdb=" O ASP E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 702 removed outlier: 4.832A pdb=" N GLU E 697 " --> pdb=" O LEU E 693 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN E 698 " --> pdb=" O MET E 694 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 702 " --> pdb=" O GLN E 698 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 748 Processing helix chain 'E' and resid 751 through 760 Processing helix chain 'E' and resid 778 through 783 removed outlier: 3.772A pdb=" N VAL E 782 " --> pdb=" O VAL E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 790 removed outlier: 3.733A pdb=" N PHE E 790 " --> pdb=" O ALA E 787 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 787 through 790' Processing helix chain 'E' and resid 791 through 796 removed outlier: 4.194A pdb=" N LYS E 795 " --> pdb=" O ALA E 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 822 Processing helix chain 'E' and resid 860 through 863 Processing helix chain 'E' and resid 871 through 875 removed outlier: 3.669A pdb=" N ALA E 875 " --> pdb=" O PRO E 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 100 Processing helix chain 'F' and resid 109 through 118 removed outlier: 4.017A pdb=" N LYS F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 184 removed outlier: 3.898A pdb=" N GLN F 179 " --> pdb=" O ASN F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 221 removed outlier: 3.625A pdb=" N ALA F 212 " --> pdb=" O ASP F 208 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE F 214 " --> pdb=" O GLU F 210 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 234 Processing helix chain 'F' and resid 253 through 266 Processing helix chain 'F' and resid 273 through 279 removed outlier: 3.732A pdb=" N ILE F 277 " --> pdb=" O ASN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 removed outlier: 3.657A pdb=" N ARG F 286 " --> pdb=" O PRO F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 338 removed outlier: 3.546A pdb=" N SER F 338 " --> pdb=" O ILE F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 361 removed outlier: 3.540A pdb=" N GLN F 352 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN F 358 " --> pdb=" O GLN F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 365 removed outlier: 3.930A pdb=" N LEU F 365 " --> pdb=" O LEU F 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 362 through 365' Processing helix chain 'F' and resid 381 through 396 removed outlier: 3.779A pdb=" N ILE F 390 " --> pdb=" O PHE F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 421 removed outlier: 3.888A pdb=" N LEU F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP F 416 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 417 " --> pdb=" O SER F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 440 Processing helix chain 'F' and resid 442 through 448 Processing helix chain 'F' and resid 461 through 470 removed outlier: 3.747A pdb=" N GLN F 468 " --> pdb=" O GLN F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 508 through 523 removed outlier: 3.849A pdb=" N GLN F 512 " --> pdb=" O HIS F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 545 removed outlier: 3.669A pdb=" N LEU F 541 " --> pdb=" O GLN F 537 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU F 543 " --> pdb=" O GLY F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 567 removed outlier: 3.997A pdb=" N CYS F 567 " --> pdb=" O THR F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 592 removed outlier: 3.811A pdb=" N LEU F 591 " --> pdb=" O SER F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 638 removed outlier: 3.698A pdb=" N ASP F 627 " --> pdb=" O GLU F 623 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 656 removed outlier: 3.774A pdb=" N ASP F 651 " --> pdb=" O SER F 647 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 656 " --> pdb=" O PHE F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 678 Processing helix chain 'F' and resid 682 through 694 removed outlier: 3.788A pdb=" N PHE F 689 " --> pdb=" O ARG F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 695 through 700 Processing helix chain 'F' and resid 742 through 748 removed outlier: 3.974A pdb=" N ARG F 747 " --> pdb=" O GLU F 743 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR F 748 " --> pdb=" O GLU F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 759 removed outlier: 4.820A pdb=" N MET F 757 " --> pdb=" O GLN F 753 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 784 Processing helix chain 'F' and resid 785 through 789 removed outlier: 4.136A pdb=" N VAL F 789 " --> pdb=" O ASP F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 821 Processing helix chain 'G' and resid 87 through 100 removed outlier: 3.848A pdb=" N LEU G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 116 removed outlier: 4.058A pdb=" N LEU G 112 " --> pdb=" O LYS G 108 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 183 removed outlier: 3.945A pdb=" N GLN G 179 " --> pdb=" O ASN G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 221 removed outlier: 3.615A pdb=" N ALA G 212 " --> pdb=" O ASP G 208 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 235 Processing helix chain 'G' and resid 253 through 266 removed outlier: 3.894A pdb=" N LEU G 264 " --> pdb=" O ASN G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 281 Processing helix chain 'G' and resid 321 through 340 removed outlier: 3.674A pdb=" N SER G 338 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL G 339 " --> pdb=" O LEU G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 348 through 361 removed outlier: 3.811A pdb=" N GLN G 352 " --> pdb=" O SER G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 365 removed outlier: 3.704A pdb=" N LEU G 365 " --> pdb=" O LEU G 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 362 through 365' Processing helix chain 'G' and resid 371 through 375 Processing helix chain 'G' and resid 381 through 396 removed outlier: 3.765A pdb=" N ILE G 390 " --> pdb=" O PHE G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 407 through 421 removed outlier: 3.598A pdb=" N LEU G 411 " --> pdb=" O ASN G 407 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TRP G 416 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 422 through 426 Processing helix chain 'G' and resid 427 through 442 Processing helix chain 'G' and resid 442 through 448 Processing helix chain 'G' and resid 461 through 470 removed outlier: 4.137A pdb=" N GLN G 468 " --> pdb=" O GLN G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 484 removed outlier: 4.073A pdb=" N TRP G 478 " --> pdb=" O GLN G 474 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN G 484 " --> pdb=" O HIS G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 522 removed outlier: 3.805A pdb=" N GLN G 512 " --> pdb=" O HIS G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 540 removed outlier: 3.695A pdb=" N SER G 535 " --> pdb=" O ASP G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 545 Processing helix chain 'G' and resid 546 through 566 removed outlier: 3.713A pdb=" N ALA G 566 " --> pdb=" O GLU G 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 594 Processing helix chain 'G' and resid 603 through 639 Processing helix chain 'G' and resid 645 through 655 Processing helix chain 'G' and resid 665 through 677 removed outlier: 3.657A pdb=" N MET G 669 " --> pdb=" O PRO G 665 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 694 removed outlier: 3.756A pdb=" N PHE G 689 " --> pdb=" O ARG G 685 " (cutoff:3.500A) Processing helix chain 'G' and resid 695 through 701 removed outlier: 3.552A pdb=" N ARG G 701 " --> pdb=" O GLU G 697 " (cutoff:3.500A) Processing helix chain 'G' and resid 742 through 746 Processing helix chain 'G' and resid 751 through 761 removed outlier: 4.649A pdb=" N MET G 757 " --> pdb=" O GLN G 753 " (cutoff:3.500A) Processing helix chain 'G' and resid 778 through 783 Processing helix chain 'G' and resid 784 through 789 removed outlier: 4.081A pdb=" N VAL G 789 " --> pdb=" O ASP G 786 " (cutoff:3.500A) Processing helix chain 'G' and resid 790 through 796 removed outlier: 3.721A pdb=" N VAL G 794 " --> pdb=" O PHE G 790 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU G 796 " --> pdb=" O GLN G 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 822 removed outlier: 3.548A pdb=" N ALA G 820 " --> pdb=" O PHE G 816 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR G 822 " --> pdb=" O LEU G 818 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 100 Processing helix chain 'H' and resid 109 through 118 removed outlier: 3.962A pdb=" N LYS H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 183 removed outlier: 3.838A pdb=" N GLN H 179 " --> pdb=" O ASN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 220 removed outlier: 4.137A pdb=" N ILE H 214 " --> pdb=" O GLU H 210 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN H 220 " --> pdb=" O ASP H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 235 removed outlier: 3.502A pdb=" N ARG H 229 " --> pdb=" O GLU H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 266 Processing helix chain 'H' and resid 273 through 281 removed outlier: 3.703A pdb=" N ILE H 277 " --> pdb=" O ASN H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 287 removed outlier: 3.653A pdb=" N ARG H 286 " --> pdb=" O PRO H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 338 removed outlier: 3.789A pdb=" N SER H 338 " --> pdb=" O ILE H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 361 Processing helix chain 'H' and resid 381 through 396 removed outlier: 3.616A pdb=" N ILE H 390 " --> pdb=" O PHE H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 421 removed outlier: 3.755A pdb=" N LEU H 411 " --> pdb=" O ASN H 407 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP H 416 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 422 through 426 removed outlier: 3.545A pdb=" N MET H 425 " --> pdb=" O PRO H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 427 through 442 Processing helix chain 'H' and resid 442 through 448 Processing helix chain 'H' and resid 461 through 470 removed outlier: 3.884A pdb=" N GLN H 468 " --> pdb=" O GLN H 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 removed outlier: 4.498A pdb=" N TRP H 478 " --> pdb=" O GLN H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 523 removed outlier: 3.834A pdb=" N GLN H 512 " --> pdb=" O HIS H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 546 removed outlier: 3.793A pdb=" N SER H 535 " --> pdb=" O ASP H 531 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU H 543 " --> pdb=" O GLY H 539 " (cutoff:3.500A) Processing helix chain 'H' and resid 546 through 567 removed outlier: 3.927A pdb=" N CYS H 567 " --> pdb=" O THR H 563 " (cutoff:3.500A) Processing helix chain 'H' and resid 584 through 594 Processing helix chain 'H' and resid 603 through 638 Processing helix chain 'H' and resid 645 through 656 removed outlier: 3.641A pdb=" N ASP H 651 " --> pdb=" O SER H 647 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU H 656 " --> pdb=" O PHE H 652 " (cutoff:3.500A) Processing helix chain 'H' and resid 666 through 678 removed outlier: 3.625A pdb=" N LEU H 678 " --> pdb=" O ASP H 674 " (cutoff:3.500A) Processing helix chain 'H' and resid 682 through 694 removed outlier: 3.610A pdb=" N PHE H 689 " --> pdb=" O ARG H 685 " (cutoff:3.500A) Processing helix chain 'H' and resid 695 through 700 Processing helix chain 'H' and resid 742 through 748 removed outlier: 3.701A pdb=" N ARG H 747 " --> pdb=" O GLU H 743 " (cutoff:3.500A) Processing helix chain 'H' and resid 751 through 759 removed outlier: 4.188A pdb=" N MET H 757 " --> pdb=" O GLN H 753 " (cutoff:3.500A) Processing helix chain 'H' and resid 778 through 783 Processing helix chain 'H' and resid 790 through 796 removed outlier: 3.884A pdb=" N VAL H 794 " --> pdb=" O PHE H 790 " (cutoff:3.500A) Processing helix chain 'H' and resid 815 through 819 Processing helix chain 'H' and resid 861 through 865 Processing helix chain 'H' and resid 871 through 875 removed outlier: 3.810A pdb=" N ALA H 875 " --> pdb=" O PRO H 872 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 100 removed outlier: 4.130A pdb=" N TYR I 95 " --> pdb=" O LYS I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 117 removed outlier: 3.848A pdb=" N LYS I 113 " --> pdb=" O GLU I 109 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU I 116 " --> pdb=" O LEU I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 183 removed outlier: 3.766A pdb=" N GLN I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 193 Processing helix chain 'I' and resid 208 through 221 removed outlier: 3.714A pdb=" N ALA I 212 " --> pdb=" O ASP I 208 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE I 214 " --> pdb=" O GLU I 210 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA I 217 " --> pdb=" O ALA I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 233 removed outlier: 3.589A pdb=" N ARG I 229 " --> pdb=" O GLU I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 266 removed outlier: 3.755A pdb=" N LEU I 264 " --> pdb=" O ASN I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 281 Processing helix chain 'I' and resid 282 through 287 removed outlier: 3.736A pdb=" N ARG I 286 " --> pdb=" O PRO I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 340 removed outlier: 3.684A pdb=" N SER I 338 " --> pdb=" O ILE I 334 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL I 339 " --> pdb=" O LEU I 335 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 348 through 361 removed outlier: 3.888A pdb=" N GLN I 352 " --> pdb=" O SER I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 365 removed outlier: 3.550A pdb=" N LEU I 365 " --> pdb=" O LEU I 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 362 through 365' Processing helix chain 'I' and resid 381 through 396 removed outlier: 3.690A pdb=" N ILE I 390 " --> pdb=" O PHE I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 421 removed outlier: 3.709A pdb=" N LEU I 411 " --> pdb=" O ASN I 407 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP I 416 " --> pdb=" O ILE I 412 " (cutoff:3.500A) Processing helix chain 'I' and resid 422 through 426 Processing helix chain 'I' and resid 427 through 440 Processing helix chain 'I' and resid 442 through 448 Processing helix chain 'I' and resid 461 through 470 removed outlier: 4.348A pdb=" N GLN I 468 " --> pdb=" O GLN I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 484 removed outlier: 3.534A pdb=" N TRP I 478 " --> pdb=" O GLN I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 522 removed outlier: 4.223A pdb=" N GLN I 512 " --> pdb=" O HIS I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 545 removed outlier: 3.721A pdb=" N SER I 535 " --> pdb=" O ASP I 531 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU I 543 " --> pdb=" O GLY I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 546 through 566 Processing helix chain 'I' and resid 584 through 594 removed outlier: 3.597A pdb=" N VAL I 588 " --> pdb=" O GLN I 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 603 through 637 Processing helix chain 'I' and resid 645 through 656 removed outlier: 3.751A pdb=" N ASP I 651 " --> pdb=" O SER I 647 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU I 656 " --> pdb=" O PHE I 652 " (cutoff:3.500A) Processing helix chain 'I' and resid 660 through 664 removed outlier: 3.645A pdb=" N ARG I 663 " --> pdb=" O ASP I 660 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL I 664 " --> pdb=" O ILE I 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 660 through 664' Processing helix chain 'I' and resid 666 through 678 removed outlier: 4.059A pdb=" N LEU I 678 " --> pdb=" O ASP I 674 " (cutoff:3.500A) Processing helix chain 'I' and resid 682 through 700 removed outlier: 3.692A pdb=" N PHE I 689 " --> pdb=" O ARG I 685 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU I 697 " --> pdb=" O LEU I 693 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLN I 698 " --> pdb=" O MET I 694 " (cutoff:3.500A) Processing helix chain 'I' and resid 751 through 760 removed outlier: 4.455A pdb=" N MET I 757 " --> pdb=" O GLN I 753 " (cutoff:3.500A) Processing helix chain 'I' and resid 778 through 783 Processing helix chain 'I' and resid 784 through 789 removed outlier: 3.606A pdb=" N ALA I 787 " --> pdb=" O LYS I 784 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL I 789 " --> pdb=" O ASP I 786 " (cutoff:3.500A) Processing helix chain 'I' and resid 790 through 796 removed outlier: 4.054A pdb=" N VAL I 794 " --> pdb=" O PHE I 790 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS I 795 " --> pdb=" O ALA I 791 " (cutoff:3.500A) Processing helix chain 'I' and resid 815 through 819 Processing helix chain 'I' and resid 841 through 845 Processing helix chain 'J' and resid 73 through 86 removed outlier: 3.853A pdb=" N LEU J 83 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS J 86 " --> pdb=" O VAL J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 100 removed outlier: 3.677A pdb=" N VAL J 93 " --> pdb=" O HIS J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 117 removed outlier: 4.031A pdb=" N LEU J 112 " --> pdb=" O LYS J 108 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS J 113 " --> pdb=" O GLU J 109 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS J 114 " --> pdb=" O SER J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 183 removed outlier: 3.960A pdb=" N GLN J 179 " --> pdb=" O ASN J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 193 removed outlier: 3.520A pdb=" N ASP J 192 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 221 removed outlier: 3.690A pdb=" N ALA J 212 " --> pdb=" O ASP J 208 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA J 217 " --> pdb=" O ALA J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 235 removed outlier: 3.696A pdb=" N ARG J 229 " --> pdb=" O GLU J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 266 Processing helix chain 'J' and resid 273 through 281 removed outlier: 3.627A pdb=" N ILE J 277 " --> pdb=" O ASN J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 321 through 340 Processing helix chain 'J' and resid 348 through 361 removed outlier: 3.903A pdb=" N GLN J 352 " --> pdb=" O SER J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 365 removed outlier: 3.678A pdb=" N LEU J 365 " --> pdb=" O LEU J 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 362 through 365' Processing helix chain 'J' and resid 381 through 396 removed outlier: 3.782A pdb=" N ILE J 390 " --> pdb=" O PHE J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 421 removed outlier: 3.822A pdb=" N LEU J 411 " --> pdb=" O ASN J 407 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TRP J 416 " --> pdb=" O ILE J 412 " (cutoff:3.500A) Processing helix chain 'J' and resid 427 through 442 Processing helix chain 'J' and resid 442 through 448 Processing helix chain 'J' and resid 461 through 470 removed outlier: 4.196A pdb=" N GLN J 468 " --> pdb=" O GLN J 464 " (cutoff:3.500A) Processing helix chain 'J' and resid 472 through 484 Processing helix chain 'J' and resid 508 through 523 removed outlier: 3.871A pdb=" N GLN J 512 " --> pdb=" O HIS J 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 530 through 545 removed outlier: 3.875A pdb=" N LEU J 543 " --> pdb=" O GLY J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 546 through 566 Processing helix chain 'J' and resid 584 through 592 removed outlier: 3.648A pdb=" N VAL J 588 " --> pdb=" O GLN J 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 603 through 638 Processing helix chain 'J' and resid 645 through 653 removed outlier: 3.601A pdb=" N VAL J 649 " --> pdb=" O MET J 645 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP J 651 " --> pdb=" O SER J 647 " (cutoff:3.500A) Processing helix chain 'J' and resid 666 through 678 removed outlier: 3.570A pdb=" N LEU J 678 " --> pdb=" O ASP J 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 682 through 702 removed outlier: 3.581A pdb=" N ASN J 695 " --> pdb=" O LEU J 691 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU J 697 " --> pdb=" O LEU J 693 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN J 698 " --> pdb=" O MET J 694 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA J 702 " --> pdb=" O GLN J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 742 through 748 removed outlier: 3.822A pdb=" N ARG J 747 " --> pdb=" O GLU J 743 " (cutoff:3.500A) Processing helix chain 'J' and resid 751 through 760 removed outlier: 3.762A pdb=" N MET J 757 " --> pdb=" O GLN J 753 " (cutoff:3.500A) Processing helix chain 'J' and resid 778 through 783 Processing helix chain 'J' and resid 785 through 789 removed outlier: 3.786A pdb=" N VAL J 789 " --> pdb=" O ASP J 786 " (cutoff:3.500A) Processing helix chain 'J' and resid 790 through 795 removed outlier: 4.428A pdb=" N VAL J 794 " --> pdb=" O PHE J 790 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 790 through 795' Processing helix chain 'J' and resid 816 through 821 removed outlier: 3.761A pdb=" N ALA J 820 " --> pdb=" O PHE J 816 " (cutoff:3.500A) Processing helix chain 'J' and resid 871 through 875 removed outlier: 3.617A pdb=" N ALA J 875 " --> pdb=" O PRO J 872 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 17 removed outlier: 3.516A pdb=" N TYR P 16 " --> pdb=" O LEU P 12 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN P 17 " --> pdb=" O SER P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 50 Processing helix chain 'P' and resid 57 through 62 removed outlier: 4.304A pdb=" N GLU P 61 " --> pdb=" O LYS P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 69 removed outlier: 3.651A pdb=" N ILE P 66 " --> pdb=" O TYR P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 90 removed outlier: 3.665A pdb=" N ARG P 87 " --> pdb=" O ASN P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 94 removed outlier: 4.099A pdb=" N LYS P 94 " --> pdb=" O LYS P 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 91 through 94' Processing helix chain 'P' and resid 114 through 118 Processing helix chain 'P' and resid 121 through 125 Processing helix chain 'P' and resid 137 through 152 Processing helix chain 'P' and resid 157 through 179 Processing helix chain 'P' and resid 192 through 197 removed outlier: 3.616A pdb=" N MET P 196 " --> pdb=" O GLU P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 215 removed outlier: 3.593A pdb=" N TRP P 206 " --> pdb=" O TYR P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 231 removed outlier: 3.622A pdb=" N VAL P 231 " --> pdb=" O ARG P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 240 through 245 Processing helix chain 'P' and resid 247 through 252 Processing helix chain 'P' and resid 253 through 255 No H-bonds generated for 'chain 'P' and resid 253 through 255' Processing helix chain 'P' and resid 282 through 299 removed outlier: 3.717A pdb=" N ASP P 286 " --> pdb=" O ASP P 282 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY P 299 " --> pdb=" O MET P 295 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 311 removed outlier: 3.524A pdb=" N LYS P 305 " --> pdb=" O THR P 301 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU P 311 " --> pdb=" O ILE P 307 " (cutoff:3.500A) Processing helix chain 'P' and resid 319 through 329 removed outlier: 3.605A pdb=" N ALA P 323 " --> pdb=" O PHE P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 338 through 347 removed outlier: 3.955A pdb=" N GLN P 346 " --> pdb=" O ALA P 342 " (cutoff:3.500A) Processing helix chain 'P' and resid 357 through 382 removed outlier: 3.770A pdb=" N GLU P 362 " --> pdb=" O GLU P 358 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU P 377 " --> pdb=" O LYS P 373 " (cutoff:3.500A) Proline residue: P 378 - end of helix Processing helix chain 'P' and resid 383 through 388 Processing helix chain 'P' and resid 388 through 396 Processing helix chain 'P' and resid 419 through 430 removed outlier: 3.963A pdb=" N ALA P 429 " --> pdb=" O MET P 425 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN P 430 " --> pdb=" O ASP P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 467 through 485 removed outlier: 3.862A pdb=" N ILE P 471 " --> pdb=" O TYR P 467 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA P 475 " --> pdb=" O ILE P 471 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL P 476 " --> pdb=" O ALA P 472 " (cutoff:3.500A) Processing helix chain 'P' and resid 531 through 547 removed outlier: 3.912A pdb=" N ARG P 535 " --> pdb=" O THR P 531 " (cutoff:3.500A) Processing helix chain 'P' and resid 551 through 569 removed outlier: 3.608A pdb=" N ILE P 555 " --> pdb=" O ASP P 551 " (cutoff:3.500A) Processing helix chain 'P' and resid 595 through 616 removed outlier: 3.668A pdb=" N SER P 613 " --> pdb=" O LYS P 609 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG P 614 " --> pdb=" O THR P 610 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE P 615 " --> pdb=" O VAL P 611 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER P 616 " --> pdb=" O LEU P 612 " (cutoff:3.500A) Processing helix chain 'P' and resid 644 through 661 Processing helix chain 'P' and resid 705 through 724 removed outlier: 3.770A pdb=" N GLN P 709 " --> pdb=" O THR P 705 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA P 710 " --> pdb=" O GLN P 706 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA P 711 " --> pdb=" O TRP P 707 " (cutoff:3.500A) Processing helix chain 'P' and resid 728 through 741 Processing helix chain 'P' and resid 753 through 758 removed outlier: 3.549A pdb=" N LEU P 757 " --> pdb=" O SER P 753 " (cutoff:3.500A) Processing helix chain 'P' and resid 778 through 793 removed outlier: 3.871A pdb=" N VAL P 782 " --> pdb=" O THR P 778 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU P 791 " --> pdb=" O ALA P 787 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER P 793 " --> pdb=" O MET P 789 " (cutoff:3.500A) Processing helix chain 'P' and resid 796 through 804 Processing helix chain 'P' and resid 805 through 818 removed outlier: 3.990A pdb=" N LYS P 809 " --> pdb=" O SER P 805 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN P 818 " --> pdb=" O ARG P 814 " (cutoff:3.500A) Processing helix chain 'P' and resid 827 through 840 removed outlier: 3.602A pdb=" N ALA P 837 " --> pdb=" O LEU P 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS P 838 " --> pdb=" O THR P 834 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN P 840 " --> pdb=" O LYS P 836 " (cutoff:3.500A) Processing helix chain 'P' and resid 842 through 862 removed outlier: 3.785A pdb=" N MET P 860 " --> pdb=" O ALA P 856 " (cutoff:3.500A) Processing helix chain 'P' and resid 873 through 882 removed outlier: 3.958A pdb=" N ILE P 877 " --> pdb=" O THR P 873 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP P 880 " --> pdb=" O ASP P 876 " (cutoff:3.500A) Processing helix chain 'P' and resid 883 through 885 No H-bonds generated for 'chain 'P' and resid 883 through 885' Processing helix chain 'P' and resid 904 through 912 Processing helix chain 'P' and resid 930 through 938 removed outlier: 3.841A pdb=" N LYS P 936 " --> pdb=" O ARG P 932 " (cutoff:3.500A) Processing helix chain 'P' and resid 943 through 951 Processing helix chain 'P' and resid 954 through 965 removed outlier: 3.626A pdb=" N ILE P 958 " --> pdb=" O HIS P 954 " (cutoff:3.500A) Processing helix chain 'P' and resid 968 through 979 removed outlier: 4.015A pdb=" N ALA P 972 " --> pdb=" O PRO P 968 " (cutoff:3.500A) Processing helix chain 'P' and resid 980 through 995 Processing helix chain 'P' and resid 1011 through 1017 removed outlier: 3.864A pdb=" N LEU P1017 " --> pdb=" O ASP P1013 " (cutoff:3.500A) Processing helix chain 'P' and resid 1026 through 1049 removed outlier: 3.598A pdb=" N THR P1030 " --> pdb=" O ILE P1026 " (cutoff:3.500A) Processing helix chain 'P' and resid 1059 through 1071 removed outlier: 3.957A pdb=" N LYS P1068 " --> pdb=" O ILE P1064 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS P1069 " --> pdb=" O LYS P1065 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP P1071 " --> pdb=" O TRP P1067 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 141 removed outlier: 4.078A pdb=" N VAL A 140 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG A 150 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 240 Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 271 Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 294 Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 492 Processing sheet with id=AA7, first strand: chain 'A' and resid 730 through 731 removed outlier: 3.562A pdb=" N GLY A 709 " --> pdb=" O TYR A 833 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 709 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY A 768 " --> pdb=" O GLY A 709 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE A 711 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 766 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 740 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ALA A 769 " --> pdb=" O ILE A 740 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 717 through 718 Processing sheet with id=AA9, first strand: chain 'A' and resid 720 through 721 Processing sheet with id=AB1, first strand: chain 'A' and resid 773 through 774 removed outlier: 6.427A pdb=" N ILE A 773 " --> pdb=" O LEU A 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 133 through 141 removed outlier: 4.239A pdb=" N VAL B 140 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG B 150 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AB4, first strand: chain 'B' and resid 238 through 240 Processing sheet with id=AB5, first strand: chain 'B' and resid 270 through 271 removed outlier: 7.313A pdb=" N ARG B 304 " --> pdb=" O TYR B 858 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 291 through 294 Processing sheet with id=AB7, first strand: chain 'B' and resid 488 through 492 Processing sheet with id=AB8, first strand: chain 'B' and resid 730 through 731 removed outlier: 3.553A pdb=" N GLY B 709 " --> pdb=" O TYR B 833 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE B 740 " --> pdb=" O VAL B 767 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 717 through 718 Processing sheet with id=AC1, first strand: chain 'B' and resid 720 through 721 Processing sheet with id=AC2, first strand: chain 'B' and resid 773 through 774 removed outlier: 6.617A pdb=" N ILE B 773 " --> pdb=" O LEU B 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 133 through 141 removed outlier: 4.024A pdb=" N VAL C 140 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG C 150 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AC5, first strand: chain 'C' and resid 238 through 240 Processing sheet with id=AC6, first strand: chain 'C' and resid 270 through 271 Processing sheet with id=AC7, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AC8, first strand: chain 'C' and resid 399 through 402 Processing sheet with id=AC9, first strand: chain 'C' and resid 488 through 492 Processing sheet with id=AD1, first strand: chain 'C' and resid 706 through 707 Processing sheet with id=AD2, first strand: chain 'C' and resid 710 through 712 removed outlier: 6.309A pdb=" N ILE C 740 " --> pdb=" O VAL C 767 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AD4, first strand: chain 'C' and resid 720 through 721 Processing sheet with id=AD5, first strand: chain 'C' and resid 730 through 731 Processing sheet with id=AD6, first strand: chain 'C' and resid 773 through 775 removed outlier: 6.656A pdb=" N ILE C 773 " --> pdb=" O LEU C 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 133 through 141 removed outlier: 4.224A pdb=" N VAL D 140 " --> pdb=" O ARG D 150 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG D 150 " --> pdb=" O VAL D 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 195 through 196 Processing sheet with id=AD9, first strand: chain 'D' and resid 238 through 240 Processing sheet with id=AE1, first strand: chain 'D' and resid 270 through 271 removed outlier: 7.338A pdb=" N ARG D 304 " --> pdb=" O TYR D 858 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 291 through 295 Processing sheet with id=AE3, first strand: chain 'D' and resid 399 through 402 removed outlier: 3.551A pdb=" N ASP D 402 " --> pdb=" O LEU D 583 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 488 through 492 Processing sheet with id=AE5, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE6, first strand: chain 'D' and resid 710 through 712 removed outlier: 6.548A pdb=" N ILE D 740 " --> pdb=" O VAL D 767 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 717 through 718 Processing sheet with id=AE8, first strand: chain 'D' and resid 727 through 728 Processing sheet with id=AE9, first strand: chain 'D' and resid 730 through 731 Processing sheet with id=AF1, first strand: chain 'E' and resid 96 through 97 removed outlier: 3.571A pdb=" N LYS P 583 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL P 580 " --> pdb=" O ASP P 577 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 133 through 141 removed outlier: 4.463A pdb=" N VAL E 140 " --> pdb=" O ARG E 150 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG E 150 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 195 through 196 Processing sheet with id=AF4, first strand: chain 'E' and resid 238 through 240 Processing sheet with id=AF5, first strand: chain 'E' and resid 270 through 271 removed outlier: 6.745A pdb=" N ARG E 304 " --> pdb=" O TYR E 858 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 291 through 295 Processing sheet with id=AF7, first strand: chain 'E' and resid 400 through 402 removed outlier: 6.220A pdb=" N SER E 400 " --> pdb=" O LEU E 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'E' and resid 488 through 492 Processing sheet with id=AF9, first strand: chain 'E' and resid 706 through 712 removed outlier: 3.557A pdb=" N GLY E 709 " --> pdb=" O GLY E 768 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY E 768 " --> pdb=" O GLY E 709 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE E 711 " --> pdb=" O LEU E 766 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU E 766 " --> pdb=" O ILE E 711 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE E 740 " --> pdb=" O VAL E 767 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ALA E 769 " --> pdb=" O ILE E 740 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 720 through 721 Processing sheet with id=AG2, first strand: chain 'E' and resid 730 through 731 Processing sheet with id=AG3, first strand: chain 'E' and resid 773 through 774 removed outlier: 6.705A pdb=" N ILE E 773 " --> pdb=" O LEU E 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'F' and resid 133 through 138 Processing sheet with id=AG5, first strand: chain 'F' and resid 195 through 196 Processing sheet with id=AG6, first strand: chain 'F' and resid 238 through 240 Processing sheet with id=AG7, first strand: chain 'F' and resid 270 through 271 removed outlier: 3.552A pdb=" N GLU F 270 " --> pdb=" O TYR F 305 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR F 305 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 291 through 294 Processing sheet with id=AG9, first strand: chain 'F' and resid 488 through 492 Processing sheet with id=AH1, first strand: chain 'F' and resid 706 through 707 Processing sheet with id=AH2, first strand: chain 'F' and resid 710 through 712 removed outlier: 6.425A pdb=" N GLN F 738 " --> pdb=" O ALA F 765 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL F 767 " --> pdb=" O GLN F 738 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE F 740 " --> pdb=" O VAL F 767 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 717 through 718 Processing sheet with id=AH4, first strand: chain 'F' and resid 730 through 731 Processing sheet with id=AH5, first strand: chain 'F' and resid 773 through 774 removed outlier: 6.047A pdb=" N ILE F 773 " --> pdb=" O LEU F 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'G' and resid 133 through 141 removed outlier: 4.336A pdb=" N VAL G 140 " --> pdb=" O ARG G 150 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG G 150 " --> pdb=" O VAL G 140 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 195 through 196 Processing sheet with id=AH8, first strand: chain 'G' and resid 238 through 240 Processing sheet with id=AH9, first strand: chain 'G' and resid 270 through 271 Processing sheet with id=AI1, first strand: chain 'G' and resid 291 through 294 Processing sheet with id=AI2, first strand: chain 'G' and resid 488 through 492 Processing sheet with id=AI3, first strand: chain 'G' and resid 730 through 731 removed outlier: 3.649A pdb=" N LEU G 770 " --> pdb=" O ALA G 707 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY G 709 " --> pdb=" O GLY G 768 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY G 768 " --> pdb=" O GLY G 709 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE G 711 " --> pdb=" O LEU G 766 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU G 766 " --> pdb=" O ILE G 711 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE G 740 " --> pdb=" O VAL G 767 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ALA G 769 " --> pdb=" O ILE G 740 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 717 through 718 Processing sheet with id=AI5, first strand: chain 'G' and resid 720 through 721 Processing sheet with id=AI6, first strand: chain 'H' and resid 133 through 141 removed outlier: 4.217A pdb=" N VAL H 140 " --> pdb=" O ARG H 150 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG H 150 " --> pdb=" O VAL H 140 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 195 through 196 Processing sheet with id=AI8, first strand: chain 'H' and resid 238 through 240 Processing sheet with id=AI9, first strand: chain 'H' and resid 270 through 271 removed outlier: 3.574A pdb=" N TYR H 305 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'H' and resid 291 through 294 Processing sheet with id=AJ2, first strand: chain 'H' and resid 488 through 492 Processing sheet with id=AJ3, first strand: chain 'H' and resid 707 through 712 removed outlier: 6.457A pdb=" N GLY H 768 " --> pdb=" O GLY H 709 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE H 711 " --> pdb=" O LEU H 766 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU H 766 " --> pdb=" O ILE H 711 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'H' and resid 720 through 721 Processing sheet with id=AJ5, first strand: chain 'H' and resid 730 through 731 Processing sheet with id=AJ6, first strand: chain 'I' and resid 133 through 141 removed outlier: 4.512A pdb=" N VAL I 140 " --> pdb=" O ARG I 150 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG I 150 " --> pdb=" O VAL I 140 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'I' and resid 195 through 196 Processing sheet with id=AJ8, first strand: chain 'I' and resid 238 through 240 Processing sheet with id=AJ9, first strand: chain 'I' and resid 270 through 271 removed outlier: 3.529A pdb=" N TYR I 305 " --> pdb=" O GLU I 270 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG I 304 " --> pdb=" O TYR I 858 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'I' and resid 291 through 294 Processing sheet with id=AK2, first strand: chain 'I' and resid 488 through 492 Processing sheet with id=AK3, first strand: chain 'I' and resid 706 through 712 removed outlier: 4.504A pdb=" N ILE I 706 " --> pdb=" O LEU I 770 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU I 770 " --> pdb=" O ILE I 706 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN I 708 " --> pdb=" O GLY I 768 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY I 768 " --> pdb=" O GLN I 708 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE I 740 " --> pdb=" O VAL I 767 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ALA I 769 " --> pdb=" O ILE I 740 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'I' and resid 720 through 721 Processing sheet with id=AK5, first strand: chain 'I' and resid 730 through 731 Processing sheet with id=AK6, first strand: chain 'I' and resid 773 through 775 removed outlier: 6.192A pdb=" N ILE I 773 " --> pdb=" O LEU I 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK6 Processing sheet with id=AK7, first strand: chain 'J' and resid 133 through 138 removed outlier: 4.587A pdb=" N GLN J 838 " --> pdb=" O TRP J 155 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'J' and resid 195 through 196 Processing sheet with id=AK9, first strand: chain 'J' and resid 238 through 240 Processing sheet with id=AL1, first strand: chain 'J' and resid 270 through 271 removed outlier: 6.685A pdb=" N ARG J 304 " --> pdb=" O TYR J 858 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'J' and resid 291 through 295 Processing sheet with id=AL3, first strand: chain 'J' and resid 488 through 492 Processing sheet with id=AL4, first strand: chain 'J' and resid 730 through 731 removed outlier: 3.678A pdb=" N GLY J 709 " --> pdb=" O GLY J 768 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY J 768 " --> pdb=" O GLY J 709 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE J 711 " --> pdb=" O LEU J 766 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU J 766 " --> pdb=" O ILE J 711 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'J' and resid 720 through 721 removed outlier: 3.634A pdb=" N GLU J 720 " --> pdb=" O VAL J 728 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'J' and resid 773 through 774 removed outlier: 6.237A pdb=" N ILE J 773 " --> pdb=" O LEU J 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL6 Processing sheet with id=AL7, first strand: chain 'P' and resid 22 through 28 removed outlier: 6.820A pdb=" N VAL P 22 " --> pdb=" O SER P 76 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER P 76 " --> pdb=" O VAL P 22 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE P 24 " --> pdb=" O ILE P 74 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE P 74 " --> pdb=" O ILE P 24 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE P 26 " --> pdb=" O LEU P 72 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'P' and resid 257 through 260 removed outlier: 4.684A pdb=" N ASN P 258 " --> pdb=" O LYS P 274 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LYS P 274 " --> pdb=" O ASN P 258 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'P' and resid 449 through 452 Processing sheet with id=AM1, first strand: chain 'P' and resid 621 through 628 removed outlier: 5.479A pdb=" N THR P 623 " --> pdb=" O GLN P 638 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLN P 638 " --> pdb=" O THR P 623 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE P 625 " --> pdb=" O VAL P 636 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU P 669 " --> pdb=" O TYR P 518 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'P' and resid 680 through 682 removed outlier: 3.665A pdb=" N TYR P 681 " --> pdb=" O PHE P 688 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'P' and resid 888 through 889 removed outlier: 3.839A pdb=" N ASN P 888 " --> pdb=" O SER P1053 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ARG P1019 " --> pdb=" O ILE P1052 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU P1054 " --> pdb=" O ARG P1019 " (cutoff:3.500A) 3193 hydrogen bonds defined for protein. 9063 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 61.83 Time building geometry restraints manager: 94.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 74340 1.03 - 1.23: 212 1.23 - 1.42: 31345 1.42 - 1.62: 43436 1.62 - 1.82: 740 Bond restraints: 150073 Sorted by residual: bond pdb=" C PHE I 525 " pdb=" N PRO I 526 " ideal model delta sigma weight residual 1.335 1.407 -0.072 1.38e-02 5.25e+03 2.75e+01 bond pdb=" CG1 ILE P 682 " pdb=" CD1 ILE P 682 " ideal model delta sigma weight residual 1.513 1.376 0.137 3.90e-02 6.57e+02 1.23e+01 bond pdb=" C ILE H 102 " pdb=" N PRO H 103 " ideal model delta sigma weight residual 1.334 1.407 -0.073 2.34e-02 1.83e+03 9.81e+00 bond pdb=" CB PRO B 665 " pdb=" CG PRO B 665 " ideal model delta sigma weight residual 1.492 1.347 0.145 5.00e-02 4.00e+02 8.41e+00 bond pdb=" CA THR P 859 " pdb=" C THR P 859 " ideal model delta sigma weight residual 1.522 1.572 -0.050 1.72e-02 3.38e+03 8.39e+00 ... (remaining 150068 not shown) Histogram of bond angle deviations from ideal: 94.99 - 102.83: 637 102.83 - 110.67: 145936 110.67 - 118.50: 57562 118.50 - 126.34: 65678 126.34 - 134.18: 1417 Bond angle restraints: 271230 Sorted by residual: angle pdb=" C ASN P 633 " pdb=" CA ASN P 633 " pdb=" CB ASN P 633 " ideal model delta sigma weight residual 109.99 99.18 10.81 1.61e+00 3.86e-01 4.51e+01 angle pdb=" N TYR P 634 " pdb=" CA TYR P 634 " pdb=" CB TYR P 634 " ideal model delta sigma weight residual 111.13 122.19 -11.06 1.79e+00 3.12e-01 3.82e+01 angle pdb=" C ALA H 143 " pdb=" N ASN H 144 " pdb=" CA ASN H 144 " ideal model delta sigma weight residual 121.54 131.72 -10.18 1.91e+00 2.74e-01 2.84e+01 angle pdb=" N THR P 459 " pdb=" CA THR P 459 " pdb=" C THR P 459 " ideal model delta sigma weight residual 108.96 100.49 8.47 1.59e+00 3.96e-01 2.84e+01 angle pdb=" N ASN B 378 " pdb=" CA ASN B 378 " pdb=" C ASN B 378 " ideal model delta sigma weight residual 110.24 117.03 -6.79 1.30e+00 5.92e-01 2.73e+01 ... (remaining 271225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 69284 33.88 - 67.76: 1070 67.76 - 101.65: 56 101.65 - 135.53: 1 135.53 - 169.41: 2 Dihedral angle restraints: 70413 sinusoidal: 39122 harmonic: 31291 Sorted by residual: dihedral pdb=" CA ILE D 102 " pdb=" C ILE D 102 " pdb=" N PRO D 103 " pdb=" CA PRO D 103 " ideal model delta harmonic sigma weight residual -180.00 -120.73 -59.27 0 5.00e+00 4.00e-02 1.41e+02 dihedral pdb=" CA LEU P 501 " pdb=" C LEU P 501 " pdb=" N SER P 502 " pdb=" CA SER P 502 " ideal model delta harmonic sigma weight residual -180.00 -124.92 -55.08 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA GLU G 106 " pdb=" C GLU G 106 " pdb=" N PRO G 107 " pdb=" CA PRO G 107 " ideal model delta harmonic sigma weight residual 180.00 -128.05 -51.95 0 5.00e+00 4.00e-02 1.08e+02 ... (remaining 70410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 9269 0.077 - 0.155: 2235 0.155 - 0.232: 265 0.232 - 0.310: 15 0.310 - 0.387: 1 Chirality restraints: 11785 Sorted by residual: chirality pdb=" CA ASP P 631 " pdb=" N ASP P 631 " pdb=" C ASP P 631 " pdb=" CB ASP P 631 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CB VAL P 244 " pdb=" CA VAL P 244 " pdb=" CG1 VAL P 244 " pdb=" CG2 VAL P 244 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB VAL E 246 " pdb=" CA VAL E 246 " pdb=" CG1 VAL E 246 " pdb=" CG2 VAL E 246 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 11782 not shown) Planarity restraints: 21926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER P 982 " -0.028 2.00e-02 2.50e+03 5.62e-02 3.16e+01 pdb=" C SER P 982 " 0.097 2.00e-02 2.50e+03 pdb=" O SER P 982 " -0.036 2.00e-02 2.50e+03 pdb=" N GLN P 983 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 955 " -0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C GLU P 955 " 0.089 2.00e-02 2.50e+03 pdb=" O GLU P 955 " -0.033 2.00e-02 2.50e+03 pdb=" N ASN P 956 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 586 " 0.024 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C THR B 586 " -0.084 2.00e-02 2.50e+03 pdb=" O THR B 586 " 0.032 2.00e-02 2.50e+03 pdb=" N SER B 587 " 0.028 2.00e-02 2.50e+03 ... (remaining 21923 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 30025 2.30 - 2.88: 340445 2.88 - 3.45: 380532 3.45 - 4.03: 518949 4.03 - 4.60: 803165 Nonbonded interactions: 2073116 Sorted by model distance: nonbonded pdb=" O LEU F 818 " pdb=" HE1 TRP F 824 " model vdw 1.731 1.850 nonbonded pdb=" H21 G T 101 " pdb=" O2 C U 110 " model vdw 1.732 1.850 nonbonded pdb=" O LEU G 818 " pdb=" HE1 TRP G 824 " model vdw 1.738 1.850 nonbonded pdb="HD22 ASN G 597 " pdb=" O GLU G 886 " model vdw 1.739 1.850 nonbonded pdb=" OE2 GLU F 467 " pdb=" HD1 HIS F 480 " model vdw 1.740 1.850 ... (remaining 2073111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD \ 13 or name HD21 or name HD22 or name HD23)) or resid 375 through 887)) selection = (chain 'B' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD \ 13 or name HD21 or name HD22 or name HD23)) or resid 375 through 887)) selection = (chain 'C' and (resid 108 through 345 or (resid 346 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 o \ r name HD22 or name HD23)) or resid 375 through 887)) selection = (chain 'D' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD \ 13 or name HD21 or name HD22 or name HD23)) or resid 375 through 887)) selection = (chain 'E' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 887)) selection = (chain 'F' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD \ 13 or name HD21 or name HD22 or name HD23)) or resid 375 through 887)) selection = (chain 'G' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD \ 13 or name HD21 or name HD22 or name HD23)) or resid 375 through 887)) selection = (chain 'H' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD \ 13 or name HD21 or name HD22 or name HD23)) or resid 375 through 887)) selection = (chain 'I' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD \ 13 or name HD21 or name HD22 or name HD23)) or resid 375 through 887)) selection = (chain 'J' and ((resid 108 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ1 or name HZ2 or name HZ3)) or resid 109 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD \ 13 or name HD21 or name HD22 or name HD23)) or resid 375 through 887)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.640 Extract box with map and model: 10.890 Check model and map are aligned: 1.610 Set scattering table: 1.040 Process input model: 349.240 Find NCS groups from input model: 5.920 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 374.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.145 75677 Z= 0.634 Angle : 1.260 11.932 102731 Z= 0.704 Chirality : 0.064 0.387 11785 Planarity : 0.008 0.109 13216 Dihedral : 10.769 169.409 28879 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.25 % Favored : 90.70 % Rotamer: Outliers : 0.01 % Allowed : 1.34 % Favored : 98.65 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 2.14 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.08), residues: 9006 helix: -1.71 (0.07), residues: 4186 sheet: -2.93 (0.15), residues: 811 loop : -2.71 (0.09), residues: 4009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP P 524 HIS 0.017 0.004 HIS I 574 PHE 0.049 0.005 PHE B 373 TYR 0.050 0.004 TYR P 191 ARG 0.019 0.002 ARG F 747 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 4075 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 4074 time to evaluate : 8.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7430 (mt-10) REVERT: A 179 GLN cc_start: 0.8833 (mt0) cc_final: 0.8631 (mt0) REVERT: A 187 TYR cc_start: 0.8448 (p90) cc_final: 0.8233 (p90) REVERT: A 353 ILE cc_start: 0.9050 (mt) cc_final: 0.8637 (tp) REVERT: A 498 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7293 (mm-40) REVERT: A 502 ASP cc_start: 0.7420 (t0) cc_final: 0.6856 (t0) REVERT: A 549 GLN cc_start: 0.8409 (mp10) cc_final: 0.8183 (mm-40) REVERT: A 565 MET cc_start: 0.8206 (ttm) cc_final: 0.7841 (tmm) REVERT: A 574 HIS cc_start: 0.7067 (t70) cc_final: 0.6287 (t70) REVERT: A 607 LEU cc_start: 0.9276 (mt) cc_final: 0.9037 (mp) REVERT: A 740 ILE cc_start: 0.8295 (mt) cc_final: 0.7455 (mt) REVERT: A 751 TYR cc_start: 0.7144 (m-80) cc_final: 0.6832 (m-80) REVERT: A 761 ASN cc_start: 0.8535 (m-40) cc_final: 0.8108 (p0) REVERT: A 777 SER cc_start: 0.9222 (t) cc_final: 0.8977 (p) REVERT: B 176 LEU cc_start: 0.9372 (tt) cc_final: 0.8675 (tp) REVERT: B 178 ASP cc_start: 0.8042 (t0) cc_final: 0.7792 (t0) REVERT: B 248 TYR cc_start: 0.8199 (m-80) cc_final: 0.7787 (m-80) REVERT: B 268 LEU cc_start: 0.8890 (mt) cc_final: 0.8415 (tp) REVERT: B 329 THR cc_start: 0.8403 (m) cc_final: 0.8165 (m) REVERT: B 363 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6662 (mm-30) REVERT: B 572 MET cc_start: 0.8035 (ptm) cc_final: 0.7790 (ptm) REVERT: B 607 LEU cc_start: 0.8641 (mt) cc_final: 0.8341 (tp) REVERT: B 651 ASP cc_start: 0.8120 (t70) cc_final: 0.7363 (t70) REVERT: B 661 ILE cc_start: 0.9197 (mp) cc_final: 0.8906 (pt) REVERT: B 708 GLN cc_start: 0.6555 (mp10) cc_final: 0.6224 (mp10) REVERT: B 724 MET cc_start: 0.8284 (pmm) cc_final: 0.7994 (pmm) REVERT: B 758 LEU cc_start: 0.9162 (mt) cc_final: 0.8934 (mt) REVERT: B 774 THR cc_start: 0.8297 (p) cc_final: 0.8053 (p) REVERT: B 776 SER cc_start: 0.8350 (m) cc_final: 0.7812 (t) REVERT: B 777 SER cc_start: 0.8537 (t) cc_final: 0.8069 (m) REVERT: C 134 GLU cc_start: 0.7312 (pm20) cc_final: 0.7050 (pm20) REVERT: C 172 TYR cc_start: 0.8250 (t80) cc_final: 0.8020 (t80) REVERT: C 227 VAL cc_start: 0.9025 (m) cc_final: 0.8592 (t) REVERT: C 234 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6504 (tm-30) REVERT: C 266 HIS cc_start: 0.7958 (m90) cc_final: 0.7648 (m90) REVERT: C 315 LEU cc_start: 0.8702 (mt) cc_final: 0.8406 (mp) REVERT: C 333 TYR cc_start: 0.8474 (t80) cc_final: 0.7964 (t80) REVERT: C 390 ILE cc_start: 0.8756 (mt) cc_final: 0.8318 (tt) REVERT: C 484 ASN cc_start: 0.8448 (m-40) cc_final: 0.8127 (t0) REVERT: C 542 LEU cc_start: 0.8744 (mt) cc_final: 0.8223 (mt) REVERT: C 552 ASP cc_start: 0.8096 (m-30) cc_final: 0.7889 (m-30) REVERT: C 712 ILE cc_start: 0.8464 (mt) cc_final: 0.8250 (mm) REVERT: C 722 ASP cc_start: 0.8105 (m-30) cc_final: 0.7780 (m-30) REVERT: C 759 LEU cc_start: 0.8373 (mt) cc_final: 0.8099 (tp) REVERT: C 761 ASN cc_start: 0.8513 (m-40) cc_final: 0.8266 (m-40) REVERT: C 809 ILE cc_start: 0.9205 (mt) cc_final: 0.8814 (mm) REVERT: C 879 ASP cc_start: 0.8697 (p0) cc_final: 0.8146 (p0) REVERT: C 880 ASN cc_start: 0.7457 (m110) cc_final: 0.6669 (m110) REVERT: C 884 MET cc_start: 0.7259 (mtp) cc_final: 0.6797 (mmt) REVERT: D 235 MET cc_start: 0.8059 (ptm) cc_final: 0.7794 (ptp) REVERT: D 261 GLU cc_start: 0.7550 (tp30) cc_final: 0.7255 (tp30) REVERT: D 266 HIS cc_start: 0.8246 (m90) cc_final: 0.7626 (m170) REVERT: D 390 ILE cc_start: 0.9156 (mt) cc_final: 0.8921 (mm) REVERT: D 484 ASN cc_start: 0.8634 (m-40) cc_final: 0.8205 (t0) REVERT: D 534 ARG cc_start: 0.8563 (ttp-170) cc_final: 0.8176 (ttt180) REVERT: D 550 LEU cc_start: 0.8957 (mt) cc_final: 0.8745 (mt) REVERT: D 608 PHE cc_start: 0.7850 (m-10) cc_final: 0.7637 (m-80) REVERT: D 644 LYS cc_start: 0.7320 (mtpt) cc_final: 0.6522 (mtpp) REVERT: D 681 VAL cc_start: 0.8762 (t) cc_final: 0.8523 (t) REVERT: D 761 ASN cc_start: 0.8669 (m-40) cc_final: 0.7488 (m110) REVERT: D 830 THR cc_start: 0.7442 (m) cc_final: 0.7188 (m) REVERT: D 843 ARG cc_start: 0.8475 (mpp80) cc_final: 0.7702 (ttt180) REVERT: D 879 ASP cc_start: 0.8337 (p0) cc_final: 0.7608 (p0) REVERT: E 205 LYS cc_start: 0.8452 (mttm) cc_final: 0.8012 (mtpt) REVERT: E 256 ASP cc_start: 0.8770 (m-30) cc_final: 0.8491 (m-30) REVERT: E 277 ILE cc_start: 0.9138 (mm) cc_final: 0.8870 (mm) REVERT: E 289 VAL cc_start: 0.8295 (m) cc_final: 0.8068 (p) REVERT: E 310 LEU cc_start: 0.7542 (mt) cc_final: 0.6878 (mp) REVERT: E 311 LEU cc_start: 0.8407 (tp) cc_final: 0.8186 (tp) REVERT: E 387 LYS cc_start: 0.8098 (ttmp) cc_final: 0.7789 (mmtp) REVERT: E 434 CYS cc_start: 0.8096 (t) cc_final: 0.7739 (t) REVERT: E 511 ASN cc_start: 0.9175 (m-40) cc_final: 0.8777 (m-40) REVERT: E 533 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7525 (mmmt) REVERT: E 550 LEU cc_start: 0.9306 (mt) cc_final: 0.9012 (mt) REVERT: E 572 MET cc_start: 0.7782 (ptm) cc_final: 0.7132 (mtm) REVERT: E 618 HIS cc_start: 0.7646 (t-170) cc_final: 0.6617 (t-170) REVERT: E 641 TYR cc_start: 0.8429 (p90) cc_final: 0.8225 (p90) REVERT: E 743 GLU cc_start: 0.5633 (pp20) cc_final: 0.3941 (pp20) REVERT: E 802 LEU cc_start: 0.9090 (tp) cc_final: 0.8857 (tp) REVERT: E 826 PRO cc_start: 0.8559 (Cg_exo) cc_final: 0.8181 (Cg_endo) REVERT: E 841 ASP cc_start: 0.8154 (t0) cc_final: 0.7898 (t0) REVERT: E 864 PHE cc_start: 0.8141 (m-80) cc_final: 0.7818 (m-10) REVERT: F 97 ILE cc_start: 0.8300 (mt) cc_final: 0.8041 (mt) REVERT: F 153 TRP cc_start: 0.7535 (m100) cc_final: 0.7321 (m-90) REVERT: F 199 ASN cc_start: 0.8779 (m-40) cc_final: 0.8402 (t0) REVERT: F 259 PHE cc_start: 0.8798 (m-80) cc_final: 0.8350 (m-80) REVERT: F 275 ASP cc_start: 0.8158 (p0) cc_final: 0.6420 (m-30) REVERT: F 276 ILE cc_start: 0.9122 (mt) cc_final: 0.8725 (mt) REVERT: F 287 ASN cc_start: 0.6668 (m110) cc_final: 0.6405 (t0) REVERT: F 313 ASP cc_start: 0.8359 (t0) cc_final: 0.7975 (m-30) REVERT: F 315 LEU cc_start: 0.8922 (mt) cc_final: 0.8637 (mp) REVERT: F 326 ASP cc_start: 0.8451 (t0) cc_final: 0.8203 (t0) REVERT: F 331 SER cc_start: 0.9227 (m) cc_final: 0.8928 (t) REVERT: F 406 THR cc_start: 0.8444 (p) cc_final: 0.8027 (p) REVERT: F 424 ASP cc_start: 0.7512 (p0) cc_final: 0.7260 (p0) REVERT: F 438 ILE cc_start: 0.9122 (mt) cc_final: 0.8905 (mt) REVERT: F 502 ASP cc_start: 0.7125 (t0) cc_final: 0.6860 (t70) REVERT: F 543 LEU cc_start: 0.9127 (mp) cc_final: 0.8917 (mp) REVERT: F 578 LEU cc_start: 0.8897 (mp) cc_final: 0.8625 (mt) REVERT: F 579 THR cc_start: 0.8623 (t) cc_final: 0.8390 (t) REVERT: F 594 LEU cc_start: 0.9076 (mt) cc_final: 0.8755 (mm) REVERT: F 621 TYR cc_start: 0.8141 (t80) cc_final: 0.7752 (t80) REVERT: F 666 ASP cc_start: 0.7826 (m-30) cc_final: 0.7484 (m-30) REVERT: F 672 LEU cc_start: 0.9558 (tp) cc_final: 0.9233 (tt) REVERT: F 773 ILE cc_start: 0.7729 (pt) cc_final: 0.6387 (pt) REVERT: F 848 MET cc_start: 0.8753 (mmm) cc_final: 0.8485 (mmm) REVERT: G 113 LYS cc_start: 0.8762 (tptm) cc_final: 0.8115 (tppt) REVERT: G 253 HIS cc_start: 0.8460 (t-90) cc_final: 0.8076 (t-90) REVERT: G 268 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7258 (pp) REVERT: G 355 LYS cc_start: 0.7977 (ptmm) cc_final: 0.7735 (ptmm) REVERT: G 374 LEU cc_start: 0.8631 (mt) cc_final: 0.8384 (pp) REVERT: G 424 ASP cc_start: 0.8314 (p0) cc_final: 0.7972 (p0) REVERT: G 426 PHE cc_start: 0.8198 (m-80) cc_final: 0.7880 (m-80) REVERT: G 434 CYS cc_start: 0.8431 (t) cc_final: 0.8161 (t) REVERT: G 565 MET cc_start: 0.8366 (ttm) cc_final: 0.7540 (ttm) REVERT: G 607 LEU cc_start: 0.9474 (mt) cc_final: 0.9236 (mt) REVERT: G 646 LYS cc_start: 0.9150 (ptpt) cc_final: 0.8614 (ptpp) REVERT: G 667 ASP cc_start: 0.7481 (p0) cc_final: 0.7251 (p0) REVERT: G 670 TYR cc_start: 0.7897 (m-80) cc_final: 0.7417 (m-80) REVERT: G 703 SER cc_start: 0.8237 (t) cc_final: 0.7892 (p) REVERT: G 708 GLN cc_start: 0.8566 (mp10) cc_final: 0.7995 (mm-40) REVERT: G 807 TYR cc_start: 0.7954 (m-80) cc_final: 0.7330 (m-80) REVERT: G 815 ASP cc_start: 0.7339 (p0) cc_final: 0.7117 (m-30) REVERT: G 879 ASP cc_start: 0.7954 (p0) cc_final: 0.7487 (p0) REVERT: G 884 MET cc_start: 0.6504 (mtp) cc_final: 0.5987 (mtp) REVERT: H 118 ILE cc_start: 0.8990 (mt) cc_final: 0.8542 (mm) REVERT: H 157 LEU cc_start: 0.8627 (mt) cc_final: 0.7799 (mt) REVERT: H 232 ILE cc_start: 0.8862 (mt) cc_final: 0.8647 (mt) REVERT: H 239 VAL cc_start: 0.8574 (t) cc_final: 0.8302 (t) REVERT: H 247 ASN cc_start: 0.7708 (m-40) cc_final: 0.7466 (t0) REVERT: H 257 HIS cc_start: 0.7729 (t70) cc_final: 0.7025 (t70) REVERT: H 275 ASP cc_start: 0.8021 (p0) cc_final: 0.7772 (p0) REVERT: H 313 ASP cc_start: 0.6498 (t0) cc_final: 0.6070 (t0) REVERT: H 326 ASP cc_start: 0.8951 (t0) cc_final: 0.8549 (t0) REVERT: H 377 ILE cc_start: 0.8686 (mm) cc_final: 0.8448 (mm) REVERT: H 480 HIS cc_start: 0.7886 (t70) cc_final: 0.7535 (t-90) REVERT: H 505 ARG cc_start: 0.8172 (mtp180) cc_final: 0.7858 (mtp180) REVERT: H 553 LEU cc_start: 0.9622 (tp) cc_final: 0.9263 (tp) REVERT: H 603 SER cc_start: 0.8563 (t) cc_final: 0.8229 (p) REVERT: H 607 LEU cc_start: 0.9609 (mt) cc_final: 0.9261 (mt) REVERT: H 621 TYR cc_start: 0.7748 (t80) cc_final: 0.7260 (t80) REVERT: H 667 ASP cc_start: 0.8867 (p0) cc_final: 0.8599 (p0) REVERT: H 694 MET cc_start: 0.7407 (ptm) cc_final: 0.5719 (tpt) REVERT: H 825 VAL cc_start: 0.9097 (t) cc_final: 0.8891 (p) REVERT: I 104 THR cc_start: 0.8961 (m) cc_final: 0.8498 (t) REVERT: I 173 PHE cc_start: 0.8853 (m-80) cc_final: 0.8629 (m-80) REVERT: I 250 SER cc_start: 0.8647 (p) cc_final: 0.8068 (p) REVERT: I 355 LYS cc_start: 0.8764 (ptmm) cc_final: 0.8561 (pttt) REVERT: I 409 MET cc_start: 0.8117 (mmm) cc_final: 0.7814 (tpp) REVERT: I 521 SER cc_start: 0.9377 (m) cc_final: 0.8950 (p) REVERT: I 550 LEU cc_start: 0.9393 (mt) cc_final: 0.9102 (mt) REVERT: I 607 LEU cc_start: 0.9473 (mt) cc_final: 0.9097 (mt) REVERT: I 661 ILE cc_start: 0.7055 (mt) cc_final: 0.6541 (tp) REVERT: I 723 GLU cc_start: 0.7592 (tp30) cc_final: 0.7075 (tp30) REVERT: I 729 ASN cc_start: 0.8967 (p0) cc_final: 0.8520 (p0) REVERT: I 732 ARG cc_start: 0.7223 (pmm-80) cc_final: 0.6860 (ptp-110) REVERT: I 761 ASN cc_start: 0.8331 (m-40) cc_final: 0.7783 (p0) REVERT: I 778 VAL cc_start: 0.9122 (t) cc_final: 0.8877 (m) REVERT: I 805 ILE cc_start: 0.8617 (mm) cc_final: 0.7957 (mm) REVERT: I 812 ASP cc_start: 0.7600 (p0) cc_final: 0.7282 (p0) REVERT: I 883 ILE cc_start: 0.8453 (tt) cc_final: 0.8186 (mp) REVERT: I 884 MET cc_start: 0.7600 (mtp) cc_final: 0.7341 (mtp) REVERT: J 166 ASP cc_start: 0.7050 (m-30) cc_final: 0.5679 (m-30) REVERT: J 193 MET cc_start: 0.8157 (ptp) cc_final: 0.7797 (ptm) REVERT: J 215 CYS cc_start: 0.7278 (m) cc_final: 0.6918 (m) REVERT: J 317 LEU cc_start: 0.9297 (mt) cc_final: 0.9082 (mp) REVERT: J 393 MET cc_start: 0.8071 (mtm) cc_final: 0.7794 (mtp) REVERT: J 584 GLN cc_start: 0.6451 (mm-40) cc_final: 0.6198 (mp10) REVERT: J 592 CYS cc_start: 0.8472 (m) cc_final: 0.8248 (t) REVERT: J 609 HIS cc_start: 0.8678 (t70) cc_final: 0.8467 (t70) REVERT: J 636 ASN cc_start: 0.7777 (m-40) cc_final: 0.7524 (t0) REVERT: J 667 ASP cc_start: 0.8387 (p0) cc_final: 0.8023 (p0) REVERT: J 706 ILE cc_start: 0.8578 (pt) cc_final: 0.8153 (pt) REVERT: J 735 ASP cc_start: 0.7144 (p0) cc_final: 0.6942 (p0) REVERT: J 744 GLU cc_start: 0.5860 (mp0) cc_final: 0.5369 (mp0) REVERT: J 756 ASN cc_start: 0.7370 (t0) cc_final: 0.6716 (t0) REVERT: J 772 PHE cc_start: 0.7939 (p90) cc_final: 0.7726 (p90) REVERT: J 801 THR cc_start: 0.8179 (t) cc_final: 0.7859 (t) REVERT: J 846 MET cc_start: 0.8114 (tmt) cc_final: 0.7604 (tmm) REVERT: J 854 THR cc_start: 0.8604 (p) cc_final: 0.8396 (t) REVERT: P 33 GLU cc_start: 0.8484 (pt0) cc_final: 0.6899 (tp30) REVERT: P 40 GLU cc_start: 0.8652 (mt-10) cc_final: 0.7810 (tt0) REVERT: P 192 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6660 (mm-30) REVERT: P 194 GLU cc_start: 0.8236 (pt0) cc_final: 0.7433 (mp0) REVERT: P 291 MET cc_start: 0.7058 (mtp) cc_final: 0.6726 (mtm) REVERT: P 374 MET cc_start: 0.7704 (mtt) cc_final: 0.6550 (mmp) REVERT: P 517 LEU cc_start: 0.8703 (pp) cc_final: 0.8390 (pt) REVERT: P 525 ASP cc_start: 0.8182 (m-30) cc_final: 0.7961 (m-30) REVERT: P 529 HIS cc_start: 0.8196 (p-80) cc_final: 0.7688 (p90) REVERT: P 544 MET cc_start: 0.7136 (mmm) cc_final: 0.6611 (mmm) REVERT: P 545 LEU cc_start: 0.9457 (mt) cc_final: 0.9208 (mt) REVERT: P 663 ASN cc_start: 0.8046 (t0) cc_final: 0.7637 (t0) REVERT: P 758 THR cc_start: 0.8488 (p) cc_final: 0.8192 (p) REVERT: P 789 MET cc_start: 0.7826 (mmm) cc_final: 0.7419 (mmt) REVERT: P 866 THR cc_start: 0.7313 (m) cc_final: 0.7084 (m) REVERT: P 931 SER cc_start: 0.7278 (m) cc_final: 0.7006 (t) REVERT: P 944 ILE cc_start: 0.4975 (pt) cc_final: 0.4660 (mt) REVERT: P 996 LEU cc_start: 0.6687 (mt) cc_final: 0.6443 (tt) REVERT: P 1058 TYR cc_start: 0.6895 (t80) cc_final: 0.6489 (t80) outliers start: 1 outliers final: 0 residues processed: 4074 average time/residue: 1.8321 time to fit residues: 12294.3149 Evaluate side-chains 2697 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2696 time to evaluate : 8.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 902 random chunks: chunk 761 optimal weight: 0.9990 chunk 683 optimal weight: 0.8980 chunk 379 optimal weight: 2.9990 chunk 233 optimal weight: 0.5980 chunk 461 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 706 optimal weight: 0.9980 chunk 273 optimal weight: 0.9990 chunk 429 optimal weight: 0.7980 chunk 526 optimal weight: 3.9990 chunk 819 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN B 460 GLN B 512 GLN B 616 ASN C 199 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS D 260 ASN ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 484 ASN D 560 ASN ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN D 642 GLN D 739 GLN D 814 ASN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN E 636 ASN E 874 ASN F 318 HIS F 545 ASN ** F 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 880 ASN G 244 ASN G 396 GLN G 440 ASN G 503 ASN G 616 ASN G 698 GLN G 718 GLN G 753 GLN ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 523 GLN H 549 GLN H 605 GLN H 642 GLN H 739 GLN I 318 HIS I 368 GLN I 477 ASN I 497 ASN I 512 GLN ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 GLN J 257 HIS J 266 HIS J 545 ASN P 498 ASN P 604 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 75677 Z= 0.195 Angle : 0.624 11.984 102731 Z= 0.337 Chirality : 0.041 0.234 11785 Planarity : 0.005 0.088 13216 Dihedral : 8.302 166.913 10332 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.04 % Favored : 92.95 % Rotamer: Outliers : 0.07 % Allowed : 1.85 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.08), residues: 9006 helix: -0.51 (0.08), residues: 4281 sheet: -2.37 (0.16), residues: 766 loop : -2.39 (0.09), residues: 3959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 416 HIS 0.007 0.001 HIS C 574 PHE 0.026 0.001 PHE C 231 TYR 0.027 0.002 TYR E 621 ARG 0.023 0.001 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 3162 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 3156 time to evaluate : 10.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6756 (mt-10) REVERT: A 164 ASP cc_start: 0.7308 (m-30) cc_final: 0.6774 (m-30) REVERT: A 187 TYR cc_start: 0.8605 (p90) cc_final: 0.8331 (p90) REVERT: A 250 SER cc_start: 0.9212 (t) cc_final: 0.8996 (t) REVERT: A 477 ASN cc_start: 0.8951 (p0) cc_final: 0.7947 (t0) REVERT: A 531 ASP cc_start: 0.8490 (p0) cc_final: 0.7009 (t70) REVERT: A 607 LEU cc_start: 0.9285 (mt) cc_final: 0.9014 (mm) REVERT: A 608 PHE cc_start: 0.8652 (m-80) cc_final: 0.8302 (m-10) REVERT: A 706 ILE cc_start: 0.9135 (pt) cc_final: 0.8602 (pt) REVERT: A 724 MET cc_start: 0.8294 (pmm) cc_final: 0.7708 (pmm) REVERT: A 725 TYR cc_start: 0.7694 (m-80) cc_final: 0.7121 (m-80) REVERT: A 761 ASN cc_start: 0.8693 (m-40) cc_final: 0.8119 (p0) REVERT: A 812 ASP cc_start: 0.8299 (t70) cc_final: 0.8080 (t70) REVERT: A 824 TRP cc_start: 0.5081 (t60) cc_final: 0.4810 (t-100) REVERT: A 825 VAL cc_start: 0.9068 (t) cc_final: 0.8815 (t) REVERT: A 846 MET cc_start: 0.8160 (tmm) cc_final: 0.7712 (tmm) REVERT: A 853 LEU cc_start: 0.8643 (tp) cc_final: 0.8377 (tt) REVERT: A 868 ASP cc_start: 0.7136 (t70) cc_final: 0.6752 (t0) REVERT: A 879 ASP cc_start: 0.7737 (p0) cc_final: 0.7277 (p0) REVERT: B 175 ASN cc_start: 0.8207 (m-40) cc_final: 0.7864 (m-40) REVERT: B 193 MET cc_start: 0.7990 (ptp) cc_final: 0.7484 (ptp) REVERT: B 268 LEU cc_start: 0.8752 (mt) cc_final: 0.8400 (tp) REVERT: B 363 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6890 (mm-30) REVERT: B 607 LEU cc_start: 0.8725 (mt) cc_final: 0.8496 (tp) REVERT: B 651 ASP cc_start: 0.7786 (t70) cc_final: 0.7477 (t70) REVERT: B 685 ARG cc_start: 0.8272 (mmt90) cc_final: 0.7843 (mpt-90) REVERT: B 700 GLU cc_start: 0.6724 (tm-30) cc_final: 0.6287 (tm-30) REVERT: B 776 SER cc_start: 0.8545 (m) cc_final: 0.7968 (t) REVERT: C 154 TYR cc_start: 0.7793 (m-80) cc_final: 0.7481 (m-10) REVERT: C 215 CYS cc_start: 0.9027 (m) cc_final: 0.8826 (m) REVERT: C 227 VAL cc_start: 0.8965 (m) cc_final: 0.8577 (t) REVERT: C 234 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6502 (tm-30) REVERT: C 266 HIS cc_start: 0.8160 (m90) cc_final: 0.7708 (m90) REVERT: C 270 GLU cc_start: 0.7602 (mp0) cc_final: 0.7397 (mp0) REVERT: C 333 TYR cc_start: 0.8039 (t80) cc_final: 0.7838 (t80) REVERT: C 484 ASN cc_start: 0.8493 (m-40) cc_final: 0.8149 (t0) REVERT: C 537 GLN cc_start: 0.7782 (tt0) cc_final: 0.7568 (tp-100) REVERT: C 650 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7825 (tm-30) REVERT: C 666 ASP cc_start: 0.7495 (t70) cc_final: 0.7123 (t70) REVERT: C 684 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7648 (mtm-85) REVERT: C 686 LEU cc_start: 0.8656 (tp) cc_final: 0.8386 (tp) REVERT: C 751 TYR cc_start: 0.7177 (m-80) cc_final: 0.6975 (m-80) REVERT: C 759 LEU cc_start: 0.8640 (mt) cc_final: 0.8393 (tp) REVERT: C 761 ASN cc_start: 0.8186 (m-40) cc_final: 0.7947 (m-40) REVERT: C 824 TRP cc_start: 0.5844 (p-90) cc_final: 0.4532 (t60) REVERT: C 854 THR cc_start: 0.8628 (m) cc_final: 0.8051 (p) REVERT: C 879 ASP cc_start: 0.8626 (p0) cc_final: 0.8079 (p0) REVERT: C 884 MET cc_start: 0.7413 (mtp) cc_final: 0.6829 (mmt) REVERT: D 81 GLU cc_start: 0.8416 (mp0) cc_final: 0.8133 (mp0) REVERT: D 134 GLU cc_start: 0.7958 (pm20) cc_final: 0.7691 (pm20) REVERT: D 261 GLU cc_start: 0.7293 (tp30) cc_final: 0.7020 (tp30) REVERT: D 349 THR cc_start: 0.8291 (p) cc_final: 0.8060 (t) REVERT: D 390 ILE cc_start: 0.9209 (mt) cc_final: 0.8972 (mm) REVERT: D 393 MET cc_start: 0.8920 (mtp) cc_final: 0.8694 (mtp) REVERT: D 484 ASN cc_start: 0.8703 (m110) cc_final: 0.8208 (t0) REVERT: D 534 ARG cc_start: 0.8527 (ttp-170) cc_final: 0.8296 (ttt180) REVERT: D 667 ASP cc_start: 0.7225 (p0) cc_final: 0.6675 (p0) REVERT: D 681 VAL cc_start: 0.8914 (t) cc_final: 0.8655 (t) REVERT: D 700 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7070 (tm-30) REVERT: D 708 GLN cc_start: 0.8634 (mp10) cc_final: 0.7399 (mp10) REVERT: D 761 ASN cc_start: 0.8397 (m-40) cc_final: 0.7652 (m-40) REVERT: D 841 ASP cc_start: 0.8439 (t70) cc_final: 0.8235 (t0) REVERT: D 843 ARG cc_start: 0.8549 (mpp80) cc_final: 0.8321 (mtm-85) REVERT: D 879 ASP cc_start: 0.8380 (p0) cc_final: 0.7863 (p0) REVERT: D 884 MET cc_start: 0.7105 (tpp) cc_final: 0.6847 (tpp) REVERT: E 164 ASP cc_start: 0.6549 (m-30) cc_final: 0.5537 (p0) REVERT: E 205 LYS cc_start: 0.8531 (mttm) cc_final: 0.7975 (mtpt) REVERT: E 277 ILE cc_start: 0.9080 (mm) cc_final: 0.8867 (mm) REVERT: E 310 LEU cc_start: 0.7565 (mt) cc_final: 0.6992 (mp) REVERT: E 434 CYS cc_start: 0.7862 (t) cc_final: 0.7487 (t) REVERT: E 509 VAL cc_start: 0.8640 (t) cc_final: 0.8346 (t) REVERT: E 511 ASN cc_start: 0.9103 (m-40) cc_final: 0.8708 (m-40) REVERT: E 572 MET cc_start: 0.7825 (ptm) cc_final: 0.7374 (mtm) REVERT: E 663 ARG cc_start: 0.8419 (mtt90) cc_final: 0.8217 (mtt90) REVERT: E 743 GLU cc_start: 0.5488 (pp20) cc_final: 0.4214 (pp20) REVERT: E 826 PRO cc_start: 0.8827 (Cg_exo) cc_final: 0.8430 (Cg_endo) REVERT: E 843 ARG cc_start: 0.7127 (tmt170) cc_final: 0.6678 (mtm-85) REVERT: E 864 PHE cc_start: 0.8066 (m-80) cc_final: 0.7800 (m-10) REVERT: F 134 GLU cc_start: 0.6798 (pt0) cc_final: 0.6262 (pt0) REVERT: F 259 PHE cc_start: 0.8958 (m-80) cc_final: 0.8477 (m-80) REVERT: F 272 LEU cc_start: 0.7303 (tp) cc_final: 0.7095 (tp) REVERT: F 313 ASP cc_start: 0.8482 (t0) cc_final: 0.7978 (m-30) REVERT: F 331 SER cc_start: 0.9302 (m) cc_final: 0.9002 (t) REVERT: F 424 ASP cc_start: 0.7628 (p0) cc_final: 0.7146 (p0) REVERT: F 509 VAL cc_start: 0.7464 (m) cc_final: 0.7219 (t) REVERT: F 514 MET cc_start: 0.8583 (mmt) cc_final: 0.8288 (tpp) REVERT: F 560 ASN cc_start: 0.8119 (m-40) cc_final: 0.7891 (m-40) REVERT: F 576 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7844 (mm-40) REVERT: F 594 LEU cc_start: 0.9010 (mt) cc_final: 0.8790 (mt) REVERT: F 621 TYR cc_start: 0.8057 (t80) cc_final: 0.7842 (t80) REVERT: F 715 ARG cc_start: 0.7850 (ptm160) cc_final: 0.7493 (ptm-80) REVERT: F 773 ILE cc_start: 0.7611 (pt) cc_final: 0.7284 (pt) REVERT: F 807 TYR cc_start: 0.8120 (m-80) cc_final: 0.7912 (m-80) REVERT: F 815 ASP cc_start: 0.6012 (p0) cc_final: 0.5681 (p0) REVERT: G 102 ILE cc_start: 0.9464 (mt) cc_final: 0.9207 (mt) REVERT: G 268 LEU cc_start: 0.7486 (pp) cc_final: 0.7200 (pp) REVERT: G 277 ILE cc_start: 0.9543 (mt) cc_final: 0.9228 (mm) REVERT: G 355 LYS cc_start: 0.8114 (ptmm) cc_final: 0.7255 (tttp) REVERT: G 423 ASN cc_start: 0.8164 (p0) cc_final: 0.7897 (p0) REVERT: G 424 ASP cc_start: 0.8417 (p0) cc_final: 0.8155 (p0) REVERT: G 434 CYS cc_start: 0.8491 (t) cc_final: 0.8254 (t) REVERT: G 565 MET cc_start: 0.8289 (ttm) cc_final: 0.7680 (ttm) REVERT: G 574 HIS cc_start: 0.6176 (t70) cc_final: 0.5705 (t70) REVERT: G 646 LYS cc_start: 0.8951 (ptpt) cc_final: 0.8565 (ptpp) REVERT: G 703 SER cc_start: 0.8290 (t) cc_final: 0.7618 (p) REVERT: G 790 PHE cc_start: 0.8447 (m-80) cc_final: 0.8238 (m-10) REVERT: G 807 TYR cc_start: 0.7991 (m-80) cc_final: 0.7345 (m-80) REVERT: G 830 THR cc_start: 0.8743 (m) cc_final: 0.8539 (m) REVERT: H 221 ASP cc_start: 0.7493 (t70) cc_final: 0.7194 (t0) REVERT: H 247 ASN cc_start: 0.8164 (m-40) cc_final: 0.7614 (t0) REVERT: H 313 ASP cc_start: 0.6717 (t0) cc_final: 0.6447 (t0) REVERT: H 326 ASP cc_start: 0.9112 (t0) cc_final: 0.8830 (t70) REVERT: H 358 GLN cc_start: 0.8704 (pt0) cc_final: 0.8356 (pt0) REVERT: H 480 HIS cc_start: 0.7932 (t70) cc_final: 0.7452 (t70) REVERT: H 553 LEU cc_start: 0.9594 (tp) cc_final: 0.9309 (tp) REVERT: H 603 SER cc_start: 0.8646 (t) cc_final: 0.8381 (m) REVERT: H 694 MET cc_start: 0.7659 (ptm) cc_final: 0.5940 (tpt) REVERT: H 717 MET cc_start: 0.5959 (mtm) cc_final: 0.5448 (mtm) REVERT: H 750 ASP cc_start: 0.6889 (p0) cc_final: 0.6677 (p0) REVERT: I 104 THR cc_start: 0.8743 (m) cc_final: 0.8311 (t) REVERT: I 160 ASP cc_start: 0.7332 (t0) cc_final: 0.7038 (t0) REVERT: I 322 GLU cc_start: 0.8073 (pm20) cc_final: 0.7763 (pm20) REVERT: I 342 ASP cc_start: 0.7628 (m-30) cc_final: 0.7378 (m-30) REVERT: I 353 ILE cc_start: 0.7958 (mm) cc_final: 0.7687 (mm) REVERT: I 451 ARG cc_start: 0.7899 (mmm-85) cc_final: 0.7200 (mmt90) REVERT: I 502 ASP cc_start: 0.6078 (t0) cc_final: 0.5783 (t0) REVERT: I 521 SER cc_start: 0.9324 (m) cc_final: 0.8942 (p) REVERT: I 607 LEU cc_start: 0.9484 (mt) cc_final: 0.9069 (mt) REVERT: I 650 GLU cc_start: 0.8218 (pp20) cc_final: 0.7823 (pp20) REVERT: I 677 ARG cc_start: 0.7549 (mtm180) cc_final: 0.7058 (tmt170) REVERT: I 697 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6919 (tm-30) REVERT: I 723 GLU cc_start: 0.7859 (tp30) cc_final: 0.7310 (tp30) REVERT: I 786 ASP cc_start: 0.7843 (p0) cc_final: 0.7626 (p0) REVERT: J 116 GLU cc_start: 0.7376 (pp20) cc_final: 0.7122 (pp20) REVERT: J 193 MET cc_start: 0.8218 (ptp) cc_final: 0.8002 (ptm) REVERT: J 218 ILE cc_start: 0.8342 (mm) cc_final: 0.7788 (tp) REVERT: J 238 ARG cc_start: 0.8119 (tpp80) cc_final: 0.7448 (mmm-85) REVERT: J 311 LEU cc_start: 0.8621 (tp) cc_final: 0.8360 (tp) REVERT: J 374 LEU cc_start: 0.9056 (mt) cc_final: 0.8796 (mt) REVERT: J 375 THR cc_start: 0.7346 (m) cc_final: 0.7012 (m) REVERT: J 444 TYR cc_start: 0.7860 (m-10) cc_final: 0.7648 (m-10) REVERT: J 523 GLN cc_start: 0.8161 (tt0) cc_final: 0.7837 (tp-100) REVERT: J 531 ASP cc_start: 0.7133 (p0) cc_final: 0.6838 (p0) REVERT: J 544 SER cc_start: 0.9378 (m) cc_final: 0.8972 (p) REVERT: J 574 HIS cc_start: 0.7626 (t-90) cc_final: 0.7265 (t-90) REVERT: J 609 HIS cc_start: 0.8464 (t70) cc_final: 0.8172 (t70) REVERT: J 612 ASN cc_start: 0.8545 (m110) cc_final: 0.8241 (m110) REVERT: J 667 ASP cc_start: 0.8370 (p0) cc_final: 0.7942 (p0) REVERT: J 756 ASN cc_start: 0.7395 (t0) cc_final: 0.6963 (t0) REVERT: J 786 ASP cc_start: 0.7934 (p0) cc_final: 0.7018 (p0) REVERT: J 854 THR cc_start: 0.8548 (p) cc_final: 0.8325 (t) REVERT: J 886 GLU cc_start: 0.7711 (tt0) cc_final: 0.7424 (tt0) REVERT: P 6 LEU cc_start: 0.8815 (mp) cc_final: 0.8611 (mt) REVERT: P 110 GLU cc_start: 0.7233 (mp0) cc_final: 0.6917 (mm-30) REVERT: P 208 ASN cc_start: 0.8830 (m110) cc_final: 0.8492 (m-40) REVERT: P 221 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6994 (mt-10) REVERT: P 365 MET cc_start: 0.8217 (ttt) cc_final: 0.8000 (ttt) REVERT: P 544 MET cc_start: 0.7160 (mmm) cc_final: 0.6793 (mmm) REVERT: P 569 MET cc_start: 0.7759 (mtm) cc_final: 0.7559 (mtm) REVERT: P 644 THR cc_start: 0.7751 (p) cc_final: 0.7477 (p) REVERT: P 663 ASN cc_start: 0.8058 (t0) cc_final: 0.7727 (t0) REVERT: P 739 MET cc_start: 0.8540 (mtp) cc_final: 0.8318 (mtt) REVERT: P 758 THR cc_start: 0.8514 (p) cc_final: 0.8250 (p) REVERT: P 785 GLN cc_start: 0.7611 (tt0) cc_final: 0.7390 (tt0) REVERT: P 789 MET cc_start: 0.7911 (mmm) cc_final: 0.7547 (mmt) REVERT: P 849 LYS cc_start: 0.8493 (ttpt) cc_final: 0.7955 (ttmm) REVERT: P 866 THR cc_start: 0.7608 (m) cc_final: 0.7369 (m) REVERT: P 931 SER cc_start: 0.7016 (m) cc_final: 0.6722 (t) REVERT: P 975 TYR cc_start: 0.5426 (t80) cc_final: 0.4524 (t80) outliers start: 6 outliers final: 2 residues processed: 3160 average time/residue: 1.7812 time to fit residues: 9388.9653 Evaluate side-chains 2591 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2589 time to evaluate : 8.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 902 random chunks: chunk 455 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 681 optimal weight: 3.9990 chunk 557 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 820 optimal weight: 7.9990 chunk 886 optimal weight: 5.9990 chunk 730 optimal weight: 4.9990 chunk 813 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 658 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 352 GLN A 453 HIS ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 GLN ** C 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN D 396 GLN ** D 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 HIS E 137 GLN E 453 HIS ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 636 ASN E 760 ASN E 874 ASN F 267 GLN ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 257 HIS ** G 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 503 ASN G 616 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 483 ASN H 523 GLN H 821 ASN I 267 GLN I 290 ASN ** I 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 368 GLN I 440 ASN I 489 GLN I 549 GLN ** I 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 483 ASN J 761 ASN P 430 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 75677 Z= 0.474 Angle : 0.760 7.345 102731 Z= 0.418 Chirality : 0.044 0.226 11785 Planarity : 0.006 0.088 13216 Dihedral : 8.179 163.202 10332 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.62 % Favored : 91.34 % Rotamer: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.08), residues: 9006 helix: -0.21 (0.08), residues: 4274 sheet: -2.16 (0.17), residues: 698 loop : -2.44 (0.09), residues: 4034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 824 HIS 0.015 0.002 HIS H 253 PHE 0.034 0.002 PHE D 790 TYR 0.040 0.002 TYR B 621 ARG 0.014 0.001 ARG G 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2895 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2891 time to evaluate : 8.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.7328 (ttm170) REVERT: A 164 ASP cc_start: 0.7441 (m-30) cc_final: 0.7132 (m-30) REVERT: A 193 MET cc_start: 0.7105 (ptp) cc_final: 0.6756 (ptp) REVERT: A 467 GLU cc_start: 0.8481 (tt0) cc_final: 0.8230 (tt0) REVERT: A 492 ILE cc_start: 0.8878 (mt) cc_final: 0.8447 (mm) REVERT: A 580 THR cc_start: 0.8655 (p) cc_final: 0.8344 (t) REVERT: A 677 ARG cc_start: 0.8961 (mtm-85) cc_final: 0.8550 (ttm110) REVERT: A 706 ILE cc_start: 0.9091 (pt) cc_final: 0.8475 (pt) REVERT: A 714 TYR cc_start: 0.8287 (m-80) cc_final: 0.7785 (m-80) REVERT: A 721 ARG cc_start: 0.7605 (mtt90) cc_final: 0.6548 (ptt-90) REVERT: A 725 TYR cc_start: 0.8042 (m-80) cc_final: 0.7318 (m-80) REVERT: A 761 ASN cc_start: 0.8883 (m-40) cc_final: 0.8266 (p0) REVERT: A 846 MET cc_start: 0.8325 (tmm) cc_final: 0.7781 (tmm) REVERT: A 868 ASP cc_start: 0.7462 (t70) cc_final: 0.6595 (t0) REVERT: B 175 ASN cc_start: 0.8517 (m-40) cc_final: 0.8303 (m-40) REVERT: B 211 THR cc_start: 0.8378 (m) cc_final: 0.8151 (m) REVERT: B 215 CYS cc_start: 0.8595 (m) cc_final: 0.8377 (m) REVERT: B 268 LEU cc_start: 0.8918 (mt) cc_final: 0.8505 (mt) REVERT: B 275 ASP cc_start: 0.7680 (m-30) cc_final: 0.7376 (t0) REVERT: B 408 TYR cc_start: 0.8430 (m-80) cc_final: 0.8213 (m-80) REVERT: B 450 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8241 (mm-40) REVERT: B 700 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7375 (tm-30) REVERT: B 708 GLN cc_start: 0.7054 (mp10) cc_final: 0.5636 (mp10) REVERT: B 879 ASP cc_start: 0.8026 (p0) cc_final: 0.6778 (t0) REVERT: B 880 ASN cc_start: 0.7575 (m110) cc_final: 0.7138 (m110) REVERT: C 215 CYS cc_start: 0.9090 (m) cc_final: 0.8857 (m) REVERT: C 227 VAL cc_start: 0.9207 (m) cc_final: 0.8912 (t) REVERT: C 234 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7111 (tm-30) REVERT: C 256 ASP cc_start: 0.8567 (m-30) cc_final: 0.8328 (m-30) REVERT: C 270 GLU cc_start: 0.7839 (mp0) cc_final: 0.7595 (mp0) REVERT: C 290 ASN cc_start: 0.8737 (m-40) cc_final: 0.8488 (m-40) REVERT: C 385 CYS cc_start: 0.8622 (t) cc_final: 0.8370 (t) REVERT: C 484 ASN cc_start: 0.8705 (m-40) cc_final: 0.8239 (t0) REVERT: C 538 ARG cc_start: 0.8786 (mtt180) cc_final: 0.8567 (ttp-110) REVERT: C 646 LYS cc_start: 0.8630 (tttt) cc_final: 0.8327 (tttt) REVERT: C 650 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7931 (tm-30) REVERT: C 729 ASN cc_start: 0.8952 (p0) cc_final: 0.8662 (p0) REVERT: C 737 PHE cc_start: 0.7493 (m-80) cc_final: 0.7228 (m-80) REVERT: C 770 LEU cc_start: 0.8378 (tp) cc_final: 0.8084 (tp) REVERT: C 854 THR cc_start: 0.8782 (m) cc_final: 0.8397 (p) REVERT: C 880 ASN cc_start: 0.7389 (m110) cc_final: 0.6968 (m110) REVERT: C 884 MET cc_start: 0.7581 (mtp) cc_final: 0.7075 (mmt) REVERT: D 77 LYS cc_start: 0.8309 (mtmm) cc_final: 0.7630 (mtmm) REVERT: D 81 GLU cc_start: 0.8572 (mp0) cc_final: 0.8098 (mp0) REVERT: D 175 ASN cc_start: 0.8749 (m-40) cc_final: 0.8515 (t0) REVERT: D 261 GLU cc_start: 0.7410 (tp30) cc_final: 0.7076 (tp30) REVERT: D 422 PRO cc_start: 0.8452 (Cg_exo) cc_final: 0.7966 (Cg_endo) REVERT: D 484 ASN cc_start: 0.8623 (m110) cc_final: 0.8191 (t0) REVERT: D 534 ARG cc_start: 0.8656 (ttp-170) cc_final: 0.8424 (ttm-80) REVERT: D 681 VAL cc_start: 0.8979 (t) cc_final: 0.8762 (t) REVERT: D 708 GLN cc_start: 0.8606 (mp10) cc_final: 0.7987 (mp10) REVERT: D 722 ASP cc_start: 0.8206 (m-30) cc_final: 0.8003 (m-30) REVERT: D 740 ILE cc_start: 0.7826 (mm) cc_final: 0.7441 (mm) REVERT: D 786 ASP cc_start: 0.8092 (p0) cc_final: 0.7815 (p0) REVERT: D 841 ASP cc_start: 0.8450 (t70) cc_final: 0.8188 (t0) REVERT: D 843 ARG cc_start: 0.8694 (mpp80) cc_final: 0.8446 (mpp80) REVERT: D 884 MET cc_start: 0.7584 (tpp) cc_final: 0.7237 (tpp) REVERT: E 164 ASP cc_start: 0.6668 (m-30) cc_final: 0.6111 (p0) REVERT: E 205 LYS cc_start: 0.8719 (mttm) cc_final: 0.8176 (mtpt) REVERT: E 210 GLU cc_start: 0.7893 (mp0) cc_final: 0.7491 (mp0) REVERT: E 272 LEU cc_start: 0.8349 (tp) cc_final: 0.8097 (tp) REVERT: E 289 VAL cc_start: 0.8186 (m) cc_final: 0.7977 (p) REVERT: E 434 CYS cc_start: 0.8285 (t) cc_final: 0.7848 (t) REVERT: E 511 ASN cc_start: 0.9291 (m-40) cc_final: 0.8839 (m-40) REVERT: E 753 GLN cc_start: 0.6903 (tp40) cc_final: 0.6651 (tp-100) REVERT: E 807 TYR cc_start: 0.8322 (m-80) cc_final: 0.7454 (m-10) REVERT: E 843 ARG cc_start: 0.7231 (tmt170) cc_final: 0.6946 (tpt-90) REVERT: F 134 GLU cc_start: 0.7146 (pt0) cc_final: 0.6927 (pt0) REVERT: F 153 TRP cc_start: 0.7730 (m100) cc_final: 0.7481 (m-90) REVERT: F 171 GLU cc_start: 0.7640 (tp30) cc_final: 0.7280 (tp30) REVERT: F 221 ASP cc_start: 0.6567 (t70) cc_final: 0.5845 (t0) REVERT: F 313 ASP cc_start: 0.8524 (t0) cc_final: 0.8222 (m-30) REVERT: F 326 ASP cc_start: 0.8658 (t0) cc_final: 0.8355 (t0) REVERT: F 331 SER cc_start: 0.9221 (m) cc_final: 0.8969 (t) REVERT: F 424 ASP cc_start: 0.7837 (p0) cc_final: 0.7535 (p0) REVERT: F 621 TYR cc_start: 0.8536 (t80) cc_final: 0.8211 (t80) REVERT: F 640 LEU cc_start: 0.8831 (mt) cc_final: 0.8592 (mt) REVERT: F 745 LEU cc_start: 0.9244 (tp) cc_final: 0.8925 (tt) REVERT: F 847 HIS cc_start: 0.7836 (m-70) cc_final: 0.7525 (m-70) REVERT: G 268 LEU cc_start: 0.7984 (pp) cc_final: 0.7654 (pp) REVERT: G 277 ILE cc_start: 0.9599 (mt) cc_final: 0.9298 (mm) REVERT: G 319 ASP cc_start: 0.8253 (p0) cc_final: 0.8017 (p0) REVERT: G 355 LYS cc_start: 0.8525 (ptmm) cc_final: 0.7681 (tttp) REVERT: G 426 PHE cc_start: 0.8228 (m-10) cc_final: 0.8005 (m-10) REVERT: G 434 CYS cc_start: 0.8532 (t) cc_final: 0.8319 (t) REVERT: G 452 MET cc_start: 0.7820 (tpp) cc_final: 0.7464 (tpt) REVERT: G 574 HIS cc_start: 0.6579 (t70) cc_final: 0.5753 (t70) REVERT: G 576 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7316 (pm20) REVERT: G 646 LYS cc_start: 0.8864 (ptpt) cc_final: 0.8481 (ptpp) REVERT: G 715 ARG cc_start: 0.7760 (ptt-90) cc_final: 0.7379 (ptt-90) REVERT: H 142 ARG cc_start: 0.7728 (ptp90) cc_final: 0.7434 (ptp90) REVERT: H 221 ASP cc_start: 0.7280 (t70) cc_final: 0.6959 (t70) REVERT: H 250 SER cc_start: 0.8759 (p) cc_final: 0.7698 (p) REVERT: H 257 HIS cc_start: 0.8374 (t70) cc_final: 0.8049 (t-90) REVERT: H 287 ASN cc_start: 0.7897 (t0) cc_final: 0.7684 (t0) REVERT: H 442 ILE cc_start: 0.8809 (mm) cc_final: 0.8543 (mm) REVERT: H 480 HIS cc_start: 0.8241 (t70) cc_final: 0.7547 (t-90) REVERT: H 553 LEU cc_start: 0.9600 (tp) cc_final: 0.9385 (tp) REVERT: H 609 HIS cc_start: 0.7669 (t70) cc_final: 0.7220 (t70) REVERT: H 645 MET cc_start: 0.7724 (mmm) cc_final: 0.7216 (mmp) REVERT: H 687 ASP cc_start: 0.8711 (t0) cc_final: 0.8503 (t0) REVERT: H 694 MET cc_start: 0.7733 (ptm) cc_final: 0.6052 (tpt) REVERT: H 744 GLU cc_start: 0.7275 (mp0) cc_final: 0.6708 (mp0) REVERT: H 746 MET cc_start: 0.8924 (ptt) cc_final: 0.8290 (tmm) REVERT: I 102 ILE cc_start: 0.9323 (mt) cc_final: 0.9116 (mt) REVERT: I 104 THR cc_start: 0.8927 (m) cc_final: 0.8531 (t) REVERT: I 146 GLU cc_start: 0.7007 (mp0) cc_final: 0.6567 (mp0) REVERT: I 265 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8460 (tt0) REVERT: I 268 LEU cc_start: 0.7529 (pp) cc_final: 0.7210 (pp) REVERT: I 322 GLU cc_start: 0.8355 (pm20) cc_final: 0.8012 (pm20) REVERT: I 323 SER cc_start: 0.9085 (m) cc_final: 0.8882 (m) REVERT: I 326 ASP cc_start: 0.8738 (t0) cc_final: 0.8422 (t0) REVERT: I 465 ILE cc_start: 0.8870 (mm) cc_final: 0.8247 (tp) REVERT: I 502 ASP cc_start: 0.6427 (t0) cc_final: 0.6194 (t70) REVERT: I 514 MET cc_start: 0.8055 (mmp) cc_final: 0.7771 (tmm) REVERT: I 607 LEU cc_start: 0.9542 (mt) cc_final: 0.9062 (mt) REVERT: I 646 LYS cc_start: 0.8719 (pptt) cc_final: 0.8355 (tmtt) REVERT: I 650 GLU cc_start: 0.8297 (pp20) cc_final: 0.7955 (pp20) REVERT: I 658 ILE cc_start: 0.8870 (pt) cc_final: 0.8138 (mp) REVERT: I 661 ILE cc_start: 0.7798 (pt) cc_final: 0.7086 (tp) REVERT: I 723 GLU cc_start: 0.7847 (tp30) cc_final: 0.7620 (tp30) REVERT: I 884 MET cc_start: 0.7546 (mtp) cc_final: 0.7220 (mtp) REVERT: J 116 GLU cc_start: 0.7069 (pp20) cc_final: 0.5688 (tm-30) REVERT: J 117 ASP cc_start: 0.7968 (m-30) cc_final: 0.7289 (p0) REVERT: J 171 GLU cc_start: 0.8144 (tp30) cc_final: 0.7833 (tp30) REVERT: J 174 LEU cc_start: 0.9519 (tt) cc_final: 0.9301 (tt) REVERT: J 193 MET cc_start: 0.8320 (ptp) cc_final: 0.7838 (mtm) REVERT: J 222 GLU cc_start: 0.5070 (tt0) cc_final: 0.4482 (tt0) REVERT: J 256 ASP cc_start: 0.8531 (m-30) cc_final: 0.8270 (m-30) REVERT: J 261 GLU cc_start: 0.6848 (pp20) cc_final: 0.5726 (mt-10) REVERT: J 313 ASP cc_start: 0.7689 (t0) cc_final: 0.7475 (t0) REVERT: J 374 LEU cc_start: 0.8956 (mt) cc_final: 0.8642 (mt) REVERT: J 544 SER cc_start: 0.9377 (m) cc_final: 0.8945 (p) REVERT: J 609 HIS cc_start: 0.8648 (t70) cc_final: 0.8371 (t-90) REVERT: J 735 ASP cc_start: 0.7378 (p0) cc_final: 0.7072 (p0) REVERT: J 854 THR cc_start: 0.8605 (p) cc_final: 0.8320 (t) REVERT: P 33 GLU cc_start: 0.8593 (pt0) cc_final: 0.7896 (pp20) REVERT: P 40 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8371 (tp30) REVERT: P 146 MET cc_start: 0.6920 (mtp) cc_final: 0.6491 (mtp) REVERT: P 291 MET cc_start: 0.7210 (mtm) cc_final: 0.6645 (mtm) REVERT: P 330 PHE cc_start: 0.8591 (m-80) cc_final: 0.8307 (m-80) REVERT: P 368 ARG cc_start: 0.8679 (ttm-80) cc_final: 0.8405 (ttp-170) REVERT: P 478 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7902 (mm-30) REVERT: P 517 LEU cc_start: 0.8764 (pp) cc_final: 0.8560 (pt) REVERT: P 518 TYR cc_start: 0.7967 (p90) cc_final: 0.7617 (p90) REVERT: P 544 MET cc_start: 0.7333 (mmm) cc_final: 0.6958 (mmm) REVERT: P 566 ILE cc_start: 0.9380 (mm) cc_final: 0.9171 (mm) REVERT: P 569 MET cc_start: 0.7873 (mtm) cc_final: 0.7442 (mtp) REVERT: P 626 ILE cc_start: 0.9158 (mt) cc_final: 0.8853 (tp) REVERT: P 644 THR cc_start: 0.8247 (p) cc_final: 0.7536 (p) REVERT: P 866 THR cc_start: 0.6660 (m) cc_final: 0.6382 (m) outliers start: 4 outliers final: 2 residues processed: 2895 average time/residue: 1.7652 time to fit residues: 8568.6209 Evaluate side-chains 2385 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2383 time to evaluate : 7.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 902 random chunks: chunk 810 optimal weight: 2.9990 chunk 616 optimal weight: 4.9990 chunk 425 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 391 optimal weight: 5.9990 chunk 551 optimal weight: 0.6980 chunk 823 optimal weight: 4.9990 chunk 871 optimal weight: 8.9990 chunk 430 optimal weight: 0.9990 chunk 780 optimal weight: 0.7980 chunk 234 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 HIS A 574 HIS B 122 GLN B 298 ASN ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 GLN C 137 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN C 512 GLN C 626 ASN C 880 ASN D 396 GLN E 508 HIS E 560 ASN E 874 ASN F 199 ASN F 497 ASN ** F 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 760 ASN ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 ASN G 318 HIS G 460 GLN ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 477 ASN G 503 ASN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 718 GLN ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 HIS I 199 ASN I 695 ASN I 760 ASN J 483 ASN ** J 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 42 HIS P 529 HIS ** P 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 75677 Z= 0.178 Angle : 0.562 10.726 102731 Z= 0.303 Chirality : 0.040 0.209 11785 Planarity : 0.005 0.085 13216 Dihedral : 7.837 163.084 10332 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.86 % Favored : 93.12 % Rotamer: Outliers : 0.04 % Allowed : 1.27 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.09), residues: 9006 helix: 0.36 (0.08), residues: 4252 sheet: -1.92 (0.17), residues: 732 loop : -2.15 (0.09), residues: 4022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 416 HIS 0.012 0.001 HIS G 257 PHE 0.028 0.001 PHE A 481 TYR 0.029 0.001 TYR E 262 ARG 0.010 0.000 ARG I 701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2905 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2902 time to evaluate : 8.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.7323 (pm20) cc_final: 0.7116 (pm20) REVERT: A 164 ASP cc_start: 0.7038 (m-30) cc_final: 0.6793 (m-30) REVERT: A 193 MET cc_start: 0.7150 (ptp) cc_final: 0.6803 (ptp) REVERT: A 373 PHE cc_start: 0.8181 (m-80) cc_final: 0.7850 (m-80) REVERT: A 477 ASN cc_start: 0.8881 (p0) cc_final: 0.8270 (t0) REVERT: A 492 ILE cc_start: 0.8862 (mt) cc_final: 0.8393 (mm) REVERT: A 502 ASP cc_start: 0.7580 (t70) cc_final: 0.7356 (t70) REVERT: A 569 THR cc_start: 0.8653 (p) cc_final: 0.8383 (t) REVERT: A 706 ILE cc_start: 0.9123 (pt) cc_final: 0.8436 (pt) REVERT: A 714 TYR cc_start: 0.8247 (m-80) cc_final: 0.7757 (m-80) REVERT: A 725 TYR cc_start: 0.7963 (m-80) cc_final: 0.7167 (m-80) REVERT: A 761 ASN cc_start: 0.8715 (m-40) cc_final: 0.8231 (p0) REVERT: A 772 PHE cc_start: 0.8274 (p90) cc_final: 0.7843 (p90) REVERT: A 812 ASP cc_start: 0.8855 (t70) cc_final: 0.8465 (t70) REVERT: A 846 MET cc_start: 0.8321 (tmm) cc_final: 0.7699 (tmm) REVERT: A 868 ASP cc_start: 0.7385 (t70) cc_final: 0.6737 (t70) REVERT: B 175 ASN cc_start: 0.8324 (m-40) cc_final: 0.7989 (m-40) REVERT: B 178 ASP cc_start: 0.8219 (t0) cc_final: 0.8017 (t0) REVERT: B 211 THR cc_start: 0.8216 (m) cc_final: 0.7951 (m) REVERT: B 218 ILE cc_start: 0.9290 (mt) cc_final: 0.9085 (tp) REVERT: B 362 LEU cc_start: 0.7931 (mp) cc_final: 0.7179 (mp) REVERT: B 363 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6908 (mm-30) REVERT: B 408 TYR cc_start: 0.8174 (m-80) cc_final: 0.7888 (m-80) REVERT: B 450 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8270 (mm-40) REVERT: B 472 ASN cc_start: 0.7727 (t0) cc_final: 0.7256 (m110) REVERT: B 651 ASP cc_start: 0.7988 (t70) cc_final: 0.7706 (t70) REVERT: B 700 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7175 (tm-30) REVERT: B 708 GLN cc_start: 0.6813 (mp10) cc_final: 0.5381 (mp10) REVERT: B 786 ASP cc_start: 0.8957 (p0) cc_final: 0.8696 (p0) REVERT: B 824 TRP cc_start: 0.3137 (t60) cc_final: 0.2843 (t60) REVERT: C 227 VAL cc_start: 0.9097 (m) cc_final: 0.8790 (t) REVERT: C 234 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6986 (tm-30) REVERT: C 250 SER cc_start: 0.9330 (p) cc_final: 0.8793 (p) REVERT: C 256 ASP cc_start: 0.8558 (m-30) cc_final: 0.8301 (m-30) REVERT: C 257 HIS cc_start: 0.8410 (t-170) cc_final: 0.8038 (t70) REVERT: C 266 HIS cc_start: 0.8421 (m90) cc_final: 0.8206 (m90) REVERT: C 270 GLU cc_start: 0.7812 (mp0) cc_final: 0.7549 (mp0) REVERT: C 291 TYR cc_start: 0.8000 (m-80) cc_final: 0.7600 (m-80) REVERT: C 380 GLN cc_start: 0.6431 (tm-30) cc_final: 0.6174 (tm-30) REVERT: C 384 ASP cc_start: 0.8600 (m-30) cc_final: 0.7849 (m-30) REVERT: C 385 CYS cc_start: 0.8403 (t) cc_final: 0.8057 (t) REVERT: C 407 ASN cc_start: 0.8840 (t0) cc_final: 0.8624 (t0) REVERT: C 484 ASN cc_start: 0.8777 (m-40) cc_final: 0.8176 (t0) REVERT: C 646 LYS cc_start: 0.8478 (tttt) cc_final: 0.8252 (tttt) REVERT: C 650 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7852 (tm-30) REVERT: C 666 ASP cc_start: 0.7578 (t70) cc_final: 0.6776 (t70) REVERT: C 770 LEU cc_start: 0.8367 (tp) cc_final: 0.8038 (tp) REVERT: C 849 LEU cc_start: 0.8786 (mt) cc_final: 0.8556 (mp) REVERT: C 884 MET cc_start: 0.7358 (mtp) cc_final: 0.7106 (tpp) REVERT: D 240 GLN cc_start: 0.8103 (pt0) cc_final: 0.7653 (tt0) REVERT: D 253 HIS cc_start: 0.8565 (t-90) cc_final: 0.8194 (t-90) REVERT: D 270 GLU cc_start: 0.7152 (mp0) cc_final: 0.6944 (mp0) REVERT: D 286 ARG cc_start: 0.8325 (mtm180) cc_final: 0.7852 (mtm-85) REVERT: D 484 ASN cc_start: 0.8557 (m110) cc_final: 0.8202 (t0) REVERT: D 534 ARG cc_start: 0.8652 (ttp-170) cc_final: 0.8313 (ttm-80) REVERT: D 708 GLN cc_start: 0.8555 (mp10) cc_final: 0.7938 (mp10) REVERT: D 751 TYR cc_start: 0.7754 (m-80) cc_final: 0.7448 (m-80) REVERT: D 841 ASP cc_start: 0.8471 (t70) cc_final: 0.8225 (t0) REVERT: D 843 ARG cc_start: 0.8671 (mpp80) cc_final: 0.8306 (mtm-85) REVERT: D 879 ASP cc_start: 0.8594 (p0) cc_final: 0.8127 (p0) REVERT: D 880 ASN cc_start: 0.8651 (m-40) cc_final: 0.8340 (t0) REVERT: D 884 MET cc_start: 0.7269 (tpp) cc_final: 0.7001 (tpp) REVERT: E 164 ASP cc_start: 0.6395 (m-30) cc_final: 0.5748 (p0) REVERT: E 205 LYS cc_start: 0.8626 (mttm) cc_final: 0.8012 (mtpt) REVERT: E 223 GLU cc_start: 0.8460 (tp30) cc_final: 0.7596 (tp30) REVERT: E 261 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7668 (tm-30) REVERT: E 270 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7281 (mt-10) REVERT: E 272 LEU cc_start: 0.8379 (tp) cc_final: 0.8141 (tp) REVERT: E 310 LEU cc_start: 0.7367 (mt) cc_final: 0.6970 (mp) REVERT: E 434 CYS cc_start: 0.8045 (t) cc_final: 0.7570 (t) REVERT: E 511 ASN cc_start: 0.9070 (m-40) cc_final: 0.8738 (m-40) REVERT: E 581 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7771 (mm-30) REVERT: E 669 MET cc_start: 0.7233 (mtt) cc_final: 0.6991 (mtt) REVERT: E 695 ASN cc_start: 0.8826 (p0) cc_final: 0.8535 (p0) REVERT: E 699 ILE cc_start: 0.9297 (mt) cc_final: 0.9095 (mt) REVERT: E 753 GLN cc_start: 0.6583 (tp40) cc_final: 0.6322 (tp-100) REVERT: E 807 TYR cc_start: 0.8210 (m-80) cc_final: 0.7279 (m-10) REVERT: E 826 PRO cc_start: 0.8971 (Cg_exo) cc_final: 0.8688 (Cg_endo) REVERT: F 171 GLU cc_start: 0.7425 (tp30) cc_final: 0.7138 (tp30) REVERT: F 221 ASP cc_start: 0.6672 (t70) cc_final: 0.5844 (t70) REVERT: F 287 ASN cc_start: 0.7231 (t0) cc_final: 0.7000 (t0) REVERT: F 313 ASP cc_start: 0.8404 (t0) cc_final: 0.8050 (m-30) REVERT: F 326 ASP cc_start: 0.8603 (t0) cc_final: 0.8315 (t0) REVERT: F 331 SER cc_start: 0.9203 (m) cc_final: 0.8947 (t) REVERT: F 335 LEU cc_start: 0.9212 (tp) cc_final: 0.8997 (tp) REVERT: F 424 ASP cc_start: 0.7708 (p0) cc_final: 0.7220 (p0) REVERT: F 452 MET cc_start: 0.7854 (ttm) cc_final: 0.7477 (ttm) REVERT: F 480 HIS cc_start: 0.7559 (t70) cc_final: 0.7213 (t-170) REVERT: F 574 HIS cc_start: 0.6842 (t70) cc_final: 0.6505 (t70) REVERT: F 586 THR cc_start: 0.8669 (p) cc_final: 0.8368 (p) REVERT: F 605 GLN cc_start: 0.8436 (pp30) cc_final: 0.8216 (pp30) REVERT: F 621 TYR cc_start: 0.8371 (t80) cc_final: 0.7947 (t80) REVERT: F 651 ASP cc_start: 0.6950 (t70) cc_final: 0.6343 (t0) REVERT: F 696 MET cc_start: 0.8145 (ppp) cc_final: 0.7661 (ptt) REVERT: G 148 GLU cc_start: 0.7429 (tp30) cc_final: 0.7104 (tp30) REVERT: G 221 ASP cc_start: 0.8122 (t70) cc_final: 0.7788 (t70) REVERT: G 277 ILE cc_start: 0.9515 (mt) cc_final: 0.9279 (mm) REVERT: G 355 LYS cc_start: 0.8387 (ptmm) cc_final: 0.7492 (tptt) REVERT: G 426 PHE cc_start: 0.8058 (m-80) cc_final: 0.7771 (m-10) REVERT: G 468 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8061 (tm-30) REVERT: G 541 LEU cc_start: 0.9378 (mm) cc_final: 0.9158 (mm) REVERT: G 576 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7199 (pm20) REVERT: H 116 GLU cc_start: 0.6676 (mt-10) cc_final: 0.6387 (mt-10) REVERT: H 221 ASP cc_start: 0.7298 (t70) cc_final: 0.7054 (t70) REVERT: H 257 HIS cc_start: 0.8329 (t70) cc_final: 0.7856 (t-90) REVERT: H 287 ASN cc_start: 0.8029 (t0) cc_final: 0.7715 (t0) REVERT: H 326 ASP cc_start: 0.8661 (t0) cc_final: 0.8425 (t0) REVERT: H 467 GLU cc_start: 0.7003 (tt0) cc_final: 0.6753 (tt0) REVERT: H 480 HIS cc_start: 0.7983 (t70) cc_final: 0.7386 (t-90) REVERT: H 550 LEU cc_start: 0.9049 (mt) cc_final: 0.8814 (mt) REVERT: H 553 LEU cc_start: 0.9602 (tp) cc_final: 0.9336 (tp) REVERT: H 609 HIS cc_start: 0.7617 (t70) cc_final: 0.7065 (t70) REVERT: H 613 VAL cc_start: 0.9294 (t) cc_final: 0.8843 (p) REVERT: H 623 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7815 (mm-30) REVERT: H 687 ASP cc_start: 0.8603 (t0) cc_final: 0.8311 (t0) REVERT: H 694 MET cc_start: 0.7619 (ptm) cc_final: 0.5969 (tpt) REVERT: H 744 GLU cc_start: 0.6956 (mp0) cc_final: 0.6352 (mp0) REVERT: H 812 ASP cc_start: 0.8521 (p0) cc_final: 0.7552 (p0) REVERT: I 104 THR cc_start: 0.8845 (m) cc_final: 0.8480 (t) REVERT: I 261 GLU cc_start: 0.6590 (pp20) cc_final: 0.5993 (pp20) REVERT: I 268 LEU cc_start: 0.7523 (pp) cc_final: 0.7151 (pp) REVERT: I 293 LEU cc_start: 0.8616 (pt) cc_final: 0.8401 (pt) REVERT: I 320 ASN cc_start: 0.7769 (t0) cc_final: 0.7535 (t0) REVERT: I 322 GLU cc_start: 0.8216 (pm20) cc_final: 0.7841 (pm20) REVERT: I 342 ASP cc_start: 0.8191 (t0) cc_final: 0.7869 (t0) REVERT: I 465 ILE cc_start: 0.8861 (mm) cc_final: 0.8228 (tp) REVERT: I 502 ASP cc_start: 0.6297 (t0) cc_final: 0.5937 (t0) REVERT: I 521 SER cc_start: 0.9581 (m) cc_final: 0.9282 (p) REVERT: I 559 TYR cc_start: 0.8674 (t80) cc_final: 0.8375 (t80) REVERT: I 644 LYS cc_start: 0.8467 (pttm) cc_final: 0.8182 (pttm) REVERT: I 646 LYS cc_start: 0.8658 (pptt) cc_final: 0.8387 (tmtt) REVERT: I 658 ILE cc_start: 0.8809 (pt) cc_final: 0.8039 (mp) REVERT: I 661 ILE cc_start: 0.7672 (pt) cc_final: 0.7008 (tp) REVERT: I 723 GLU cc_start: 0.7684 (tp30) cc_final: 0.7290 (tp30) REVERT: I 786 ASP cc_start: 0.7917 (p0) cc_final: 0.7567 (p0) REVERT: I 805 ILE cc_start: 0.9182 (mm) cc_final: 0.8964 (mm) REVERT: J 116 GLU cc_start: 0.6916 (pp20) cc_final: 0.6438 (pp20) REVERT: J 193 MET cc_start: 0.8211 (ptp) cc_final: 0.7769 (mtm) REVERT: J 218 ILE cc_start: 0.8824 (mm) cc_final: 0.8299 (tp) REVERT: J 238 ARG cc_start: 0.8158 (tpp80) cc_final: 0.7741 (mmm-85) REVERT: J 256 ASP cc_start: 0.8402 (m-30) cc_final: 0.8107 (m-30) REVERT: J 557 LEU cc_start: 0.9456 (tp) cc_final: 0.9246 (tp) REVERT: J 585 LEU cc_start: 0.8786 (mm) cc_final: 0.8362 (mm) REVERT: J 592 CYS cc_start: 0.9089 (m) cc_final: 0.8556 (t) REVERT: J 609 HIS cc_start: 0.8510 (t70) cc_final: 0.8204 (t-90) REVERT: J 714 TYR cc_start: 0.7373 (m-80) cc_final: 0.7083 (m-80) REVERT: J 735 ASP cc_start: 0.7430 (p0) cc_final: 0.7165 (p0) REVERT: J 854 THR cc_start: 0.8498 (p) cc_final: 0.8197 (t) REVERT: P 27 TYR cc_start: 0.7594 (m-80) cc_final: 0.7326 (m-80) REVERT: P 33 GLU cc_start: 0.8402 (pt0) cc_final: 0.7607 (pp20) REVERT: P 40 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8133 (tp30) REVERT: P 146 MET cc_start: 0.6707 (mtp) cc_final: 0.6260 (mtp) REVERT: P 208 ASN cc_start: 0.9029 (m110) cc_final: 0.8769 (m-40) REVERT: P 215 MET cc_start: 0.9092 (mmm) cc_final: 0.8844 (mmm) REVERT: P 221 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7395 (mt-10) REVERT: P 291 MET cc_start: 0.7218 (mtm) cc_final: 0.6825 (mtm) REVERT: P 328 TRP cc_start: 0.8437 (m100) cc_final: 0.8072 (m100) REVERT: P 330 PHE cc_start: 0.8461 (m-80) cc_final: 0.8169 (m-80) REVERT: P 478 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7810 (mm-30) REVERT: P 518 TYR cc_start: 0.7935 (p90) cc_final: 0.7529 (p90) REVERT: P 544 MET cc_start: 0.7036 (mmm) cc_final: 0.6755 (mmm) REVERT: P 597 LYS cc_start: 0.7369 (tttm) cc_final: 0.7027 (tppt) REVERT: P 644 THR cc_start: 0.8053 (p) cc_final: 0.7471 (p) REVERT: P 736 ILE cc_start: 0.8822 (mt) cc_final: 0.8615 (mt) REVERT: P 785 GLN cc_start: 0.7645 (tt0) cc_final: 0.7431 (tt0) REVERT: P 903 LEU cc_start: 0.8770 (mt) cc_final: 0.8406 (mt) outliers start: 3 outliers final: 1 residues processed: 2904 average time/residue: 1.7271 time to fit residues: 8448.9136 Evaluate side-chains 2441 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2440 time to evaluate : 8.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 902 random chunks: chunk 726 optimal weight: 5.9990 chunk 494 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 649 optimal weight: 4.9990 chunk 359 optimal weight: 3.9990 chunk 744 optimal weight: 6.9990 chunk 602 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 445 optimal weight: 4.9990 chunk 782 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN B 718 GLN ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN D 512 GLN D 576 GLN ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 695 ASN F 760 ASN F 761 ASN ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 718 GLN H 199 ASN I 695 ASN ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 483 ASN ** J 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 738 GLN P 529 HIS P 595 GLN ** P 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 912 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 75677 Z= 0.351 Angle : 0.638 7.689 102731 Z= 0.349 Chirality : 0.041 0.193 11785 Planarity : 0.005 0.099 13216 Dihedral : 7.815 161.080 10332 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.64 % Favored : 91.33 % Rotamer: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.09), residues: 9006 helix: 0.29 (0.08), residues: 4297 sheet: -1.93 (0.18), residues: 712 loop : -2.25 (0.09), residues: 3997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 416 HIS 0.013 0.002 HIS G 257 PHE 0.022 0.002 PHE P 509 TYR 0.031 0.002 TYR B 621 ARG 0.017 0.001 ARG P 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2720 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2718 time to evaluate : 8.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.7241 (ptp) cc_final: 0.6968 (ptp) REVERT: A 425 MET cc_start: 0.8412 (tpp) cc_final: 0.8156 (ttt) REVERT: A 492 ILE cc_start: 0.8839 (mt) cc_final: 0.8419 (mm) REVERT: A 562 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 569 THR cc_start: 0.8870 (p) cc_final: 0.8583 (t) REVERT: A 605 GLN cc_start: 0.8936 (mp10) cc_final: 0.8482 (mp10) REVERT: A 607 LEU cc_start: 0.9562 (mt) cc_final: 0.8995 (mt) REVERT: A 677 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8526 (ttm110) REVERT: A 689 PHE cc_start: 0.8984 (t80) cc_final: 0.8764 (t80) REVERT: A 706 ILE cc_start: 0.9116 (pt) cc_final: 0.8475 (pt) REVERT: A 714 TYR cc_start: 0.8270 (m-80) cc_final: 0.7871 (m-80) REVERT: A 725 TYR cc_start: 0.7950 (m-80) cc_final: 0.7241 (m-80) REVERT: A 761 ASN cc_start: 0.8814 (m-40) cc_final: 0.8318 (p0) REVERT: A 846 MET cc_start: 0.8325 (tmm) cc_final: 0.7884 (tmm) REVERT: A 868 ASP cc_start: 0.7520 (t70) cc_final: 0.6895 (t70) REVERT: B 211 THR cc_start: 0.8276 (m) cc_final: 0.8013 (m) REVERT: B 230 ARG cc_start: 0.7697 (mtt-85) cc_final: 0.7425 (ttp-170) REVERT: B 268 LEU cc_start: 0.9010 (mt) cc_final: 0.8511 (mt) REVERT: B 362 LEU cc_start: 0.7989 (mp) cc_final: 0.7200 (mt) REVERT: B 363 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7085 (mm-30) REVERT: B 408 TYR cc_start: 0.8352 (m-80) cc_final: 0.8136 (m-80) REVERT: B 450 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8361 (mm-40) REVERT: B 700 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7214 (tm-30) REVERT: B 708 GLN cc_start: 0.6919 (mp10) cc_final: 0.5442 (mp10) REVERT: B 824 TRP cc_start: 0.3945 (t60) cc_final: 0.3032 (t60) REVERT: B 879 ASP cc_start: 0.7963 (p0) cc_final: 0.6713 (t0) REVERT: B 880 ASN cc_start: 0.7514 (m110) cc_final: 0.7127 (m110) REVERT: C 227 VAL cc_start: 0.9151 (m) cc_final: 0.8881 (t) REVERT: C 234 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7203 (tm-30) REVERT: C 250 SER cc_start: 0.9257 (p) cc_final: 0.8945 (p) REVERT: C 256 ASP cc_start: 0.8636 (m-30) cc_final: 0.8293 (m-30) REVERT: C 270 GLU cc_start: 0.7827 (mp0) cc_final: 0.7548 (mp0) REVERT: C 385 CYS cc_start: 0.8428 (t) cc_final: 0.8167 (t) REVERT: C 429 GLU cc_start: 0.8130 (pm20) cc_final: 0.7573 (pt0) REVERT: C 484 ASN cc_start: 0.8761 (m-40) cc_final: 0.8238 (t0) REVERT: C 645 MET cc_start: 0.8151 (mmm) cc_final: 0.7939 (mmm) REVERT: C 646 LYS cc_start: 0.8640 (tttt) cc_final: 0.8385 (tttt) REVERT: C 686 LEU cc_start: 0.8720 (tp) cc_final: 0.8455 (tp) REVERT: C 729 ASN cc_start: 0.8883 (p0) cc_final: 0.8607 (p0) REVERT: C 770 LEU cc_start: 0.8437 (tp) cc_final: 0.8125 (tp) REVERT: C 802 LEU cc_start: 0.8747 (tp) cc_final: 0.8517 (tp) REVERT: C 849 LEU cc_start: 0.8874 (mt) cc_final: 0.8628 (mp) REVERT: C 854 THR cc_start: 0.8795 (m) cc_final: 0.8376 (t) REVERT: D 240 GLN cc_start: 0.8273 (pt0) cc_final: 0.7957 (tt0) REVERT: D 261 GLU cc_start: 0.7426 (tp30) cc_final: 0.7083 (tp30) REVERT: D 422 PRO cc_start: 0.8493 (Cg_exo) cc_final: 0.8097 (Cg_endo) REVERT: D 484 ASN cc_start: 0.8506 (m110) cc_final: 0.8226 (t0) REVERT: D 490 VAL cc_start: 0.8921 (p) cc_final: 0.8710 (m) REVERT: D 534 ARG cc_start: 0.8746 (ttp-170) cc_final: 0.8359 (ttt180) REVERT: D 751 TYR cc_start: 0.7982 (m-80) cc_final: 0.7621 (m-80) REVERT: D 843 ARG cc_start: 0.8723 (mpp80) cc_final: 0.8395 (mpp80) REVERT: D 879 ASP cc_start: 0.8507 (p0) cc_final: 0.8208 (p0) REVERT: D 884 MET cc_start: 0.7376 (tpp) cc_final: 0.6780 (tpp) REVERT: E 164 ASP cc_start: 0.6554 (m-30) cc_final: 0.6191 (p0) REVERT: E 205 LYS cc_start: 0.8701 (mttm) cc_final: 0.8002 (mtpp) REVERT: E 434 CYS cc_start: 0.8199 (t) cc_final: 0.7760 (t) REVERT: E 511 ASN cc_start: 0.9143 (m-40) cc_final: 0.8891 (m-40) REVERT: E 568 ILE cc_start: 0.9428 (mt) cc_final: 0.9118 (tp) REVERT: E 753 GLN cc_start: 0.6864 (tp40) cc_final: 0.6582 (tp-100) REVERT: E 757 MET cc_start: 0.7750 (mtt) cc_final: 0.7282 (mtt) REVERT: E 807 TYR cc_start: 0.8165 (m-80) cc_final: 0.7245 (m-10) REVERT: E 826 PRO cc_start: 0.9066 (Cg_exo) cc_final: 0.8835 (Cg_endo) REVERT: F 171 GLU cc_start: 0.7513 (tp30) cc_final: 0.7118 (tp30) REVERT: F 268 LEU cc_start: 0.7729 (pp) cc_final: 0.7067 (pp) REVERT: F 313 ASP cc_start: 0.8469 (t0) cc_final: 0.8155 (m-30) REVERT: F 326 ASP cc_start: 0.8658 (t0) cc_final: 0.8347 (t0) REVERT: F 331 SER cc_start: 0.9260 (m) cc_final: 0.8958 (t) REVERT: F 424 ASP cc_start: 0.7693 (p0) cc_final: 0.7437 (p0) REVERT: F 605 GLN cc_start: 0.8450 (pp30) cc_final: 0.8173 (pp30) REVERT: F 621 TYR cc_start: 0.8491 (t80) cc_final: 0.8088 (t80) REVERT: F 640 LEU cc_start: 0.8926 (mt) cc_final: 0.8657 (mt) REVERT: F 672 LEU cc_start: 0.9536 (tt) cc_final: 0.9328 (tt) REVERT: F 696 MET cc_start: 0.8272 (ppp) cc_final: 0.7841 (ptt) REVERT: F 869 THR cc_start: 0.7723 (t) cc_final: 0.7447 (t) REVERT: G 261 GLU cc_start: 0.5086 (pp20) cc_final: 0.4157 (pp20) REVERT: G 268 LEU cc_start: 0.7975 (pp) cc_final: 0.7768 (pp) REVERT: G 277 ILE cc_start: 0.9572 (mt) cc_final: 0.9369 (mm) REVERT: G 291 TYR cc_start: 0.8874 (m-80) cc_final: 0.8576 (m-10) REVERT: G 316 ASN cc_start: 0.8414 (m-40) cc_final: 0.8200 (m-40) REVERT: G 355 LYS cc_start: 0.8578 (ptmm) cc_final: 0.7646 (tptt) REVERT: G 379 SER cc_start: 0.8528 (m) cc_final: 0.7823 (p) REVERT: G 380 GLN cc_start: 0.7816 (mt0) cc_final: 0.7604 (mp10) REVERT: G 396 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8462 (mm-40) REVERT: G 399 MET cc_start: 0.8892 (pmm) cc_final: 0.8504 (ptp) REVERT: G 452 MET cc_start: 0.8168 (tpp) cc_final: 0.7688 (tpt) REVERT: G 458 ASP cc_start: 0.8820 (t0) cc_final: 0.8615 (t0) REVERT: G 464 GLN cc_start: 0.8044 (mt0) cc_final: 0.7323 (mt0) REVERT: G 468 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8194 (tm-30) REVERT: G 484 ASN cc_start: 0.8561 (m-40) cc_final: 0.7569 (t0) REVERT: G 576 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7186 (pm20) REVERT: G 807 TYR cc_start: 0.8405 (m-80) cc_final: 0.8136 (m-10) REVERT: H 112 LEU cc_start: 0.8415 (tp) cc_final: 0.8181 (tp) REVERT: H 216 ASP cc_start: 0.7487 (p0) cc_final: 0.7246 (p0) REVERT: H 221 ASP cc_start: 0.7555 (t70) cc_final: 0.7183 (t70) REVERT: H 287 ASN cc_start: 0.8136 (t0) cc_final: 0.7829 (t0) REVERT: H 313 ASP cc_start: 0.7550 (t0) cc_final: 0.7290 (t0) REVERT: H 425 MET cc_start: 0.8063 (ttm) cc_final: 0.7835 (ttm) REVERT: H 550 LEU cc_start: 0.9093 (mt) cc_final: 0.8893 (mt) REVERT: H 553 LEU cc_start: 0.9595 (tp) cc_final: 0.9337 (tp) REVERT: H 560 ASN cc_start: 0.8801 (m-40) cc_final: 0.8519 (m-40) REVERT: H 613 VAL cc_start: 0.9327 (t) cc_final: 0.9018 (p) REVERT: H 687 ASP cc_start: 0.8676 (t0) cc_final: 0.8402 (t0) REVERT: H 694 MET cc_start: 0.7673 (ptm) cc_final: 0.5865 (tmm) REVERT: H 698 GLN cc_start: 0.8839 (tp40) cc_final: 0.8406 (tp-100) REVERT: H 706 ILE cc_start: 0.9105 (pt) cc_final: 0.8589 (pt) REVERT: H 744 GLU cc_start: 0.7512 (mp0) cc_final: 0.6611 (mp0) REVERT: H 848 MET cc_start: 0.8101 (tpp) cc_final: 0.6800 (ttm) REVERT: I 102 ILE cc_start: 0.9359 (mt) cc_final: 0.9104 (mt) REVERT: I 104 THR cc_start: 0.8871 (m) cc_final: 0.8510 (t) REVERT: I 146 GLU cc_start: 0.7284 (mp0) cc_final: 0.6827 (mp0) REVERT: I 150 ARG cc_start: 0.4937 (ptp-170) cc_final: 0.4352 (ptp-170) REVERT: I 171 GLU cc_start: 0.8194 (tp30) cc_final: 0.7791 (tp30) REVERT: I 268 LEU cc_start: 0.8018 (pp) cc_final: 0.7726 (pp) REVERT: I 322 GLU cc_start: 0.8311 (pm20) cc_final: 0.7908 (pm20) REVERT: I 323 SER cc_start: 0.9154 (m) cc_final: 0.8939 (m) REVERT: I 342 ASP cc_start: 0.8241 (t0) cc_final: 0.7918 (t0) REVERT: I 465 ILE cc_start: 0.9032 (mm) cc_final: 0.8428 (tp) REVERT: I 521 SER cc_start: 0.9571 (m) cc_final: 0.9341 (p) REVERT: I 559 TYR cc_start: 0.8792 (t80) cc_final: 0.8462 (t80) REVERT: I 644 LYS cc_start: 0.8500 (pttm) cc_final: 0.8217 (pttm) REVERT: I 650 GLU cc_start: 0.8307 (pp20) cc_final: 0.7856 (pp20) REVERT: I 658 ILE cc_start: 0.8879 (pt) cc_final: 0.8255 (mp) REVERT: I 661 ILE cc_start: 0.7748 (pt) cc_final: 0.7209 (tp) REVERT: I 723 GLU cc_start: 0.7843 (tp30) cc_final: 0.7555 (tp30) REVERT: I 729 ASN cc_start: 0.8860 (p0) cc_final: 0.8350 (p0) REVERT: J 193 MET cc_start: 0.8204 (ptp) cc_final: 0.7822 (mtm) REVERT: J 218 ILE cc_start: 0.9006 (mm) cc_final: 0.8470 (tp) REVERT: J 256 ASP cc_start: 0.8504 (m-30) cc_final: 0.8169 (m-30) REVERT: J 261 GLU cc_start: 0.6187 (pp20) cc_final: 0.5967 (tm-30) REVERT: J 609 HIS cc_start: 0.8627 (t70) cc_final: 0.8272 (t-90) REVERT: J 714 TYR cc_start: 0.7499 (m-80) cc_final: 0.7284 (m-80) REVERT: J 735 ASP cc_start: 0.7451 (p0) cc_final: 0.7138 (p0) REVERT: J 854 THR cc_start: 0.8571 (p) cc_final: 0.8224 (t) REVERT: P 33 GLU cc_start: 0.8504 (pt0) cc_final: 0.7858 (pp20) REVERT: P 40 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7863 (tp30) REVERT: P 225 ILE cc_start: 0.9374 (mt) cc_final: 0.9141 (mt) REVERT: P 291 MET cc_start: 0.7510 (mtm) cc_final: 0.7147 (mtm) REVERT: P 328 TRP cc_start: 0.8567 (m100) cc_final: 0.8332 (m100) REVERT: P 462 ILE cc_start: 0.8398 (mm) cc_final: 0.8074 (mm) REVERT: P 518 TYR cc_start: 0.8054 (p90) cc_final: 0.7616 (p90) REVERT: P 544 MET cc_start: 0.7066 (mmm) cc_final: 0.6846 (mmm) REVERT: P 597 LYS cc_start: 0.7524 (tttm) cc_final: 0.7115 (tppt) REVERT: P 624 LYS cc_start: 0.8691 (mmmt) cc_final: 0.8424 (mmmt) REVERT: P 626 ILE cc_start: 0.9146 (mt) cc_final: 0.8693 (tp) REVERT: P 884 PHE cc_start: 0.8262 (m-80) cc_final: 0.8026 (m-80) outliers start: 2 outliers final: 1 residues processed: 2719 average time/residue: 1.7184 time to fit residues: 7858.7454 Evaluate side-chains 2336 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2335 time to evaluate : 7.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 902 random chunks: chunk 293 optimal weight: 5.9990 chunk 785 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 511 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 872 optimal weight: 4.9990 chunk 724 optimal weight: 5.9990 chunk 404 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 458 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN A 574 HIS A 668 GLN ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 695 ASN B 880 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN D 396 GLN D 477 ASN ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 GLN E 423 ASN E 501 ASN E 880 ASN F 760 ASN ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN G 503 ASN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 257 HIS ** I 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 380 GLN J 483 ASN ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 529 HIS P 697 ASN ** P 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 75677 Z= 0.218 Angle : 0.566 11.445 102731 Z= 0.305 Chirality : 0.040 0.167 11785 Planarity : 0.005 0.098 13216 Dihedral : 7.637 160.850 10332 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.17 % Favored : 92.82 % Rotamer: Outliers : 0.04 % Allowed : 1.21 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.09), residues: 9006 helix: 0.56 (0.08), residues: 4315 sheet: -1.74 (0.18), residues: 721 loop : -2.08 (0.09), residues: 3970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 416 HIS 0.013 0.001 HIS G 257 PHE 0.021 0.001 PHE A 816 TYR 0.029 0.002 TYR B 621 ARG 0.011 0.001 ARG P 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2726 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2723 time to evaluate : 8.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LEU cc_start: 0.7977 (tt) cc_final: 0.7662 (tt) REVERT: A 193 MET cc_start: 0.7227 (ptp) cc_final: 0.6960 (ptp) REVERT: A 272 LEU cc_start: 0.8401 (tp) cc_final: 0.8130 (tt) REVERT: A 399 MET cc_start: 0.8516 (pmm) cc_final: 0.8049 (pmm) REVERT: A 477 ASN cc_start: 0.8931 (p0) cc_final: 0.8306 (t0) REVERT: A 492 ILE cc_start: 0.8838 (mt) cc_final: 0.8451 (mm) REVERT: A 502 ASP cc_start: 0.7796 (t70) cc_final: 0.7452 (t70) REVERT: A 569 THR cc_start: 0.8845 (p) cc_final: 0.8596 (t) REVERT: A 605 GLN cc_start: 0.8838 (mp10) cc_final: 0.8460 (mp10) REVERT: A 607 LEU cc_start: 0.9534 (mt) cc_final: 0.9070 (mt) REVERT: A 677 ARG cc_start: 0.8850 (mtm-85) cc_final: 0.8542 (ttm110) REVERT: A 706 ILE cc_start: 0.9074 (pt) cc_final: 0.8431 (pt) REVERT: A 714 TYR cc_start: 0.8269 (m-80) cc_final: 0.7891 (m-80) REVERT: A 725 TYR cc_start: 0.7872 (m-80) cc_final: 0.7160 (m-80) REVERT: A 761 ASN cc_start: 0.8791 (m-40) cc_final: 0.8196 (p0) REVERT: A 812 ASP cc_start: 0.8899 (t70) cc_final: 0.8522 (t70) REVERT: A 846 MET cc_start: 0.8263 (tmm) cc_final: 0.7797 (tmm) REVERT: A 868 ASP cc_start: 0.7608 (t70) cc_final: 0.6952 (t70) REVERT: A 884 MET cc_start: 0.7625 (mmm) cc_final: 0.7289 (mmm) REVERT: B 193 MET cc_start: 0.8879 (pmm) cc_final: 0.8609 (pmm) REVERT: B 211 THR cc_start: 0.8254 (m) cc_final: 0.7986 (m) REVERT: B 215 CYS cc_start: 0.8675 (m) cc_final: 0.8381 (m) REVERT: B 362 LEU cc_start: 0.8066 (mp) cc_final: 0.7422 (mt) REVERT: B 363 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6873 (mm-30) REVERT: B 408 TYR cc_start: 0.8299 (m-80) cc_final: 0.8045 (m-80) REVERT: B 450 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8271 (mm-40) REVERT: B 685 ARG cc_start: 0.8280 (mpt-90) cc_final: 0.8036 (mpt-90) REVERT: B 700 GLU cc_start: 0.7728 (tm-30) cc_final: 0.6814 (tm-30) REVERT: B 762 GLN cc_start: 0.7481 (mt0) cc_final: 0.7123 (mt0) REVERT: B 824 TRP cc_start: 0.4272 (t60) cc_final: 0.3168 (t60) REVERT: B 830 THR cc_start: 0.7952 (m) cc_final: 0.7687 (m) REVERT: B 848 MET cc_start: 0.8731 (mmt) cc_final: 0.8338 (mmm) REVERT: B 879 ASP cc_start: 0.7877 (p0) cc_final: 0.6508 (t0) REVERT: B 880 ASN cc_start: 0.7539 (m-40) cc_final: 0.7211 (m-40) REVERT: C 227 VAL cc_start: 0.9175 (m) cc_final: 0.8890 (t) REVERT: C 234 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7062 (tm-30) REVERT: C 250 SER cc_start: 0.9237 (p) cc_final: 0.8925 (p) REVERT: C 266 HIS cc_start: 0.8567 (m90) cc_final: 0.8329 (m-70) REVERT: C 291 TYR cc_start: 0.8094 (m-80) cc_final: 0.7704 (m-80) REVERT: C 356 MET cc_start: 0.8518 (tpp) cc_final: 0.8188 (tpp) REVERT: C 385 CYS cc_start: 0.8350 (t) cc_final: 0.8089 (t) REVERT: C 429 GLU cc_start: 0.8050 (pm20) cc_final: 0.7612 (pt0) REVERT: C 484 ASN cc_start: 0.8741 (m110) cc_final: 0.8200 (t0) REVERT: C 618 HIS cc_start: 0.7896 (t-170) cc_final: 0.7565 (t70) REVERT: C 641 TYR cc_start: 0.7760 (p90) cc_final: 0.7485 (p90) REVERT: C 770 LEU cc_start: 0.8326 (tp) cc_final: 0.8050 (tp) REVERT: C 802 LEU cc_start: 0.8656 (tp) cc_final: 0.8400 (tp) REVERT: C 882 ARG cc_start: 0.6909 (ttm-80) cc_final: 0.6371 (ttm110) REVERT: D 240 GLN cc_start: 0.8286 (pt0) cc_final: 0.7942 (tt0) REVERT: D 253 HIS cc_start: 0.8529 (t-90) cc_final: 0.8183 (t-90) REVERT: D 295 MET cc_start: 0.7795 (ptp) cc_final: 0.7575 (ptp) REVERT: D 358 GLN cc_start: 0.7732 (mp10) cc_final: 0.7418 (pt0) REVERT: D 396 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7901 (mm110) REVERT: D 484 ASN cc_start: 0.8491 (m110) cc_final: 0.8183 (t0) REVERT: D 534 ARG cc_start: 0.8731 (ttp-170) cc_final: 0.8300 (ttt180) REVERT: D 751 TYR cc_start: 0.7921 (m-80) cc_final: 0.7512 (m-80) REVERT: D 807 TYR cc_start: 0.8400 (m-10) cc_final: 0.8006 (m-10) REVERT: D 843 ARG cc_start: 0.8603 (mpp80) cc_final: 0.8344 (mtm-85) REVERT: D 879 ASP cc_start: 0.8456 (p0) cc_final: 0.8119 (p0) REVERT: D 884 MET cc_start: 0.7279 (tpp) cc_final: 0.6749 (tpp) REVERT: E 164 ASP cc_start: 0.6666 (m-30) cc_final: 0.6325 (p0) REVERT: E 205 LYS cc_start: 0.8698 (mttm) cc_final: 0.7899 (mtpp) REVERT: E 220 GLN cc_start: 0.7700 (mp10) cc_final: 0.7450 (mp10) REVERT: E 223 GLU cc_start: 0.8879 (tp30) cc_final: 0.8462 (tp30) REVERT: E 298 ASN cc_start: 0.7235 (t0) cc_final: 0.6891 (t0) REVERT: E 310 LEU cc_start: 0.7628 (mt) cc_final: 0.6925 (mp) REVERT: E 434 CYS cc_start: 0.8263 (t) cc_final: 0.7831 (t) REVERT: E 511 ASN cc_start: 0.9170 (m-40) cc_final: 0.8779 (m-40) REVERT: E 753 GLN cc_start: 0.6756 (tp40) cc_final: 0.6463 (tp-100) REVERT: E 757 MET cc_start: 0.7777 (mtt) cc_final: 0.7300 (mtt) REVERT: E 826 PRO cc_start: 0.8938 (Cg_exo) cc_final: 0.8680 (Cg_endo) REVERT: F 268 LEU cc_start: 0.7559 (pp) cc_final: 0.7168 (pp) REVERT: F 313 ASP cc_start: 0.8387 (t0) cc_final: 0.8146 (m-30) REVERT: F 326 ASP cc_start: 0.8631 (t0) cc_final: 0.8338 (t0) REVERT: F 331 SER cc_start: 0.9215 (m) cc_final: 0.8979 (t) REVERT: F 356 MET cc_start: 0.7993 (ttm) cc_final: 0.7682 (ttm) REVERT: F 424 ASP cc_start: 0.7764 (p0) cc_final: 0.7468 (p0) REVERT: F 545 ASN cc_start: 0.8825 (m-40) cc_final: 0.8579 (m-40) REVERT: F 599 THR cc_start: 0.5795 (m) cc_final: 0.5477 (m) REVERT: F 621 TYR cc_start: 0.8423 (t80) cc_final: 0.7907 (t80) REVERT: F 696 MET cc_start: 0.8150 (ppp) cc_final: 0.7686 (ptt) REVERT: G 148 GLU cc_start: 0.7782 (tp30) cc_final: 0.7465 (tp30) REVERT: G 268 LEU cc_start: 0.7955 (pp) cc_final: 0.7731 (pp) REVERT: G 283 GLU cc_start: 0.7274 (mp0) cc_final: 0.7044 (mp0) REVERT: G 291 TYR cc_start: 0.8786 (m-80) cc_final: 0.8448 (m-10) REVERT: G 342 ASP cc_start: 0.8590 (m-30) cc_final: 0.8373 (m-30) REVERT: G 379 SER cc_start: 0.8379 (m) cc_final: 0.7618 (p) REVERT: G 380 GLN cc_start: 0.7823 (mt0) cc_final: 0.7567 (mp10) REVERT: G 452 MET cc_start: 0.8148 (tpp) cc_final: 0.7560 (tpt) REVERT: G 464 GLN cc_start: 0.7960 (mt0) cc_final: 0.7269 (mt0) REVERT: G 468 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8131 (tm-30) REVERT: G 484 ASN cc_start: 0.8591 (m-40) cc_final: 0.7615 (t0) REVERT: G 541 LEU cc_start: 0.9407 (mm) cc_final: 0.9154 (mm) REVERT: G 545 ASN cc_start: 0.8548 (m110) cc_final: 0.8260 (m-40) REVERT: G 576 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7145 (pm20) REVERT: G 668 GLN cc_start: 0.8108 (mt0) cc_final: 0.7848 (mt0) REVERT: G 790 PHE cc_start: 0.8622 (m-80) cc_final: 0.8406 (m-10) REVERT: H 221 ASP cc_start: 0.7519 (t70) cc_final: 0.7152 (t70) REVERT: H 425 MET cc_start: 0.8160 (ttm) cc_final: 0.7910 (ttm) REVERT: H 429 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7418 (mm-30) REVERT: H 553 LEU cc_start: 0.9587 (tp) cc_final: 0.9360 (tp) REVERT: H 560 ASN cc_start: 0.8733 (m-40) cc_final: 0.8464 (m-40) REVERT: H 613 VAL cc_start: 0.9275 (t) cc_final: 0.8926 (p) REVERT: H 687 ASP cc_start: 0.8601 (t0) cc_final: 0.8397 (t0) REVERT: H 706 ILE cc_start: 0.9071 (pt) cc_final: 0.8556 (pt) REVERT: H 744 GLU cc_start: 0.7239 (mp0) cc_final: 0.6387 (mp0) REVERT: H 848 MET cc_start: 0.8074 (tpp) cc_final: 0.6900 (ttm) REVERT: I 102 ILE cc_start: 0.9382 (mt) cc_final: 0.9098 (mt) REVERT: I 104 THR cc_start: 0.8835 (m) cc_final: 0.8490 (t) REVERT: I 261 GLU cc_start: 0.6478 (pp20) cc_final: 0.5894 (pp20) REVERT: I 295 MET cc_start: 0.7646 (mmm) cc_final: 0.4825 (ppp) REVERT: I 320 ASN cc_start: 0.7878 (t0) cc_final: 0.7443 (t0) REVERT: I 322 GLU cc_start: 0.8388 (pm20) cc_final: 0.7961 (pm20) REVERT: I 323 SER cc_start: 0.9171 (m) cc_final: 0.8960 (m) REVERT: I 326 ASP cc_start: 0.8570 (t0) cc_final: 0.8364 (t0) REVERT: I 342 ASP cc_start: 0.8155 (t0) cc_final: 0.7918 (t0) REVERT: I 451 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.8221 (mmt-90) REVERT: I 465 ILE cc_start: 0.9036 (mm) cc_final: 0.8426 (tp) REVERT: I 502 ASP cc_start: 0.6542 (t0) cc_final: 0.6151 (t0) REVERT: I 519 GLN cc_start: 0.8517 (tp-100) cc_final: 0.8172 (tp-100) REVERT: I 559 TYR cc_start: 0.8718 (t80) cc_final: 0.8239 (t80) REVERT: I 650 GLU cc_start: 0.8141 (pp20) cc_final: 0.7681 (pp20) REVERT: I 658 ILE cc_start: 0.8729 (pt) cc_final: 0.8116 (mp) REVERT: I 673 ARG cc_start: 0.8636 (mtm110) cc_final: 0.8289 (mtm110) REVERT: I 729 ASN cc_start: 0.8517 (p0) cc_final: 0.7878 (p0) REVERT: J 116 GLU cc_start: 0.6966 (pp20) cc_final: 0.6345 (pp20) REVERT: J 193 MET cc_start: 0.8230 (ptp) cc_final: 0.7850 (mtm) REVERT: J 218 ILE cc_start: 0.8876 (mm) cc_final: 0.8485 (tp) REVERT: J 243 ARG cc_start: 0.8727 (mmm160) cc_final: 0.8265 (mmm160) REVERT: J 256 ASP cc_start: 0.8413 (m-30) cc_final: 0.8194 (m-30) REVERT: J 261 GLU cc_start: 0.6213 (pp20) cc_final: 0.5754 (tm-30) REVERT: J 609 HIS cc_start: 0.8541 (t70) cc_final: 0.8232 (t-90) REVERT: J 727 TYR cc_start: 0.8066 (m-80) cc_final: 0.7865 (m-80) REVERT: J 735 ASP cc_start: 0.7600 (p0) cc_final: 0.7318 (p0) REVERT: J 799 VAL cc_start: 0.8171 (p) cc_final: 0.7923 (p) REVERT: J 854 THR cc_start: 0.8476 (p) cc_final: 0.8143 (t) REVERT: P 40 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7825 (tp30) REVERT: P 146 MET cc_start: 0.6778 (mtp) cc_final: 0.6498 (mtp) REVERT: P 215 MET cc_start: 0.9195 (mmm) cc_final: 0.8907 (mmm) REVERT: P 225 ILE cc_start: 0.9376 (mt) cc_final: 0.9151 (mt) REVERT: P 416 PHE cc_start: 0.7948 (m-80) cc_final: 0.7640 (m-10) REVERT: P 462 ILE cc_start: 0.8403 (mm) cc_final: 0.8170 (mm) REVERT: P 464 ILE cc_start: 0.9003 (mm) cc_final: 0.8730 (mm) REVERT: P 518 TYR cc_start: 0.7994 (p90) cc_final: 0.7548 (p90) REVERT: P 544 MET cc_start: 0.7125 (mmm) cc_final: 0.6868 (mmm) REVERT: P 624 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8446 (mmmt) REVERT: P 626 ILE cc_start: 0.9307 (mt) cc_final: 0.8907 (tp) REVERT: P 644 THR cc_start: 0.8106 (p) cc_final: 0.7879 (p) REVERT: P 884 PHE cc_start: 0.8303 (m-80) cc_final: 0.8082 (m-80) REVERT: P 903 LEU cc_start: 0.8829 (mt) cc_final: 0.8621 (mt) outliers start: 3 outliers final: 1 residues processed: 2724 average time/residue: 1.6757 time to fit residues: 7693.4129 Evaluate side-chains 2365 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2364 time to evaluate : 8.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 902 random chunks: chunk 841 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 497 optimal weight: 3.9990 chunk 637 optimal weight: 6.9990 chunk 493 optimal weight: 0.0010 chunk 734 optimal weight: 7.9990 chunk 487 optimal weight: 0.7980 chunk 869 optimal weight: 8.9990 chunk 544 optimal weight: 4.9990 chunk 530 optimal weight: 0.9980 chunk 401 optimal weight: 3.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 537 GLN B 695 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 GLN D 477 ASN ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 GLN E 501 ASN E 545 ASN ** E 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 760 ASN ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 718 GLN I 89 HIS ** I 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 260 ASN J 267 GLN J 483 ASN J 523 GLN ** J 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 473 GLN P 529 HIS ** P 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 75677 Z= 0.183 Angle : 0.538 8.738 102731 Z= 0.288 Chirality : 0.040 0.175 11785 Planarity : 0.005 0.099 13216 Dihedral : 7.473 160.621 10332 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.66 % Favored : 92.33 % Rotamer: Outliers : 0.01 % Allowed : 0.90 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.83 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.09), residues: 9006 helix: 0.77 (0.08), residues: 4316 sheet: -1.61 (0.18), residues: 755 loop : -1.94 (0.10), residues: 3935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P1051 HIS 0.016 0.001 HIS F 847 PHE 0.019 0.001 PHE A 373 TYR 0.039 0.002 TYR F 262 ARG 0.012 0.000 ARG I 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2727 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2726 time to evaluate : 7.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.7248 (ptp) cc_final: 0.6996 (ptp) REVERT: A 272 LEU cc_start: 0.8418 (tp) cc_final: 0.8137 (tt) REVERT: A 399 MET cc_start: 0.8516 (pmm) cc_final: 0.8081 (pmm) REVERT: A 477 ASN cc_start: 0.8838 (p0) cc_final: 0.8231 (t0) REVERT: A 492 ILE cc_start: 0.8862 (mt) cc_final: 0.8447 (mm) REVERT: A 502 ASP cc_start: 0.7806 (t70) cc_final: 0.7525 (t70) REVERT: A 569 THR cc_start: 0.8765 (p) cc_final: 0.8540 (t) REVERT: A 580 THR cc_start: 0.8821 (p) cc_final: 0.8502 (t) REVERT: A 605 GLN cc_start: 0.8898 (mp10) cc_final: 0.8511 (mp10) REVERT: A 607 LEU cc_start: 0.9528 (mt) cc_final: 0.9054 (mt) REVERT: A 646 LYS cc_start: 0.8280 (ptpp) cc_final: 0.7845 (pttm) REVERT: A 677 ARG cc_start: 0.8825 (mtm-85) cc_final: 0.8593 (ttm110) REVERT: A 706 ILE cc_start: 0.9078 (pt) cc_final: 0.8499 (pt) REVERT: A 714 TYR cc_start: 0.8216 (m-80) cc_final: 0.7925 (m-80) REVERT: A 725 TYR cc_start: 0.7903 (m-80) cc_final: 0.7165 (m-80) REVERT: A 761 ASN cc_start: 0.8711 (m-40) cc_final: 0.8107 (p0) REVERT: A 812 ASP cc_start: 0.8913 (t70) cc_final: 0.8562 (t70) REVERT: A 846 MET cc_start: 0.8346 (tmm) cc_final: 0.7873 (tmm) REVERT: A 868 ASP cc_start: 0.7603 (t70) cc_final: 0.6874 (t70) REVERT: B 155 TRP cc_start: 0.8037 (m100) cc_final: 0.7578 (m100) REVERT: B 193 MET cc_start: 0.8829 (pmm) cc_final: 0.8536 (pmm) REVERT: B 211 THR cc_start: 0.8208 (m) cc_final: 0.7984 (m) REVERT: B 215 CYS cc_start: 0.8658 (m) cc_final: 0.8395 (m) REVERT: B 268 LEU cc_start: 0.8982 (mt) cc_final: 0.8513 (mt) REVERT: B 362 LEU cc_start: 0.7970 (mp) cc_final: 0.7229 (mt) REVERT: B 363 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6963 (mm-30) REVERT: B 450 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8371 (mm-40) REVERT: B 685 ARG cc_start: 0.8261 (mpt-90) cc_final: 0.8030 (mpt-90) REVERT: B 757 MET cc_start: 0.7447 (ttm) cc_final: 0.7222 (ttm) REVERT: B 824 TRP cc_start: 0.4079 (t60) cc_final: 0.2962 (t60) REVERT: B 830 THR cc_start: 0.7980 (m) cc_final: 0.7698 (m) REVERT: B 879 ASP cc_start: 0.7896 (p0) cc_final: 0.6457 (t0) REVERT: B 880 ASN cc_start: 0.7602 (m-40) cc_final: 0.6264 (m-40) REVERT: C 227 VAL cc_start: 0.9166 (m) cc_final: 0.8860 (t) REVERT: C 234 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7196 (tm-30) REVERT: C 250 SER cc_start: 0.9097 (p) cc_final: 0.8780 (m) REVERT: C 256 ASP cc_start: 0.8639 (m-30) cc_final: 0.8317 (m-30) REVERT: C 257 HIS cc_start: 0.8464 (t-170) cc_final: 0.8003 (t70) REVERT: C 266 HIS cc_start: 0.8517 (m90) cc_final: 0.8302 (m-70) REVERT: C 291 TYR cc_start: 0.8073 (m-80) cc_final: 0.7701 (m-80) REVERT: C 484 ASN cc_start: 0.8714 (m110) cc_final: 0.8157 (t0) REVERT: C 641 TYR cc_start: 0.7617 (p90) cc_final: 0.7355 (p90) REVERT: C 770 LEU cc_start: 0.8309 (tp) cc_final: 0.8023 (tp) REVERT: C 802 LEU cc_start: 0.8691 (tp) cc_final: 0.8448 (tp) REVERT: C 848 MET cc_start: 0.8861 (mmm) cc_final: 0.8576 (mmt) REVERT: C 854 THR cc_start: 0.8698 (m) cc_final: 0.8213 (t) REVERT: C 884 MET cc_start: 0.7772 (mtp) cc_final: 0.7518 (mmt) REVERT: D 240 GLN cc_start: 0.8136 (pt0) cc_final: 0.7710 (tt0) REVERT: D 290 ASN cc_start: 0.8745 (m-40) cc_final: 0.8527 (m110) REVERT: D 295 MET cc_start: 0.7948 (ptp) cc_final: 0.7730 (ptp) REVERT: D 358 GLN cc_start: 0.7913 (mp10) cc_final: 0.7521 (pt0) REVERT: D 484 ASN cc_start: 0.8509 (m110) cc_final: 0.8202 (t0) REVERT: D 506 ASN cc_start: 0.7610 (p0) cc_final: 0.6542 (p0) REVERT: D 534 ARG cc_start: 0.8747 (ttp-170) cc_final: 0.8419 (ttt180) REVERT: D 609 HIS cc_start: 0.7995 (t-90) cc_final: 0.7601 (t-90) REVERT: D 751 TYR cc_start: 0.7894 (m-80) cc_final: 0.7513 (m-80) REVERT: D 807 TYR cc_start: 0.8437 (m-10) cc_final: 0.7968 (m-10) REVERT: D 843 ARG cc_start: 0.8571 (mpp80) cc_final: 0.8334 (mtm-85) REVERT: D 879 ASP cc_start: 0.8430 (p0) cc_final: 0.8089 (p0) REVERT: D 884 MET cc_start: 0.7351 (tpp) cc_final: 0.6901 (tpp) REVERT: E 164 ASP cc_start: 0.6542 (m-30) cc_final: 0.6231 (p0) REVERT: E 205 LYS cc_start: 0.8654 (mttm) cc_final: 0.7892 (mtpp) REVERT: E 298 ASN cc_start: 0.7156 (t0) cc_final: 0.6710 (t0) REVERT: E 434 CYS cc_start: 0.8227 (t) cc_final: 0.7839 (t) REVERT: E 511 ASN cc_start: 0.9116 (m-40) cc_final: 0.8767 (m-40) REVERT: E 695 ASN cc_start: 0.8812 (p0) cc_final: 0.8535 (p0) REVERT: E 753 GLN cc_start: 0.6653 (tp40) cc_final: 0.6328 (tp-100) REVERT: E 757 MET cc_start: 0.7730 (mtt) cc_final: 0.7222 (mtt) REVERT: E 826 PRO cc_start: 0.8878 (Cg_exo) cc_final: 0.8568 (Cg_endo) REVERT: F 268 LEU cc_start: 0.7651 (pp) cc_final: 0.7246 (pp) REVERT: F 313 ASP cc_start: 0.8299 (t0) cc_final: 0.7818 (t0) REVERT: F 326 ASP cc_start: 0.8615 (t0) cc_final: 0.8271 (t0) REVERT: F 331 SER cc_start: 0.9201 (m) cc_final: 0.8962 (t) REVERT: F 356 MET cc_start: 0.7894 (ttm) cc_final: 0.7545 (ttm) REVERT: F 416 TRP cc_start: 0.9099 (t60) cc_final: 0.8884 (t60) REVERT: F 424 ASP cc_start: 0.7796 (p0) cc_final: 0.7496 (p0) REVERT: F 594 LEU cc_start: 0.9135 (mt) cc_final: 0.8861 (mt) REVERT: F 621 TYR cc_start: 0.8391 (t80) cc_final: 0.7801 (t80) REVERT: F 696 MET cc_start: 0.8107 (ppp) cc_final: 0.7655 (ptt) REVERT: F 743 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6394 (tm-30) REVERT: F 775 ASP cc_start: 0.8129 (t0) cc_final: 0.7860 (t0) REVERT: G 148 GLU cc_start: 0.7805 (tp30) cc_final: 0.7513 (tp30) REVERT: G 268 LEU cc_start: 0.7932 (pp) cc_final: 0.7700 (pp) REVERT: G 291 TYR cc_start: 0.8795 (m-80) cc_final: 0.8469 (m-10) REVERT: G 342 ASP cc_start: 0.8592 (m-30) cc_final: 0.8369 (m-30) REVERT: G 355 LYS cc_start: 0.8510 (ptmm) cc_final: 0.7890 (tptt) REVERT: G 379 SER cc_start: 0.8431 (m) cc_final: 0.7577 (p) REVERT: G 380 GLN cc_start: 0.7792 (mt0) cc_final: 0.7586 (mp10) REVERT: G 399 MET cc_start: 0.8933 (pmm) cc_final: 0.8321 (ptp) REVERT: G 452 MET cc_start: 0.8196 (tpp) cc_final: 0.7822 (tpt) REVERT: G 468 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8120 (tm-30) REVERT: G 484 ASN cc_start: 0.8576 (m-40) cc_final: 0.7625 (t0) REVERT: G 545 ASN cc_start: 0.8523 (m110) cc_final: 0.8217 (m-40) REVERT: G 576 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7209 (pm20) REVERT: G 615 VAL cc_start: 0.9386 (t) cc_final: 0.9174 (p) REVERT: G 746 MET cc_start: 0.8240 (ptm) cc_final: 0.6871 (tmm) REVERT: G 773 ILE cc_start: 0.8123 (pt) cc_final: 0.7802 (pt) REVERT: G 807 TYR cc_start: 0.7829 (m-10) cc_final: 0.7540 (m-10) REVERT: H 96 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8186 (tm-30) REVERT: H 221 ASP cc_start: 0.7551 (t70) cc_final: 0.7179 (t70) REVERT: H 326 ASP cc_start: 0.8867 (t0) cc_final: 0.8511 (t0) REVERT: H 425 MET cc_start: 0.8245 (ttm) cc_final: 0.8019 (ttm) REVERT: H 429 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7380 (mm-30) REVERT: H 553 LEU cc_start: 0.9594 (tp) cc_final: 0.9350 (tp) REVERT: H 560 ASN cc_start: 0.8658 (m-40) cc_final: 0.8444 (m-40) REVERT: H 613 VAL cc_start: 0.9277 (t) cc_final: 0.9054 (p) REVERT: H 687 ASP cc_start: 0.8576 (t0) cc_final: 0.8359 (t0) REVERT: H 694 MET cc_start: 0.7681 (ptm) cc_final: 0.5928 (tmm) REVERT: H 706 ILE cc_start: 0.9062 (pt) cc_final: 0.8546 (pt) REVERT: H 744 GLU cc_start: 0.7106 (mp0) cc_final: 0.6239 (mp0) REVERT: H 848 MET cc_start: 0.8029 (tpp) cc_final: 0.6835 (ttm) REVERT: I 102 ILE cc_start: 0.9382 (mt) cc_final: 0.9137 (mt) REVERT: I 104 THR cc_start: 0.8782 (m) cc_final: 0.8410 (t) REVERT: I 261 GLU cc_start: 0.6585 (pp20) cc_final: 0.5936 (pp20) REVERT: I 294 ASN cc_start: 0.7237 (m110) cc_final: 0.6981 (m110) REVERT: I 295 MET cc_start: 0.7704 (mmm) cc_final: 0.4852 (ppp) REVERT: I 320 ASN cc_start: 0.7885 (t0) cc_final: 0.7533 (t0) REVERT: I 326 ASP cc_start: 0.8585 (t0) cc_final: 0.8321 (t0) REVERT: I 327 THR cc_start: 0.9391 (m) cc_final: 0.9087 (m) REVERT: I 342 ASP cc_start: 0.8164 (t0) cc_final: 0.7922 (t0) REVERT: I 465 ILE cc_start: 0.9035 (mm) cc_final: 0.8424 (tp) REVERT: I 502 ASP cc_start: 0.6262 (t0) cc_final: 0.5877 (t0) REVERT: I 559 TYR cc_start: 0.8640 (t80) cc_final: 0.8244 (t80) REVERT: I 673 ARG cc_start: 0.8594 (mtm110) cc_final: 0.8382 (mtm110) REVERT: I 729 ASN cc_start: 0.8560 (p0) cc_final: 0.7912 (p0) REVERT: I 786 ASP cc_start: 0.7997 (p0) cc_final: 0.7685 (p0) REVERT: J 116 GLU cc_start: 0.6753 (pp20) cc_final: 0.5768 (tm-30) REVERT: J 193 MET cc_start: 0.8218 (ptp) cc_final: 0.7879 (mtm) REVERT: J 218 ILE cc_start: 0.8882 (mm) cc_final: 0.8480 (tp) REVERT: J 235 MET cc_start: 0.7938 (tmm) cc_final: 0.7534 (tmm) REVERT: J 256 ASP cc_start: 0.8430 (m-30) cc_final: 0.8169 (m-30) REVERT: J 261 GLU cc_start: 0.6302 (pp20) cc_final: 0.5760 (tm-30) REVERT: J 377 ILE cc_start: 0.8843 (mm) cc_final: 0.8539 (mm) REVERT: J 378 ASN cc_start: 0.8299 (p0) cc_final: 0.7826 (p0) REVERT: J 609 HIS cc_start: 0.8515 (t70) cc_final: 0.8239 (t-90) REVERT: J 727 TYR cc_start: 0.8085 (m-80) cc_final: 0.7748 (m-80) REVERT: J 735 ASP cc_start: 0.7542 (p0) cc_final: 0.7291 (p0) REVERT: J 799 VAL cc_start: 0.8193 (p) cc_final: 0.7903 (p) REVERT: J 854 THR cc_start: 0.8387 (p) cc_final: 0.8060 (t) REVERT: P 40 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7805 (tp30) REVERT: P 79 TYR cc_start: 0.3890 (m-80) cc_final: 0.3643 (m-80) REVERT: P 146 MET cc_start: 0.6812 (mtp) cc_final: 0.6443 (mtp) REVERT: P 215 MET cc_start: 0.9153 (mmm) cc_final: 0.8909 (mmm) REVERT: P 416 PHE cc_start: 0.7920 (m-80) cc_final: 0.7618 (m-10) REVERT: P 518 TYR cc_start: 0.7954 (p90) cc_final: 0.7433 (p90) REVERT: P 525 ASP cc_start: 0.8104 (m-30) cc_final: 0.7864 (m-30) REVERT: P 544 MET cc_start: 0.7078 (mmm) cc_final: 0.6877 (mmm) REVERT: P 624 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8551 (mmmt) REVERT: P 626 ILE cc_start: 0.9274 (mt) cc_final: 0.8906 (tp) REVERT: P 644 THR cc_start: 0.8226 (p) cc_final: 0.7732 (p) outliers start: 1 outliers final: 1 residues processed: 2726 average time/residue: 1.6619 time to fit residues: 7637.7351 Evaluate side-chains 2365 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2364 time to evaluate : 8.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 902 random chunks: chunk 537 optimal weight: 4.9990 chunk 347 optimal weight: 6.9990 chunk 519 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 552 optimal weight: 2.9990 chunk 592 optimal weight: 2.9990 chunk 429 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 683 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 HIS ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 695 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN E 545 ASN E 609 HIS ** E 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 622 ASN F 760 ASN ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 464 GLN ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN G 503 ASN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 718 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 483 ASN J 523 GLN J 761 ASN P 529 HIS P 565 GLN P 595 GLN ** P 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.7017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 75677 Z= 0.302 Angle : 0.599 8.346 102731 Z= 0.326 Chirality : 0.041 0.182 11785 Planarity : 0.005 0.097 13216 Dihedral : 7.533 159.979 10332 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.76 % Favored : 91.23 % Rotamer: Outliers : 0.04 % Allowed : 1.04 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.09), residues: 9006 helix: 0.62 (0.08), residues: 4323 sheet: -1.66 (0.18), residues: 732 loop : -2.02 (0.10), residues: 3951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 478 HIS 0.015 0.001 HIS F 257 PHE 0.020 0.002 PHE P1055 TYR 0.038 0.002 TYR C 807 ARG 0.011 0.001 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2637 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2634 time to evaluate : 8.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8046 (tt) cc_final: 0.7615 (tt) REVERT: A 193 MET cc_start: 0.7187 (ptp) cc_final: 0.6567 (ptp) REVERT: A 272 LEU cc_start: 0.8486 (tp) cc_final: 0.8220 (tt) REVERT: A 390 ILE cc_start: 0.9461 (mm) cc_final: 0.9131 (tp) REVERT: A 399 MET cc_start: 0.8619 (pmm) cc_final: 0.8227 (pmm) REVERT: A 477 ASN cc_start: 0.8791 (p0) cc_final: 0.8298 (t0) REVERT: A 492 ILE cc_start: 0.8914 (mt) cc_final: 0.8488 (mm) REVERT: A 502 ASP cc_start: 0.8014 (t70) cc_final: 0.7772 (t70) REVERT: A 569 THR cc_start: 0.8882 (p) cc_final: 0.8658 (t) REVERT: A 605 GLN cc_start: 0.8937 (mp10) cc_final: 0.8555 (mp10) REVERT: A 607 LEU cc_start: 0.9518 (mt) cc_final: 0.9083 (mt) REVERT: A 677 ARG cc_start: 0.8804 (mtm-85) cc_final: 0.8542 (ttm110) REVERT: A 706 ILE cc_start: 0.9120 (pt) cc_final: 0.8585 (pt) REVERT: A 714 TYR cc_start: 0.8241 (m-80) cc_final: 0.7918 (m-80) REVERT: A 725 TYR cc_start: 0.8058 (m-80) cc_final: 0.7310 (m-80) REVERT: A 757 MET cc_start: 0.8525 (mmp) cc_final: 0.7952 (mmp) REVERT: A 761 ASN cc_start: 0.8796 (m-40) cc_final: 0.8061 (p0) REVERT: A 808 LYS cc_start: 0.8569 (tttt) cc_final: 0.8344 (tttt) REVERT: A 812 ASP cc_start: 0.8987 (t70) cc_final: 0.8705 (t70) REVERT: A 846 MET cc_start: 0.8336 (tmm) cc_final: 0.7864 (tmm) REVERT: A 868 ASP cc_start: 0.7723 (t70) cc_final: 0.7090 (t70) REVERT: A 884 MET cc_start: 0.7826 (mmm) cc_final: 0.7367 (mmm) REVERT: B 193 MET cc_start: 0.8991 (pmm) cc_final: 0.8619 (pmm) REVERT: B 211 THR cc_start: 0.8369 (m) cc_final: 0.8115 (m) REVERT: B 215 CYS cc_start: 0.8672 (m) cc_final: 0.8378 (m) REVERT: B 268 LEU cc_start: 0.9040 (mt) cc_final: 0.8558 (mt) REVERT: B 363 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7025 (mm-30) REVERT: B 409 MET cc_start: 0.7318 (ttp) cc_final: 0.7034 (ttp) REVERT: B 450 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8309 (mm-40) REVERT: B 830 THR cc_start: 0.8241 (m) cc_final: 0.8001 (m) REVERT: B 880 ASN cc_start: 0.7324 (m-40) cc_final: 0.6963 (m-40) REVERT: C 227 VAL cc_start: 0.9216 (m) cc_final: 0.8929 (t) REVERT: C 234 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7160 (tm-30) REVERT: C 236 ARG cc_start: 0.6209 (ptt180) cc_final: 0.5954 (ptm160) REVERT: C 250 SER cc_start: 0.9333 (p) cc_final: 0.9068 (p) REVERT: C 256 ASP cc_start: 0.8680 (m-30) cc_final: 0.8366 (m-30) REVERT: C 270 GLU cc_start: 0.7814 (mp0) cc_final: 0.7395 (mp0) REVERT: C 356 MET cc_start: 0.8330 (tpp) cc_final: 0.8091 (mmm) REVERT: C 484 ASN cc_start: 0.8714 (m110) cc_final: 0.8192 (t0) REVERT: C 568 ILE cc_start: 0.9225 (mt) cc_final: 0.8971 (mm) REVERT: C 618 HIS cc_start: 0.7957 (t-170) cc_final: 0.7660 (t70) REVERT: C 641 TYR cc_start: 0.7919 (p90) cc_final: 0.7595 (p90) REVERT: C 646 LYS cc_start: 0.9063 (tptp) cc_final: 0.8838 (tptp) REVERT: C 729 ASN cc_start: 0.9013 (p0) cc_final: 0.8765 (p0) REVERT: C 770 LEU cc_start: 0.8368 (tp) cc_final: 0.8067 (tp) REVERT: C 786 ASP cc_start: 0.7658 (t70) cc_final: 0.6929 (t70) REVERT: C 798 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7710 (mtmm) REVERT: C 802 LEU cc_start: 0.8734 (tp) cc_final: 0.8516 (tp) REVERT: C 805 ILE cc_start: 0.9291 (mm) cc_final: 0.9077 (mm) REVERT: C 807 TYR cc_start: 0.8199 (m-10) cc_final: 0.7706 (m-10) REVERT: C 848 MET cc_start: 0.8883 (mmm) cc_final: 0.8641 (mmt) REVERT: C 854 THR cc_start: 0.8702 (m) cc_final: 0.8295 (t) REVERT: D 240 GLN cc_start: 0.8025 (pt0) cc_final: 0.7701 (tt0) REVERT: D 290 ASN cc_start: 0.8843 (m-40) cc_final: 0.8596 (m110) REVERT: D 295 MET cc_start: 0.8138 (ptp) cc_final: 0.7899 (ptp) REVERT: D 422 PRO cc_start: 0.8359 (Cg_exo) cc_final: 0.8018 (Cg_endo) REVERT: D 484 ASN cc_start: 0.8514 (m110) cc_final: 0.8219 (t0) REVERT: D 534 ARG cc_start: 0.8665 (ttp-170) cc_final: 0.8411 (ttt180) REVERT: D 536 ILE cc_start: 0.9432 (mm) cc_final: 0.9228 (mm) REVERT: D 609 HIS cc_start: 0.8205 (t-90) cc_final: 0.7966 (t-90) REVERT: D 720 GLU cc_start: 0.8044 (tt0) cc_final: 0.7836 (tt0) REVERT: D 751 TYR cc_start: 0.7961 (m-80) cc_final: 0.7543 (m-80) REVERT: D 807 TYR cc_start: 0.8481 (m-10) cc_final: 0.8064 (m-10) REVERT: D 879 ASP cc_start: 0.8398 (p0) cc_final: 0.8084 (p0) REVERT: E 205 LYS cc_start: 0.8723 (mttm) cc_final: 0.8193 (mtpt) REVERT: E 434 CYS cc_start: 0.8397 (t) cc_final: 0.8005 (t) REVERT: E 511 ASN cc_start: 0.9104 (m-40) cc_final: 0.8839 (m-40) REVERT: E 695 ASN cc_start: 0.8934 (p0) cc_final: 0.8653 (p0) REVERT: E 699 ILE cc_start: 0.9370 (mt) cc_final: 0.9167 (mt) REVERT: E 753 GLN cc_start: 0.6855 (tp40) cc_final: 0.6531 (tp-100) REVERT: E 757 MET cc_start: 0.7745 (mtt) cc_final: 0.7312 (mtt) REVERT: E 775 ASP cc_start: 0.6827 (t0) cc_final: 0.6617 (t0) REVERT: E 781 LEU cc_start: 0.9497 (tp) cc_final: 0.9296 (tp) REVERT: E 807 TYR cc_start: 0.8288 (m-80) cc_final: 0.7348 (m-10) REVERT: E 826 PRO cc_start: 0.8918 (Cg_exo) cc_final: 0.8412 (Cg_endo) REVERT: F 171 GLU cc_start: 0.7578 (tp30) cc_final: 0.7228 (tp30) REVERT: F 268 LEU cc_start: 0.7602 (pp) cc_final: 0.7081 (pp) REVERT: F 313 ASP cc_start: 0.8423 (t0) cc_final: 0.7922 (t0) REVERT: F 326 ASP cc_start: 0.8660 (t0) cc_final: 0.8330 (t0) REVERT: F 331 SER cc_start: 0.9242 (m) cc_final: 0.8978 (t) REVERT: F 356 MET cc_start: 0.7995 (ttm) cc_final: 0.7614 (ttm) REVERT: F 424 ASP cc_start: 0.7871 (p0) cc_final: 0.7583 (p0) REVERT: F 480 HIS cc_start: 0.8068 (t70) cc_final: 0.7743 (t-170) REVERT: F 592 CYS cc_start: 0.8402 (m) cc_final: 0.8181 (m) REVERT: F 599 THR cc_start: 0.6306 (m) cc_final: 0.6063 (m) REVERT: F 621 TYR cc_start: 0.8480 (t80) cc_final: 0.7920 (t80) REVERT: F 640 LEU cc_start: 0.8948 (mt) cc_final: 0.8677 (mt) REVERT: F 696 MET cc_start: 0.8198 (ppp) cc_final: 0.7748 (ptt) REVERT: F 743 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6526 (tm-30) REVERT: F 744 GLU cc_start: 0.6974 (mp0) cc_final: 0.6624 (mp0) REVERT: F 773 ILE cc_start: 0.7741 (pt) cc_final: 0.7472 (pt) REVERT: G 148 GLU cc_start: 0.8064 (tp30) cc_final: 0.7823 (tp30) REVERT: G 268 LEU cc_start: 0.7921 (pp) cc_final: 0.7716 (pp) REVERT: G 291 TYR cc_start: 0.8897 (m-80) cc_final: 0.8585 (m-10) REVERT: G 316 ASN cc_start: 0.8403 (m-40) cc_final: 0.8197 (m-40) REVERT: G 342 ASP cc_start: 0.8688 (m-30) cc_final: 0.8486 (m-30) REVERT: G 355 LYS cc_start: 0.8347 (ptmm) cc_final: 0.7882 (tptt) REVERT: G 399 MET cc_start: 0.8944 (pmm) cc_final: 0.8332 (ptp) REVERT: G 452 MET cc_start: 0.8370 (tpp) cc_final: 0.7926 (tpt) REVERT: G 468 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8110 (tm-30) REVERT: G 484 ASN cc_start: 0.8628 (m-40) cc_final: 0.7653 (t0) REVERT: G 576 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7322 (pm20) REVERT: G 689 PHE cc_start: 0.8712 (t80) cc_final: 0.8491 (t80) REVERT: G 746 MET cc_start: 0.8280 (ptm) cc_final: 0.6921 (tmm) REVERT: G 790 PHE cc_start: 0.8632 (m-80) cc_final: 0.8413 (m-10) REVERT: H 221 ASP cc_start: 0.7563 (t70) cc_final: 0.7207 (t70) REVERT: H 261 GLU cc_start: 0.7159 (pp20) cc_final: 0.6959 (pp20) REVERT: H 326 ASP cc_start: 0.8926 (t0) cc_final: 0.8625 (t0) REVERT: H 425 MET cc_start: 0.8246 (ttm) cc_final: 0.8044 (ttm) REVERT: H 429 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7671 (mm-30) REVERT: H 553 LEU cc_start: 0.9592 (tp) cc_final: 0.9364 (tp) REVERT: H 560 ASN cc_start: 0.8766 (m-40) cc_final: 0.8474 (m-40) REVERT: H 694 MET cc_start: 0.7707 (ptm) cc_final: 0.7053 (ttp) REVERT: H 706 ILE cc_start: 0.9026 (pt) cc_final: 0.8564 (pt) REVERT: H 848 MET cc_start: 0.8081 (tpp) cc_final: 0.6987 (ttm) REVERT: I 102 ILE cc_start: 0.9353 (mt) cc_final: 0.9110 (mt) REVERT: I 104 THR cc_start: 0.8814 (m) cc_final: 0.8428 (t) REVERT: I 261 GLU cc_start: 0.6775 (pp20) cc_final: 0.6107 (pp20) REVERT: I 326 ASP cc_start: 0.8596 (t0) cc_final: 0.8359 (t0) REVERT: I 327 THR cc_start: 0.9346 (m) cc_final: 0.9101 (m) REVERT: I 342 ASP cc_start: 0.8294 (t0) cc_final: 0.8051 (t0) REVERT: I 455 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7344 (tpp80) REVERT: I 465 ILE cc_start: 0.9095 (mm) cc_final: 0.8503 (tp) REVERT: I 502 ASP cc_start: 0.6173 (t0) cc_final: 0.5860 (t0) REVERT: I 559 TYR cc_start: 0.8689 (t80) cc_final: 0.8337 (t80) REVERT: I 593 MET cc_start: 0.8366 (mmt) cc_final: 0.8111 (mmt) REVERT: I 650 GLU cc_start: 0.8189 (pp20) cc_final: 0.7788 (pp20) REVERT: I 729 ASN cc_start: 0.8764 (p0) cc_final: 0.8093 (p0) REVERT: I 841 ASP cc_start: 0.7943 (t0) cc_final: 0.7689 (t0) REVERT: I 876 VAL cc_start: 0.8903 (t) cc_final: 0.8684 (t) REVERT: J 193 MET cc_start: 0.8268 (ptp) cc_final: 0.7561 (mtm) REVERT: J 218 ILE cc_start: 0.8953 (mm) cc_final: 0.8530 (tp) REVERT: J 235 MET cc_start: 0.8030 (tmm) cc_final: 0.7673 (tmm) REVERT: J 243 ARG cc_start: 0.8823 (mmm160) cc_final: 0.8542 (mmm160) REVERT: J 256 ASP cc_start: 0.8398 (m-30) cc_final: 0.8171 (m-30) REVERT: J 261 GLU cc_start: 0.6496 (pp20) cc_final: 0.5589 (tm-30) REVERT: J 609 HIS cc_start: 0.8611 (t70) cc_final: 0.8283 (t-90) REVERT: J 727 TYR cc_start: 0.8063 (m-80) cc_final: 0.7759 (m-80) REVERT: J 735 ASP cc_start: 0.7486 (p0) cc_final: 0.7241 (p0) REVERT: J 750 ASP cc_start: 0.7543 (t0) cc_final: 0.7340 (t0) REVERT: J 799 VAL cc_start: 0.8257 (p) cc_final: 0.8033 (p) REVERT: J 854 THR cc_start: 0.8322 (p) cc_final: 0.7996 (t) REVERT: P 79 TYR cc_start: 0.3747 (m-80) cc_final: 0.3515 (m-80) REVERT: P 146 MET cc_start: 0.6883 (mtp) cc_final: 0.6559 (mtp) REVERT: P 215 MET cc_start: 0.9234 (mmm) cc_final: 0.9034 (mmm) REVERT: P 291 MET cc_start: 0.7450 (mtm) cc_final: 0.7229 (mtm) REVERT: P 416 PHE cc_start: 0.7999 (m-80) cc_final: 0.7700 (m-10) REVERT: P 420 LYS cc_start: 0.8540 (mttt) cc_final: 0.8315 (mttp) REVERT: P 464 ILE cc_start: 0.9003 (mm) cc_final: 0.8721 (mm) REVERT: P 518 TYR cc_start: 0.7976 (p90) cc_final: 0.7541 (p90) REVERT: P 525 ASP cc_start: 0.8281 (m-30) cc_final: 0.8034 (m-30) REVERT: P 544 MET cc_start: 0.7181 (mmm) cc_final: 0.6937 (mmm) REVERT: P 624 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8546 (mmmt) REVERT: P 626 ILE cc_start: 0.9276 (mt) cc_final: 0.8837 (tp) REVERT: P 644 THR cc_start: 0.8362 (p) cc_final: 0.7654 (p) REVERT: P 1063 MET cc_start: 0.7680 (mtt) cc_final: 0.7394 (mtt) outliers start: 3 outliers final: 1 residues processed: 2636 average time/residue: 1.6509 time to fit residues: 7308.2837 Evaluate side-chains 2327 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2326 time to evaluate : 8.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 902 random chunks: chunk 790 optimal weight: 6.9990 chunk 832 optimal weight: 5.9990 chunk 759 optimal weight: 5.9990 chunk 810 optimal weight: 1.9990 chunk 487 optimal weight: 5.9990 chunk 352 optimal weight: 5.9990 chunk 636 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 732 optimal weight: 3.9990 chunk 766 optimal weight: 4.9990 chunk 807 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN B 199 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 695 ASN B 718 GLN B 761 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN E 545 ASN E 609 HIS ** E 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 622 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 545 ASN F 760 ASN ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 642 GLN ** H 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 739 GLN ** I 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 483 ASN J 597 ASN J 761 ASN P 529 HIS P 595 GLN ** P 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 912 GLN ** P 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 75677 Z= 0.396 Angle : 0.676 11.944 102731 Z= 0.370 Chirality : 0.043 0.216 11785 Planarity : 0.006 0.117 13216 Dihedral : 7.767 158.947 10332 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.49 % Favored : 90.48 % Rotamer: Outliers : 0.04 % Allowed : 0.64 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.09), residues: 9006 helix: 0.23 (0.08), residues: 4337 sheet: -1.86 (0.17), residues: 759 loop : -2.21 (0.09), residues: 3910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 416 HIS 0.016 0.002 HIS G 257 PHE 0.038 0.002 PHE F 105 TYR 0.028 0.002 TYR B 621 ARG 0.017 0.001 ARG E 715 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2616 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2613 time to evaluate : 8.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ILE cc_start: 0.9370 (mt) cc_final: 0.9077 (mm) REVERT: A 152 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8341 (ttp80) REVERT: A 193 MET cc_start: 0.7097 (ptp) cc_final: 0.6573 (ptp) REVERT: A 272 LEU cc_start: 0.8548 (tp) cc_final: 0.8338 (tt) REVERT: A 399 MET cc_start: 0.8717 (pmm) cc_final: 0.8338 (pmm) REVERT: A 423 ASN cc_start: 0.7660 (m110) cc_final: 0.7404 (m110) REVERT: A 431 LEU cc_start: 0.8628 (pt) cc_final: 0.8391 (pt) REVERT: A 532 TYR cc_start: 0.7664 (t80) cc_final: 0.7126 (t80) REVERT: A 569 THR cc_start: 0.8979 (p) cc_final: 0.8745 (t) REVERT: A 580 THR cc_start: 0.8882 (p) cc_final: 0.8673 (t) REVERT: A 594 LEU cc_start: 0.9517 (mp) cc_final: 0.9317 (mp) REVERT: A 607 LEU cc_start: 0.9528 (mt) cc_final: 0.9084 (mt) REVERT: A 677 ARG cc_start: 0.8922 (mtm-85) cc_final: 0.8531 (ttm110) REVERT: A 706 ILE cc_start: 0.9126 (pt) cc_final: 0.8597 (pt) REVERT: A 714 TYR cc_start: 0.8203 (m-80) cc_final: 0.7881 (m-80) REVERT: A 725 TYR cc_start: 0.8068 (m-80) cc_final: 0.7443 (m-80) REVERT: A 757 MET cc_start: 0.8591 (mmp) cc_final: 0.8067 (mmp) REVERT: A 761 ASN cc_start: 0.8857 (m-40) cc_final: 0.8102 (p0) REVERT: A 807 TYR cc_start: 0.8029 (m-80) cc_final: 0.7675 (m-10) REVERT: A 846 MET cc_start: 0.8277 (tmm) cc_final: 0.7888 (tmm) REVERT: B 215 CYS cc_start: 0.8638 (m) cc_final: 0.8381 (m) REVERT: B 219 PHE cc_start: 0.7673 (t80) cc_final: 0.7455 (t80) REVERT: B 268 LEU cc_start: 0.9112 (mt) cc_final: 0.8632 (mt) REVERT: B 362 LEU cc_start: 0.7946 (mp) cc_final: 0.7413 (mt) REVERT: B 363 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7071 (mm-30) REVERT: B 450 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8409 (mm-40) REVERT: B 627 ASP cc_start: 0.8310 (m-30) cc_final: 0.7947 (m-30) REVERT: C 227 VAL cc_start: 0.9258 (m) cc_final: 0.9052 (t) REVERT: C 234 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7059 (tm-30) REVERT: C 250 SER cc_start: 0.9188 (p) cc_final: 0.8948 (m) REVERT: C 256 ASP cc_start: 0.8701 (m-30) cc_final: 0.8378 (m-30) REVERT: C 257 HIS cc_start: 0.8675 (t-170) cc_final: 0.8198 (t-90) REVERT: C 270 GLU cc_start: 0.7890 (mp0) cc_final: 0.7483 (mp0) REVERT: C 568 ILE cc_start: 0.9233 (mt) cc_final: 0.9031 (mm) REVERT: C 641 TYR cc_start: 0.8151 (p90) cc_final: 0.7692 (p90) REVERT: C 729 ASN cc_start: 0.8974 (p0) cc_final: 0.8755 (p0) REVERT: C 786 ASP cc_start: 0.7740 (t70) cc_final: 0.6931 (t0) REVERT: C 807 TYR cc_start: 0.8427 (m-10) cc_final: 0.7778 (m-10) REVERT: C 848 MET cc_start: 0.8930 (mmm) cc_final: 0.8681 (mmt) REVERT: D 256 ASP cc_start: 0.8630 (m-30) cc_final: 0.8219 (m-30) REVERT: D 290 ASN cc_start: 0.8912 (m-40) cc_final: 0.8527 (m110) REVERT: D 422 PRO cc_start: 0.8580 (Cg_exo) cc_final: 0.8133 (Cg_endo) REVERT: D 484 ASN cc_start: 0.8435 (m110) cc_final: 0.8220 (t0) REVERT: D 506 ASN cc_start: 0.7810 (p0) cc_final: 0.6919 (p0) REVERT: D 534 ARG cc_start: 0.8915 (ttp-170) cc_final: 0.8600 (ttt180) REVERT: D 536 ILE cc_start: 0.9470 (mm) cc_final: 0.9260 (mm) REVERT: D 751 TYR cc_start: 0.7923 (m-80) cc_final: 0.7468 (m-80) REVERT: E 205 LYS cc_start: 0.8763 (mttm) cc_final: 0.8192 (mtpp) REVERT: E 261 GLU cc_start: 0.8437 (pp20) cc_final: 0.7683 (pp20) REVERT: E 265 GLN cc_start: 0.8982 (mp10) cc_final: 0.8284 (mp10) REVERT: E 434 CYS cc_start: 0.8573 (t) cc_final: 0.8183 (t) REVERT: E 511 ASN cc_start: 0.9111 (m-40) cc_final: 0.8806 (m-40) REVERT: E 753 GLN cc_start: 0.7040 (tp40) cc_final: 0.6707 (tp-100) REVERT: E 757 MET cc_start: 0.7868 (mtt) cc_final: 0.7411 (mtt) REVERT: E 807 TYR cc_start: 0.8345 (m-80) cc_final: 0.7467 (m-10) REVERT: F 171 GLU cc_start: 0.7579 (tp30) cc_final: 0.7266 (tp30) REVERT: F 208 ASP cc_start: 0.7859 (t0) cc_final: 0.7617 (t0) REVERT: F 268 LEU cc_start: 0.7758 (pp) cc_final: 0.7432 (pp) REVERT: F 313 ASP cc_start: 0.8480 (t0) cc_final: 0.7984 (t0) REVERT: F 326 ASP cc_start: 0.8626 (t0) cc_final: 0.8288 (t0) REVERT: F 331 SER cc_start: 0.9226 (m) cc_final: 0.8987 (t) REVERT: F 356 MET cc_start: 0.8063 (ttm) cc_final: 0.7727 (ttm) REVERT: F 424 ASP cc_start: 0.7782 (p0) cc_final: 0.7498 (p0) REVERT: F 511 ASN cc_start: 0.9022 (m-40) cc_final: 0.8151 (t0) REVERT: F 621 TYR cc_start: 0.8594 (t80) cc_final: 0.7956 (t80) REVERT: F 696 MET cc_start: 0.8332 (ppp) cc_final: 0.7856 (ptt) REVERT: F 734 LEU cc_start: 0.8924 (tp) cc_final: 0.8651 (tp) REVERT: F 881 MET cc_start: 0.7560 (mmp) cc_final: 0.7346 (mmm) REVERT: G 268 LEU cc_start: 0.7942 (pp) cc_final: 0.7726 (pp) REVERT: G 291 TYR cc_start: 0.8988 (m-80) cc_final: 0.8646 (m-10) REVERT: G 342 ASP cc_start: 0.8688 (m-30) cc_final: 0.8436 (m-30) REVERT: G 399 MET cc_start: 0.8879 (pmm) cc_final: 0.8403 (ptp) REVERT: G 452 MET cc_start: 0.8474 (tpp) cc_final: 0.8090 (tpt) REVERT: G 468 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8114 (tm-30) REVERT: G 545 ASN cc_start: 0.8590 (m110) cc_final: 0.8379 (m-40) REVERT: G 572 MET cc_start: 0.8396 (ptp) cc_final: 0.7978 (ptp) REVERT: G 576 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7426 (pm20) REVERT: G 644 LYS cc_start: 0.8279 (pttm) cc_final: 0.7896 (ptmm) REVERT: G 668 GLN cc_start: 0.8018 (mt0) cc_final: 0.7799 (mt0) REVERT: G 689 PHE cc_start: 0.8855 (t80) cc_final: 0.8543 (t80) REVERT: G 746 MET cc_start: 0.8223 (ptm) cc_final: 0.7084 (tmm) REVERT: G 803 LYS cc_start: 0.7940 (tppt) cc_final: 0.7140 (ttpp) REVERT: H 221 ASP cc_start: 0.7407 (t70) cc_final: 0.7152 (t70) REVERT: H 261 GLU cc_start: 0.7305 (pp20) cc_final: 0.7072 (pp20) REVERT: H 326 ASP cc_start: 0.8802 (t0) cc_final: 0.8527 (t0) REVERT: H 393 MET cc_start: 0.8888 (mtm) cc_final: 0.8672 (mtm) REVERT: H 553 LEU cc_start: 0.9598 (tp) cc_final: 0.9364 (tp) REVERT: H 627 ASP cc_start: 0.8552 (t0) cc_final: 0.8337 (t70) REVERT: H 694 MET cc_start: 0.7746 (ptm) cc_final: 0.7094 (ttp) REVERT: H 848 MET cc_start: 0.7699 (mmp) cc_final: 0.6942 (ttm) REVERT: I 104 THR cc_start: 0.8832 (m) cc_final: 0.8472 (t) REVERT: I 150 ARG cc_start: 0.5062 (ptp-170) cc_final: 0.4726 (ptp-170) REVERT: I 171 GLU cc_start: 0.8219 (tp30) cc_final: 0.7849 (tp30) REVERT: I 295 MET cc_start: 0.7722 (mmm) cc_final: 0.5110 (ppp) REVERT: I 326 ASP cc_start: 0.8635 (t0) cc_final: 0.8424 (t0) REVERT: I 327 THR cc_start: 0.9323 (m) cc_final: 0.9035 (m) REVERT: I 409 MET cc_start: 0.8514 (tpp) cc_final: 0.8177 (tpp) REVERT: I 502 ASP cc_start: 0.6311 (t0) cc_final: 0.5970 (t0) REVERT: I 559 TYR cc_start: 0.8559 (t80) cc_final: 0.8187 (t80) REVERT: I 593 MET cc_start: 0.8435 (mmt) cc_final: 0.8166 (mmt) REVERT: I 650 GLU cc_start: 0.8196 (pp20) cc_final: 0.7913 (pp20) REVERT: I 658 ILE cc_start: 0.9106 (pt) cc_final: 0.8584 (mp) REVERT: I 729 ASN cc_start: 0.8876 (p0) cc_final: 0.8336 (p0) REVERT: I 841 ASP cc_start: 0.8298 (t0) cc_final: 0.7928 (t0) REVERT: J 193 MET cc_start: 0.7992 (ptp) cc_final: 0.7774 (mtm) REVERT: J 218 ILE cc_start: 0.9007 (mm) cc_final: 0.8537 (tp) REVERT: J 235 MET cc_start: 0.8044 (tmm) cc_final: 0.7706 (tmm) REVERT: J 304 ARG cc_start: 0.8612 (mmt-90) cc_final: 0.8351 (mmt90) REVERT: J 378 ASN cc_start: 0.8259 (p0) cc_final: 0.7834 (p0) REVERT: J 413 SER cc_start: 0.9502 (m) cc_final: 0.9264 (t) REVERT: J 530 VAL cc_start: 0.8517 (m) cc_final: 0.8238 (p) REVERT: J 585 LEU cc_start: 0.8976 (mm) cc_final: 0.8696 (mm) REVERT: J 609 HIS cc_start: 0.8554 (t70) cc_final: 0.8274 (t-90) REVERT: J 727 TYR cc_start: 0.8248 (m-80) cc_final: 0.7981 (m-80) REVERT: J 735 ASP cc_start: 0.7555 (p0) cc_final: 0.7254 (p0) REVERT: J 833 TYR cc_start: 0.7959 (t80) cc_final: 0.7702 (t80) REVERT: J 854 THR cc_start: 0.8262 (p) cc_final: 0.8011 (t) REVERT: P 282 ASP cc_start: 0.8128 (p0) cc_final: 0.7771 (p0) REVERT: P 416 PHE cc_start: 0.8157 (m-80) cc_final: 0.7870 (m-10) REVERT: P 420 LYS cc_start: 0.8552 (mttt) cc_final: 0.8335 (mttp) REVERT: P 464 ILE cc_start: 0.9128 (mm) cc_final: 0.8833 (mm) REVERT: P 518 TYR cc_start: 0.7941 (p90) cc_final: 0.7556 (p90) REVERT: P 525 ASP cc_start: 0.8147 (m-30) cc_final: 0.7918 (m-30) REVERT: P 544 MET cc_start: 0.7322 (mmm) cc_final: 0.6995 (mmm) REVERT: P 597 LYS cc_start: 0.7650 (tttm) cc_final: 0.7249 (tppt) REVERT: P 624 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8589 (mmmt) REVERT: P 644 THR cc_start: 0.8510 (p) cc_final: 0.7973 (p) outliers start: 3 outliers final: 1 residues processed: 2615 average time/residue: 1.6443 time to fit residues: 7233.0938 Evaluate side-chains 2298 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2297 time to evaluate : 8.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 902 random chunks: chunk 532 optimal weight: 3.9990 chunk 856 optimal weight: 6.9990 chunk 522 optimal weight: 1.9990 chunk 406 optimal weight: 0.8980 chunk 595 optimal weight: 3.9990 chunk 898 optimal weight: 0.9990 chunk 827 optimal weight: 6.9990 chunk 715 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 552 optimal weight: 3.9990 chunk 438 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 ASN B 126 GLN B 199 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 695 ASN B 761 ASN C 122 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 HIS C 368 GLN C 512 GLN D 287 ASN D 396 GLN ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN E 609 HIS E 614 ASN E 622 ASN ** F 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 760 ASN ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 483 ASN G 503 ASN ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 718 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 483 ASN J 626 ASN J 761 ASN ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 529 HIS P 595 GLN ** P 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.7445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 75677 Z= 0.190 Angle : 0.570 11.898 102731 Z= 0.305 Chirality : 0.040 0.164 11785 Planarity : 0.005 0.104 13216 Dihedral : 7.568 159.309 10332 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.81 % Favored : 92.18 % Rotamer: Outliers : 0.02 % Allowed : 0.18 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.09), residues: 9006 helix: 0.57 (0.08), residues: 4322 sheet: -1.70 (0.18), residues: 743 loop : -1.97 (0.10), residues: 3941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 416 HIS 0.016 0.001 HIS G 253 PHE 0.025 0.001 PHE F 105 TYR 0.038 0.002 TYR E 262 ARG 0.016 0.001 ARG I 455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18012 Ramachandran restraints generated. 9006 Oldfield, 0 Emsley, 9006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 868 is missing expected H atoms. Skipping. Evaluate side-chains 2646 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2644 time to evaluate : 8.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.7041 (ptp) cc_final: 0.6513 (ptp) REVERT: A 208 ASP cc_start: 0.8078 (t0) cc_final: 0.7793 (t0) REVERT: A 356 MET cc_start: 0.8081 (mmt) cc_final: 0.7557 (mmt) REVERT: A 399 MET cc_start: 0.8704 (pmm) cc_final: 0.8374 (pmm) REVERT: A 431 LEU cc_start: 0.8582 (pt) cc_final: 0.8302 (pt) REVERT: A 532 TYR cc_start: 0.7571 (t80) cc_final: 0.7131 (t80) REVERT: A 569 THR cc_start: 0.8969 (p) cc_final: 0.8705 (t) REVERT: A 607 LEU cc_start: 0.9569 (mt) cc_final: 0.9242 (mt) REVERT: A 677 ARG cc_start: 0.8849 (mtm-85) cc_final: 0.8592 (ttm110) REVERT: A 706 ILE cc_start: 0.9146 (pt) cc_final: 0.8598 (pt) REVERT: A 724 MET cc_start: 0.8085 (pmm) cc_final: 0.7783 (pmm) REVERT: A 725 TYR cc_start: 0.7992 (m-80) cc_final: 0.7262 (m-80) REVERT: A 761 ASN cc_start: 0.8823 (m-40) cc_final: 0.8181 (p0) REVERT: A 812 ASP cc_start: 0.8898 (t70) cc_final: 0.8592 (t70) REVERT: A 818 LEU cc_start: 0.8702 (mp) cc_final: 0.8305 (mp) REVERT: A 846 MET cc_start: 0.8420 (tmm) cc_final: 0.7914 (tmm) REVERT: A 868 ASP cc_start: 0.7751 (t70) cc_final: 0.7198 (t70) REVERT: B 193 MET cc_start: 0.9073 (pmm) cc_final: 0.8745 (pmm) REVERT: B 199 ASN cc_start: 0.8260 (m-40) cc_final: 0.8042 (m110) REVERT: B 211 THR cc_start: 0.8358 (m) cc_final: 0.8094 (m) REVERT: B 215 CYS cc_start: 0.8614 (m) cc_final: 0.8254 (m) REVERT: B 219 PHE cc_start: 0.7495 (t80) cc_final: 0.7277 (t80) REVERT: B 268 LEU cc_start: 0.9051 (mt) cc_final: 0.8601 (mt) REVERT: B 363 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7011 (mm-30) REVERT: B 409 MET cc_start: 0.7416 (ttp) cc_final: 0.7083 (ttp) REVERT: B 450 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8372 (mm-40) REVERT: B 795 LYS cc_start: 0.8258 (tmmt) cc_final: 0.7756 (mmtt) REVERT: B 824 TRP cc_start: 0.4711 (t60) cc_final: 0.3147 (t60) REVERT: B 830 THR cc_start: 0.8284 (m) cc_final: 0.8047 (m) REVERT: B 879 ASP cc_start: 0.7922 (p0) cc_final: 0.7280 (t0) REVERT: C 227 VAL cc_start: 0.9246 (m) cc_final: 0.8966 (t) REVERT: C 234 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6899 (tm-30) REVERT: C 250 SER cc_start: 0.9147 (p) cc_final: 0.8945 (m) REVERT: C 256 ASP cc_start: 0.8631 (m-30) cc_final: 0.8258 (m-30) REVERT: C 257 HIS cc_start: 0.8523 (t-170) cc_final: 0.8008 (t-90) REVERT: C 291 TYR cc_start: 0.8161 (m-80) cc_final: 0.7722 (m-80) REVERT: C 356 MET cc_start: 0.8507 (mmm) cc_final: 0.8147 (mmm) REVERT: C 484 ASN cc_start: 0.8712 (m110) cc_final: 0.8221 (t0) REVERT: C 641 TYR cc_start: 0.8046 (p90) cc_final: 0.7671 (p90) REVERT: C 761 ASN cc_start: 0.8231 (m110) cc_final: 0.7951 (m110) REVERT: C 786 ASP cc_start: 0.7767 (t70) cc_final: 0.6869 (t0) REVERT: C 807 TYR cc_start: 0.8231 (m-10) cc_final: 0.7624 (m-10) REVERT: C 848 MET cc_start: 0.9018 (mmm) cc_final: 0.8736 (mmt) REVERT: C 854 THR cc_start: 0.8660 (m) cc_final: 0.8233 (t) REVERT: D 290 ASN cc_start: 0.8589 (m-40) cc_final: 0.8367 (m110) REVERT: D 396 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7728 (mm110) REVERT: D 422 PRO cc_start: 0.8460 (Cg_exo) cc_final: 0.8043 (Cg_endo) REVERT: D 484 ASN cc_start: 0.8486 (m110) cc_final: 0.8190 (t0) REVERT: D 534 ARG cc_start: 0.8911 (ttp-170) cc_final: 0.8559 (ttt180) REVERT: D 536 ILE cc_start: 0.9420 (mm) cc_final: 0.9179 (mm) REVERT: D 723 GLU cc_start: 0.5847 (mt-10) cc_final: 0.5647 (mt-10) REVERT: D 751 TYR cc_start: 0.7881 (m-80) cc_final: 0.7400 (m-80) REVERT: E 205 LYS cc_start: 0.8670 (mttm) cc_final: 0.8064 (mtpp) REVERT: E 265 GLN cc_start: 0.8690 (mp10) cc_final: 0.8183 (mp10) REVERT: E 434 CYS cc_start: 0.8531 (t) cc_final: 0.8101 (t) REVERT: E 511 ASN cc_start: 0.9055 (m-40) cc_final: 0.8693 (m-40) REVERT: E 695 ASN cc_start: 0.8940 (p0) cc_final: 0.8607 (p0) REVERT: E 699 ILE cc_start: 0.9331 (mt) cc_final: 0.9096 (mt) REVERT: E 753 GLN cc_start: 0.6822 (tp40) cc_final: 0.6499 (tp-100) REVERT: E 757 MET cc_start: 0.7812 (mtt) cc_final: 0.7350 (mtt) REVERT: E 807 TYR cc_start: 0.8278 (m-80) cc_final: 0.7447 (m-10) REVERT: F 171 GLU cc_start: 0.7526 (tp30) cc_final: 0.7210 (tp30) REVERT: F 268 LEU cc_start: 0.7719 (pp) cc_final: 0.7467 (pp) REVERT: F 313 ASP cc_start: 0.8417 (t0) cc_final: 0.8023 (t0) REVERT: F 331 SER cc_start: 0.9214 (m) cc_final: 0.8934 (t) REVERT: F 356 MET cc_start: 0.8034 (ttm) cc_final: 0.7701 (ttm) REVERT: F 416 TRP cc_start: 0.9229 (t60) cc_final: 0.8987 (t60) REVERT: F 424 ASP cc_start: 0.7787 (p0) cc_final: 0.7468 (p0) REVERT: F 480 HIS cc_start: 0.7957 (t-170) cc_final: 0.7548 (t-170) REVERT: F 776 SER cc_start: 0.8339 (t) cc_final: 0.8108 (t) REVERT: F 881 MET cc_start: 0.7565 (mmp) cc_final: 0.7337 (mmm) REVERT: G 268 LEU cc_start: 0.7868 (pp) cc_final: 0.7654 (pp) REVERT: G 291 TYR cc_start: 0.8774 (m-80) cc_final: 0.8421 (m-10) REVERT: G 355 LYS cc_start: 0.8303 (ptmm) cc_final: 0.7754 (tptt) REVERT: G 399 MET cc_start: 0.8880 (pmm) cc_final: 0.8355 (ptp) REVERT: G 452 MET cc_start: 0.8355 (tpp) cc_final: 0.7981 (tpt) REVERT: G 468 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8082 (tm-30) REVERT: G 503 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8878 (t0) REVERT: G 523 GLN cc_start: 0.7910 (tt0) cc_final: 0.7449 (tt0) REVERT: G 576 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7294 (pm20) REVERT: G 668 GLN cc_start: 0.8100 (mt0) cc_final: 0.7835 (mt0) REVERT: G 746 MET cc_start: 0.8307 (ptm) cc_final: 0.6949 (tmm) REVERT: H 221 ASP cc_start: 0.7404 (t70) cc_final: 0.7158 (t70) REVERT: H 326 ASP cc_start: 0.8738 (t0) cc_final: 0.8444 (t0) REVERT: H 429 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7552 (mm-30) REVERT: H 627 ASP cc_start: 0.8452 (t0) cc_final: 0.8177 (t70) REVERT: H 697 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7314 (tp30) REVERT: H 706 ILE cc_start: 0.9224 (pt) cc_final: 0.8702 (pt) REVERT: H 744 GLU cc_start: 0.7173 (mp0) cc_final: 0.6231 (mp0) REVERT: H 848 MET cc_start: 0.7846 (mmp) cc_final: 0.6538 (ttm) REVERT: I 102 ILE cc_start: 0.9390 (mt) cc_final: 0.9155 (mt) REVERT: I 104 THR cc_start: 0.8796 (m) cc_final: 0.8346 (t) REVERT: I 171 GLU cc_start: 0.8132 (tp30) cc_final: 0.7824 (tp30) REVERT: I 261 GLU cc_start: 0.6915 (pp20) cc_final: 0.6241 (tm-30) REVERT: I 295 MET cc_start: 0.7653 (mmm) cc_final: 0.5010 (ppp) REVERT: I 326 ASP cc_start: 0.8531 (t0) cc_final: 0.8297 (t0) REVERT: I 409 MET cc_start: 0.8272 (tpp) cc_final: 0.8038 (tpp) REVERT: I 502 ASP cc_start: 0.6132 (t0) cc_final: 0.5828 (t0) REVERT: I 559 TYR cc_start: 0.8434 (t80) cc_final: 0.8085 (t80) REVERT: I 593 MET cc_start: 0.8374 (mmt) cc_final: 0.8097 (mmt) REVERT: I 723 GLU cc_start: 0.8050 (tp30) cc_final: 0.7734 (tp30) REVERT: I 725 TYR cc_start: 0.7046 (m-10) cc_final: 0.6762 (m-10) REVERT: I 729 ASN cc_start: 0.8793 (p0) cc_final: 0.8202 (p0) REVERT: I 841 ASP cc_start: 0.8036 (t0) cc_final: 0.7742 (t0) REVERT: J 116 GLU cc_start: 0.6776 (pp20) cc_final: 0.5748 (tm-30) REVERT: J 193 MET cc_start: 0.7880 (ptp) cc_final: 0.7668 (mtm) REVERT: J 218 ILE cc_start: 0.8817 (mm) cc_final: 0.8465 (tp) REVERT: J 235 MET cc_start: 0.8074 (tmm) cc_final: 0.7786 (tmm) REVERT: J 304 ARG cc_start: 0.8614 (mmt-90) cc_final: 0.8215 (mpt180) REVERT: J 378 ASN cc_start: 0.8209 (p0) cc_final: 0.7717 (p0) REVERT: J 609 HIS cc_start: 0.8485 (t70) cc_final: 0.8253 (t-90) REVERT: J 727 TYR cc_start: 0.8106 (m-80) cc_final: 0.7680 (m-80) REVERT: J 735 ASP cc_start: 0.7597 (p0) cc_final: 0.7344 (p0) REVERT: J 743 GLU cc_start: 0.6837 (pm20) cc_final: 0.6434 (pp20) REVERT: J 799 VAL cc_start: 0.8269 (p) cc_final: 0.7978 (p) REVERT: J 854 THR cc_start: 0.8156 (p) cc_final: 0.7935 (t) REVERT: P 33 GLU cc_start: 0.8539 (pt0) cc_final: 0.7902 (pp20) REVERT: P 40 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7646 (tp30) REVERT: P 146 MET cc_start: 0.6774 (mtp) cc_final: 0.6355 (mtp) REVERT: P 268 GLU cc_start: 0.5019 (mm-30) cc_final: 0.4398 (mm-30) REVERT: P 282 ASP cc_start: 0.8154 (p0) cc_final: 0.7719 (p0) REVERT: P 353 GLU cc_start: 0.7931 (mp0) cc_final: 0.7255 (mm-30) REVERT: P 416 PHE cc_start: 0.8089 (m-80) cc_final: 0.7830 (m-10) REVERT: P 464 ILE cc_start: 0.8968 (mm) cc_final: 0.8731 (mm) REVERT: P 518 TYR cc_start: 0.7875 (p90) cc_final: 0.7505 (p90) REVERT: P 525 ASP cc_start: 0.8107 (m-30) cc_final: 0.7741 (m-30) REVERT: P 597 LYS cc_start: 0.7634 (tttm) cc_final: 0.7220 (tppt) REVERT: P 624 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8605 (mmmt) REVERT: P 970 ILE cc_start: 0.8709 (tp) cc_final: 0.8341 (tp) REVERT: P 1063 MET cc_start: 0.7834 (mtt) cc_final: 0.7559 (mtt) outliers start: 2 outliers final: 0 residues processed: 2645 average time/residue: 1.6601 time to fit residues: 7402.7428 Evaluate side-chains 2353 residues out of total 8293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2352 time to evaluate : 8.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 902 random chunks: chunk 568 optimal weight: 5.9990 chunk 762 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 659 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 716 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 chunk 735 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 132 optimal weight: 0.0870 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 GLN ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 695 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 HIS C 368 GLN D 287 ASN ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN E 609 HIS ** E 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 761 ASN ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 396 GLN ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 483 ASN ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 483 ASN J 484 ASN J 597 ASN J 761 ASN ** P 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 595 GLN ** P 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121967 restraints weight = 501523.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125835 restraints weight = 208038.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128108 restraints weight = 103396.838| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.7549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 75677 Z= 0.219 Angle : 0.568 12.087 102731 Z= 0.305 Chirality : 0.040 0.165 11785 Planarity : 0.005 0.102 13216 Dihedral : 7.497 158.618 10332 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.37 % Favored : 91.62 % Rotamer: Outliers : 0.02 % Allowed : 0.28 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.09), residues: 9006 helix: 0.67 (0.08), residues: 4327 sheet: -1.61 (0.18), residues: 733 loop : -1.94 (0.10), residues: 3946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 416 HIS 0.013 0.001 HIS G 257 PHE 0.025 0.001 PHE F 173 TYR 0.035 0.002 TYR E 262 ARG 0.015 0.001 ARG I 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 93271.89 seconds wall clock time: 1585 minutes 43.87 seconds (95143.87 seconds total)