Starting phenix.real_space_refine on Wed Mar 20 14:03:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe5_20323/03_2024/6pe5_20323.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe5_20323/03_2024/6pe5_20323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe5_20323/03_2024/6pe5_20323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe5_20323/03_2024/6pe5_20323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe5_20323/03_2024/6pe5_20323.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe5_20323/03_2024/6pe5_20323.pdb" } resolution = 3.2 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= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 173 5.16 5 C 17925 2.51 5 N 4492 2.21 5 O 5052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ARG 799": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "H ARG 161": "NH1" <-> "NH2" Residue "I ARG 46": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I ARG 124": "NH1" <-> "NH2" Residue "I ARG 153": "NH1" <-> "NH2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J ARG 124": "NH1" <-> "NH2" Residue "J ARG 153": "NH1" <-> "NH2" Residue "K ARG 46": "NH1" <-> "NH2" Residue "K ARG 117": "NH1" <-> "NH2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "L ARG 117": "NH1" <-> "NH2" Residue "L ARG 153": "NH1" <-> "NH2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 117": "NH1" <-> "NH2" Residue "M ARG 124": "NH1" <-> "NH2" Residue "M ARG 153": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 117": "NH1" <-> "NH2" Residue "N ARG 124": "NH1" <-> "NH2" Residue "N ARG 153": "NH1" <-> "NH2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 117": "NH1" <-> "NH2" Residue "O ARG 124": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "P ARG 46": "NH1" <-> "NH2" Residue "P ARG 117": "NH1" <-> "NH2" Residue "P ARG 124": "NH1" <-> "NH2" Residue "P ARG 153": "NH1" <-> "NH2" Residue "Q ARG 108": "NH1" <-> "NH2" Residue "Q ARG 224": "NH1" <-> "NH2" Residue "R ARG 108": "NH1" <-> "NH2" Residue "R ARG 224": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27642 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 6142 Classifications: {'peptide': 758} Link IDs: {'PTRANS': 21, 'TRANS': 736} Chain breaks: 2 Chain: "B" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 406 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "D" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2802 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 335} Chain: "E" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 554 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "F" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 561 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "G" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1484 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 196} Chain: "H" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1149 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "I" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "J" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "K" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "L" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "M" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "N" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "O" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "P" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "Q" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2712 Classifications: {'peptide': 369} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 20, 'TRANS': 348} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "R" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2712 Classifications: {'peptide': 369} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 20, 'TRANS': 348} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 13.96, per 1000 atoms: 0.51 Number of scatterers: 27642 At special positions: 0 Unit cell: (157.29, 170.13, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 173 16.00 O 5052 8.00 N 4492 7.00 C 17925 6.00 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: 9.86 Conformation dependent library (CDL) restraints added in 5.4 seconds 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6642 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 8 sheets defined 69.8% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.791A pdb=" N TYR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 removed outlier: 4.252A pdb=" N LEU A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 77 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 128 removed outlier: 4.391A pdb=" N GLU A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 4.152A pdb=" N ASP A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.771A pdb=" N LEU A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.512A pdb=" N ARG A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.697A pdb=" N LYS A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 removed outlier: 3.545A pdb=" N PHE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.693A pdb=" N GLN A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 Processing helix chain 'A' and resid 407 through 423 removed outlier: 3.700A pdb=" N THR A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix removed outlier: 4.091A pdb=" N MET A 422 " --> pdb=" O MET A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 441 removed outlier: 3.780A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 447 removed outlier: 4.018A pdb=" N ILE A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 460 Processing helix chain 'A' and resid 461 through 479 Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.525A pdb=" N TRP A 522 " --> pdb=" O ASP A 519 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 523 " --> pdb=" O TRP A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 519 through 523' Processing helix chain 'A' and resid 527 through 552 removed outlier: 3.535A pdb=" N PHE A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 removed outlier: 3.941A pdb=" N LEU A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 596 removed outlier: 3.691A pdb=" N ILE A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 569 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Proline residue: A 574 - end of helix removed outlier: 3.610A pdb=" N ILE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 602 removed outlier: 3.677A pdb=" N ASP A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 removed outlier: 4.025A pdb=" N PHE A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.833A pdb=" N VAL A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 650 through 658 removed outlier: 3.623A pdb=" N PHE A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 724 through 732 removed outlier: 3.605A pdb=" N SER A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 754 removed outlier: 3.657A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.809A pdb=" N PHE A 759 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 760 " --> pdb=" O ILE A 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 756 through 760' Processing helix chain 'A' and resid 763 through 784 removed outlier: 4.004A pdb=" N VAL A 767 " --> pdb=" O GLY A 763 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A 768 " --> pdb=" O PHE A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 803 removed outlier: 3.535A pdb=" N THR A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 801 " --> pdb=" O SER A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 removed outlier: 3.521A pdb=" N ALA A 830 " --> pdb=" O ASP A 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 246 removed outlier: 3.733A pdb=" N ASN B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'D' and resid 6 through 22 removed outlier: 7.072A pdb=" N PHE D 12 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 35 Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.626A pdb=" N LEU D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.697A pdb=" N LEU D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 116 removed outlier: 3.556A pdb=" N LYS D 93 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY D 101 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR D 102 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 Processing helix chain 'D' and resid 135 through 141 removed outlier: 3.545A pdb=" N THR D 138 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 140 " --> pdb=" O PRO D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 150 Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.819A pdb=" N PHE D 162 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 200 removed outlier: 3.707A pdb=" N GLU D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 198 " --> pdb=" O ASN D 194 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 227 removed outlier: 3.736A pdb=" N CYS D 207 " --> pdb=" O PRO D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 251 through 258 removed outlier: 4.009A pdb=" N HIS D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.523A pdb=" N VAL D 265 " --> pdb=" O ASP D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 299 removed outlier: 3.856A pdb=" N HIS D 287 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE D 288 " --> pdb=" O LEU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'D' and resid 306 through 332 removed outlier: 4.339A pdb=" N TRP D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 removed outlier: 3.758A pdb=" N ARG D 337 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 334 through 338' Processing helix chain 'E' and resid 4 through 23 removed outlier: 3.713A pdb=" N ILE E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 53 removed outlier: 4.041A pdb=" N ILE E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 42 " --> pdb=" O ILE E 38 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP E 48 " --> pdb=" O MET E 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 33 removed outlier: 3.664A pdb=" N CYS F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU F 16 " --> pdb=" O CYS F 12 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 73 removed outlier: 3.724A pdb=" N ALA F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN F 72 " --> pdb=" O PHE F 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 40 removed outlier: 3.754A pdb=" N GLY G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 53 removed outlier: 3.584A pdb=" N PHE G 50 " --> pdb=" O ASN G 46 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU G 51 " --> pdb=" O PHE G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 90 removed outlier: 3.936A pdb=" N TRP G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 97 removed outlier: 3.578A pdb=" N ILE G 96 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR G 97 " --> pdb=" O PRO G 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 93 through 97' Processing helix chain 'G' and resid 101 through 122 removed outlier: 3.834A pdb=" N CYS G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL G 110 " --> pdb=" O PHE G 106 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA G 111 " --> pdb=" O CYS G 107 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 135 through 177 removed outlier: 3.537A pdb=" N ASP G 177 " --> pdb=" O SER G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 192 removed outlier: 3.925A pdb=" N VAL G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 206 removed outlier: 4.151A pdb=" N LEU G 196 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 48 removed outlier: 4.012A pdb=" N GLY H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.601A pdb=" N LEU H 55 " --> pdb=" O LYS H 52 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE H 56 " --> pdb=" O PRO H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 52 through 56' Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.683A pdb=" N ILE H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 126 removed outlier: 3.588A pdb=" N GLY H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 163 removed outlier: 3.658A pdb=" N VAL H 146 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU H 147 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY H 148 " --> pdb=" O SER H 144 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER H 163 " --> pdb=" O ASN H 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 43 removed outlier: 4.153A pdb=" N GLY I 13 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE I 21 " --> pdb=" O CYS I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 50 Processing helix chain 'I' and resid 54 through 76 removed outlier: 4.153A pdb=" N ILE I 63 " --> pdb=" O MET I 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 120 removed outlier: 3.504A pdb=" N GLY I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 152 removed outlier: 4.451A pdb=" N GLY I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU I 139 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 43 removed outlier: 4.154A pdb=" N GLY J 13 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 54 through 76 removed outlier: 4.154A pdb=" N ILE J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 120 removed outlier: 3.503A pdb=" N GLY J 87 " --> pdb=" O ALA J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 124 No H-bonds generated for 'chain 'J' and resid 122 through 124' Processing helix chain 'J' and resid 125 through 152 removed outlier: 4.430A pdb=" N LEU J 139 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 43 removed outlier: 4.154A pdb=" N GLY K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE K 21 " --> pdb=" O CYS K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 50 Processing helix chain 'K' and resid 54 through 76 removed outlier: 4.153A pdb=" N ILE K 63 " --> pdb=" O MET K 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 120 removed outlier: 3.504A pdb=" N GLY K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 124 No H-bonds generated for 'chain 'K' and resid 122 through 124' Processing helix chain 'K' and resid 125 through 152 removed outlier: 4.430A pdb=" N LEU K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY K 140 " --> pdb=" O ALA K 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 43 removed outlier: 4.153A pdb=" N GLY L 13 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE L 21 " --> pdb=" O CYS L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 50 Processing helix chain 'L' and resid 54 through 76 removed outlier: 4.154A pdb=" N ILE L 63 " --> pdb=" O MET L 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 120 removed outlier: 3.503A pdb=" N GLY L 87 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 124 No H-bonds generated for 'chain 'L' and resid 122 through 124' Processing helix chain 'L' and resid 125 through 152 removed outlier: 4.430A pdb=" N LEU L 139 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY L 140 " --> pdb=" O ALA L 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 43 removed outlier: 4.154A pdb=" N GLY M 13 " --> pdb=" O ALA M 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 50 Processing helix chain 'M' and resid 54 through 76 removed outlier: 4.153A pdb=" N ILE M 63 " --> pdb=" O MET M 59 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 120 removed outlier: 3.504A pdb=" N GLY M 87 " --> pdb=" O ALA M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 152 removed outlier: 4.451A pdb=" N GLY M 128 " --> pdb=" O ARG M 124 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU M 139 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 43 removed outlier: 4.154A pdb=" N GLY N 13 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE N 21 " --> pdb=" O CYS N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 50 Processing helix chain 'N' and resid 54 through 76 removed outlier: 4.154A pdb=" N ILE N 63 " --> pdb=" O MET N 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA N 64 " --> pdb=" O ALA N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 120 removed outlier: 3.503A pdb=" N GLY N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 152 removed outlier: 4.452A pdb=" N GLY N 128 " --> pdb=" O ARG N 124 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU N 139 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY N 140 " --> pdb=" O ALA N 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 43 removed outlier: 4.153A pdb=" N GLY O 13 " --> pdb=" O ALA O 9 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE O 21 " --> pdb=" O CYS O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 50 Processing helix chain 'O' and resid 54 through 76 removed outlier: 4.153A pdb=" N ILE O 63 " --> pdb=" O MET O 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA O 64 " --> pdb=" O ALA O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 120 removed outlier: 3.504A pdb=" N GLY O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 152 removed outlier: 4.451A pdb=" N GLY O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU O 139 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY O 140 " --> pdb=" O ALA O 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 43 removed outlier: 4.153A pdb=" N GLY P 13 " --> pdb=" O ALA P 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE P 21 " --> pdb=" O CYS P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 50 Processing helix chain 'P' and resid 54 through 76 removed outlier: 4.153A pdb=" N ILE P 63 " --> pdb=" O MET P 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA P 64 " --> pdb=" O ALA P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 120 removed outlier: 3.504A pdb=" N GLY P 87 " --> pdb=" O ALA P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 152 removed outlier: 4.451A pdb=" N GLY P 128 " --> pdb=" O ARG P 124 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU P 139 " --> pdb=" O PHE P 135 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY P 140 " --> pdb=" O ALA P 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 65 Processing helix chain 'Q' and resid 75 through 81 removed outlier: 4.227A pdb=" N LYS Q 81 " --> pdb=" O GLN Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 93 removed outlier: 3.821A pdb=" N ALA Q 91 " --> pdb=" O THR Q 87 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 117 Processing helix chain 'Q' and resid 125 through 134 Processing helix chain 'Q' and resid 140 through 147 removed outlier: 3.727A pdb=" N GLN Q 144 " --> pdb=" O ASP Q 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 186 through 211 removed outlier: 3.775A pdb=" N GLU Q 195 " --> pdb=" O ALA Q 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS Q 198 " --> pdb=" O ARG Q 194 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN Q 202 " --> pdb=" O LYS Q 198 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA Q 207 " --> pdb=" O GLY Q 203 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS Q 209 " --> pdb=" O ALA Q 205 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 253 removed outlier: 3.781A pdb=" N MET Q 229 " --> pdb=" O LEU Q 225 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN Q 230 " --> pdb=" O SER Q 226 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU Q 233 " --> pdb=" O MET Q 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU Q 240 " --> pdb=" O GLY Q 236 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA Q 245 " --> pdb=" O SER Q 241 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY Q 247 " --> pdb=" O GLU Q 243 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 310 Processing helix chain 'Q' and resid 337 through 348 removed outlier: 3.868A pdb=" N ALA Q 346 " --> pdb=" O ARG Q 342 " (cutoff:3.500A) Processing helix chain 'Q' and resid 365 through 380 removed outlier: 3.526A pdb=" N ALA Q 370 " --> pdb=" O GLN Q 366 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA Q 371 " --> pdb=" O GLU Q 367 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU Q 375 " --> pdb=" O ALA Q 371 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET Q 378 " --> pdb=" O THR Q 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 419 Processing helix chain 'Q' and resid 425 through 434 removed outlier: 3.928A pdb=" N LYS Q 434 " --> pdb=" O ARG Q 430 " (cutoff:3.500A) Processing helix chain 'Q' and resid 439 through 444 Processing helix chain 'Q' and resid 466 through 476 removed outlier: 3.704A pdb=" N LEU Q 473 " --> pdb=" O GLN Q 469 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP Q 474 " --> pdb=" O LEU Q 470 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU Q 476 " --> pdb=" O ALA Q 472 " (cutoff:3.500A) Processing helix chain 'Q' and resid 480 through 488 Processing helix chain 'R' and resid 61 through 65 Processing helix chain 'R' and resid 75 through 81 removed outlier: 4.227A pdb=" N LYS R 81 " --> pdb=" O GLN R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 93 removed outlier: 3.822A pdb=" N ALA R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 117 Processing helix chain 'R' and resid 125 through 134 Processing helix chain 'R' and resid 140 through 147 removed outlier: 3.727A pdb=" N GLN R 144 " --> pdb=" O ASP R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 211 removed outlier: 3.775A pdb=" N GLU R 195 " --> pdb=" O ALA R 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS R 198 " --> pdb=" O ARG R 194 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN R 202 " --> pdb=" O LYS R 198 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS R 209 " --> pdb=" O ALA R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 253 removed outlier: 3.781A pdb=" N MET R 229 " --> pdb=" O LEU R 225 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN R 230 " --> pdb=" O SER R 226 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU R 233 " --> pdb=" O MET R 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA R 245 " --> pdb=" O SER R 241 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY R 247 " --> pdb=" O GLU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 310 Processing helix chain 'R' and resid 337 through 348 removed outlier: 3.868A pdb=" N ALA R 346 " --> pdb=" O ARG R 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 380 removed outlier: 3.525A pdb=" N ALA R 370 " --> pdb=" O GLN R 366 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA R 371 " --> pdb=" O GLU R 367 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU R 375 " --> pdb=" O ALA R 371 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET R 378 " --> pdb=" O THR R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 419 Processing helix chain 'R' and resid 425 through 434 removed outlier: 3.928A pdb=" N LYS R 434 " --> pdb=" O ARG R 430 " (cutoff:3.500A) Processing helix chain 'R' and resid 439 through 444 Processing helix chain 'R' and resid 466 through 476 removed outlier: 3.704A pdb=" N LEU R 473 " --> pdb=" O GLN R 469 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP R 474 " --> pdb=" O LEU R 470 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU R 476 " --> pdb=" O ALA R 472 " (cutoff:3.500A) Processing helix chain 'R' and resid 480 through 488 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.317A pdb=" N LEU A 16 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 214 through 217 removed outlier: 3.655A pdb=" N VAL A 216 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 189 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR A 188 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 323 through 326 removed outlier: 3.543A pdb=" N GLY Q 329 " --> pdb=" O ASN Q 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Q' and resid 446 through 448 Processing sheet with id=AA6, first strand: chain 'R' and resid 323 through 326 removed outlier: 3.543A pdb=" N GLY R 329 " --> pdb=" O ASN R 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 446 through 448 Processing sheet with id=AA8, first strand: chain 'R' and resid 451 through 452 removed outlier: 3.555A pdb=" N GLY R 455 " --> pdb=" O ALA R 452 " (cutoff:3.500A) 1805 hydrogen bonds defined for protein. 5313 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: 9.16 Time building geometry restraints manager: 10.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7613 1.34 - 1.46: 5128 1.46 - 1.57: 15150 1.57 - 1.69: 0 1.69 - 1.81: 280 Bond restraints: 28171 Sorted by residual: bond pdb=" CG1 ILE A 245 " pdb=" CD1 ILE A 245 " ideal model delta sigma weight residual 1.513 1.358 0.155 3.90e-02 6.57e+02 1.58e+01 bond pdb=" N ILE D 245 " pdb=" CA ILE D 245 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" CB TRP G 77 " pdb=" CG TRP G 77 " ideal model delta sigma weight residual 1.498 1.392 0.106 3.10e-02 1.04e+03 1.16e+01 bond pdb=" N GLN J 122 " pdb=" CA GLN J 122 " ideal model delta sigma weight residual 1.463 1.489 -0.027 8.80e-03 1.29e+04 9.09e+00 bond pdb=" N GLN L 122 " pdb=" CA GLN L 122 " ideal model delta sigma weight residual 1.463 1.489 -0.026 8.80e-03 1.29e+04 9.05e+00 ... (remaining 28166 not shown) Histogram of bond angle deviations from ideal: 96.82 - 104.27: 393 104.27 - 111.73: 12089 111.73 - 119.18: 10903 119.18 - 126.64: 14501 126.64 - 134.10: 345 Bond angle restraints: 38231 Sorted by residual: angle pdb=" C ILE O 54 " pdb=" N VAL O 55 " pdb=" CA VAL O 55 " ideal model delta sigma weight residual 120.24 126.21 -5.97 6.30e-01 2.52e+00 8.97e+01 angle pdb=" C ILE P 54 " pdb=" N VAL P 55 " pdb=" CA VAL P 55 " ideal model delta sigma weight residual 120.24 126.20 -5.96 6.30e-01 2.52e+00 8.95e+01 angle pdb=" C ILE L 54 " pdb=" N VAL L 55 " pdb=" CA VAL L 55 " ideal model delta sigma weight residual 120.24 126.17 -5.93 6.30e-01 2.52e+00 8.85e+01 angle pdb=" C ILE J 54 " pdb=" N VAL J 55 " pdb=" CA VAL J 55 " ideal model delta sigma weight residual 120.24 126.16 -5.92 6.30e-01 2.52e+00 8.84e+01 angle pdb=" C ILE N 54 " pdb=" N VAL N 55 " pdb=" CA VAL N 55 " ideal model delta sigma weight residual 120.24 126.16 -5.92 6.30e-01 2.52e+00 8.83e+01 ... (remaining 38226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 15688 15.22 - 30.45: 657 30.45 - 45.67: 199 45.67 - 60.90: 24 60.90 - 76.12: 26 Dihedral angle restraints: 16594 sinusoidal: 6167 harmonic: 10427 Sorted by residual: dihedral pdb=" CA ASN F 43 " pdb=" C ASN F 43 " pdb=" N ASP F 44 " pdb=" CA ASP F 44 " ideal model delta harmonic sigma weight residual -180.00 -136.83 -43.17 0 5.00e+00 4.00e-02 7.46e+01 dihedral pdb=" CD ARG R 456 " pdb=" NE ARG R 456 " pdb=" CZ ARG R 456 " pdb=" NH1 ARG R 456 " ideal model delta sinusoidal sigma weight residual 0.00 -75.58 75.58 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CD ARG J 124 " pdb=" NE ARG J 124 " pdb=" CZ ARG J 124 " pdb=" NH1 ARG J 124 " ideal model delta sinusoidal sigma weight residual 0.00 75.49 -75.49 1 1.00e+01 1.00e-02 7.19e+01 ... (remaining 16591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3624 0.066 - 0.132: 771 0.132 - 0.197: 97 0.197 - 0.263: 18 0.263 - 0.329: 4 Chirality restraints: 4514 Sorted by residual: chirality pdb=" CA PHE D 133 " pdb=" N PHE D 133 " pdb=" C PHE D 133 " pdb=" CB PHE D 133 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB ILE A 482 " pdb=" CA ILE A 482 " pdb=" CG1 ILE A 482 " pdb=" CG2 ILE A 482 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB VAL R 120 " pdb=" CA VAL R 120 " pdb=" CG1 VAL R 120 " pdb=" CG2 VAL R 120 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 4511 not shown) Planarity restraints: 4807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 456 " -1.063 9.50e-02 1.11e+02 4.76e-01 1.37e+02 pdb=" NE ARG R 456 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG R 456 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG R 456 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG R 456 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 124 " 1.062 9.50e-02 1.11e+02 4.76e-01 1.37e+02 pdb=" NE ARG J 124 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG J 124 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 124 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG J 124 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 46 " -0.884 9.50e-02 1.11e+02 3.96e-01 9.52e+01 pdb=" NE ARG J 46 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG J 46 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 46 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG J 46 " -0.024 2.00e-02 2.50e+03 ... (remaining 4804 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 447 2.69 - 3.24: 26449 3.24 - 3.80: 42160 3.80 - 4.35: 56897 4.35 - 4.90: 94429 Nonbonded interactions: 220382 Sorted by model distance: nonbonded pdb=" O TYR D 97 " pdb=" OH TYR D 188 " model vdw 2.138 2.440 nonbonded pdb=" OG SER F 41 " pdb=" OD1 ASN F 43 " model vdw 2.237 2.440 nonbonded pdb=" O MET Q 345 " pdb=" OH TYR Q 486 " model vdw 2.253 2.440 nonbonded pdb=" O MET R 345 " pdb=" OH TYR R 486 " model vdw 2.254 2.440 nonbonded pdb=" O THR A 383 " pdb=" OG1 THR A 387 " model vdw 2.293 2.440 ... (remaining 220377 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 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.870 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: 0.020 Extract box with map and model: 6.370 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 68.810 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.190 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: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.007 0.155 28171 Z= 0.470 Angle : 1.071 17.080 38231 Z= 0.573 Chirality : 0.056 0.329 4514 Planarity : 0.015 0.476 4807 Dihedral : 10.653 76.121 9952 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.41 % Favored : 93.37 % Rotamer: Outliers : 0.45 % Allowed : 3.37 % Favored : 96.19 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.44 (0.11), residues: 3620 helix: -1.78 (0.08), residues: 2426 sheet: -1.67 (0.56), residues: 72 loop : -3.15 (0.15), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 312 HIS 0.021 0.002 HIS A 796 PHE 0.053 0.004 PHE F 65 TYR 0.034 0.002 TYR G 57 ARG 0.011 0.001 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 667 time to evaluate : 3.137 Fit side-chains revert: symmetry clash REVERT: A 563 ASN cc_start: 0.7722 (t0) cc_final: 0.7441 (t0) REVERT: E 17 MET cc_start: 0.7362 (ptm) cc_final: 0.7152 (ptp) REVERT: E 20 LEU cc_start: 0.9064 (tm) cc_final: 0.8593 (tp) REVERT: G 27 ILE cc_start: 0.9183 (mt) cc_final: 0.8943 (mt) REVERT: G 47 PHE cc_start: 0.8324 (t80) cc_final: 0.8061 (t80) REVERT: G 205 MET cc_start: 0.9163 (mtp) cc_final: 0.8921 (mtp) REVERT: L 42 THR cc_start: 0.8059 (m) cc_final: 0.7682 (m) REVERT: Q 206 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: R 318 VAL cc_start: 0.8810 (t) cc_final: 0.8564 (m) REVERT: R 407 GLU cc_start: 0.6669 (pt0) cc_final: 0.6468 (pt0) outliers start: 13 outliers final: 6 residues processed: 677 average time/residue: 0.4237 time to fit residues: 435.6909 Evaluate side-chains 400 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 393 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain Q residue 206 GLU Chi-restraints excluded: chain Q residue 454 ASN Chi-restraints excluded: chain R residue 454 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 6.9990 chunk 267 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 320 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 123 GLN A 630 GLN A 796 HIS D 7 ASN D 244 ASN E 55 GLN F 72 GLN I 90 GLN J 90 GLN J 122 GLN K 53 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 GLN O 90 GLN P 90 GLN Q 217 GLN Q 411 ASN ** Q 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** R 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28171 Z= 0.217 Angle : 0.637 13.700 38231 Z= 0.324 Chirality : 0.041 0.216 4514 Planarity : 0.005 0.055 4807 Dihedral : 5.166 57.336 3923 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.03 % Rotamer: Outliers : 2.61 % Allowed : 9.38 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.83 (0.14), residues: 3620 helix: 0.35 (0.10), residues: 2435 sheet: -1.15 (0.60), residues: 76 loop : -2.49 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 48 HIS 0.004 0.001 HIS A 381 PHE 0.034 0.002 PHE D 133 TYR 0.016 0.001 TYR A 285 ARG 0.007 0.001 ARG J 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 424 time to evaluate : 3.190 Fit side-chains revert: symmetry clash REVERT: A 143 PHE cc_start: 0.8834 (t80) cc_final: 0.8558 (t80) REVERT: A 344 ASP cc_start: 0.7073 (p0) cc_final: 0.6520 (p0) REVERT: A 453 GLU cc_start: 0.6357 (tp30) cc_final: 0.5932 (tp30) REVERT: A 487 MET cc_start: 0.7577 (mmt) cc_final: 0.6889 (mmt) REVERT: A 563 ASN cc_start: 0.7779 (t0) cc_final: 0.7501 (t0) REVERT: D 122 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6763 (tm-30) REVERT: D 236 ASP cc_start: 0.8204 (m-30) cc_final: 0.7906 (m-30) REVERT: E 20 LEU cc_start: 0.8874 (tm) cc_final: 0.8590 (tp) REVERT: G 27 ILE cc_start: 0.9174 (mt) cc_final: 0.8895 (mt) REVERT: K 144 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9004 (tp) REVERT: P 137 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7119 (mm-30) outliers start: 76 outliers final: 35 residues processed: 475 average time/residue: 0.3916 time to fit residues: 294.2385 Evaluate side-chains 401 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 364 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 190 PHE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 121 GLN Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 451 ASP Chi-restraints excluded: chain R residue 235 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 321 optimal weight: 10.0000 chunk 346 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 318 optimal weight: 50.0000 chunk 109 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN I 90 GLN J 53 ASN J 90 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN ** O 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 GLN Q 202 ASN Q 469 GLN R 469 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28171 Z= 0.304 Angle : 0.649 16.044 38231 Z= 0.329 Chirality : 0.042 0.260 4514 Planarity : 0.004 0.041 4807 Dihedral : 4.871 59.979 3908 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 3.06 % Allowed : 10.99 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.07 (0.14), residues: 3620 helix: 1.09 (0.11), residues: 2422 sheet: -0.81 (0.59), residues: 81 loop : -2.25 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 77 HIS 0.005 0.001 HIS A 796 PHE 0.035 0.002 PHE D 133 TYR 0.020 0.001 TYR L 8 ARG 0.007 0.000 ARG J 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 373 time to evaluate : 3.335 Fit side-chains revert: symmetry clash REVERT: A 344 ASP cc_start: 0.7040 (p0) cc_final: 0.6607 (p0) REVERT: A 453 GLU cc_start: 0.6337 (tp30) cc_final: 0.6112 (tp30) REVERT: A 487 MET cc_start: 0.7487 (mmt) cc_final: 0.6879 (mmt) REVERT: A 556 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8943 (tp) REVERT: B 246 ASN cc_start: 0.8769 (m110) cc_final: 0.8537 (m-40) REVERT: D 122 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6966 (tm-30) REVERT: D 150 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: D 236 ASP cc_start: 0.8231 (m-30) cc_final: 0.7535 (t0) REVERT: D 262 PHE cc_start: 0.9011 (t80) cc_final: 0.8727 (t80) REVERT: E 20 LEU cc_start: 0.8977 (tm) cc_final: 0.8718 (tp) REVERT: G 27 ILE cc_start: 0.9234 (mt) cc_final: 0.8965 (mt) REVERT: G 108 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8209 (tm-30) REVERT: G 133 MET cc_start: 0.8064 (tpt) cc_final: 0.7569 (tpt) REVERT: K 144 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8929 (tp) REVERT: O 68 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9268 (tp) REVERT: P 137 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: R 326 ASN cc_start: 0.7931 (p0) cc_final: 0.7100 (p0) outliers start: 89 outliers final: 53 residues processed: 441 average time/residue: 0.3882 time to fit residues: 270.4118 Evaluate side-chains 394 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 336 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 317 optimal weight: 50.0000 chunk 241 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 322 optimal weight: 3.9990 chunk 341 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 305 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 499 HIS D 303 GLN J 53 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28171 Z= 0.230 Angle : 0.586 17.530 38231 Z= 0.296 Chirality : 0.040 0.215 4514 Planarity : 0.004 0.046 4807 Dihedral : 4.602 59.983 3908 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.02 % Allowed : 12.33 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.65 (0.14), residues: 3620 helix: 1.58 (0.11), residues: 2420 sheet: -0.80 (0.58), residues: 81 loop : -2.13 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 77 HIS 0.005 0.001 HIS A 796 PHE 0.034 0.001 PHE D 133 TYR 0.015 0.001 TYR L 8 ARG 0.006 0.000 ARG J 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 365 time to evaluate : 3.123 Fit side-chains revert: symmetry clash REVERT: A 344 ASP cc_start: 0.7086 (p0) cc_final: 0.6700 (p0) REVERT: A 556 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8963 (tp) REVERT: B 246 ASN cc_start: 0.8717 (m110) cc_final: 0.8482 (m-40) REVERT: D 150 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: D 236 ASP cc_start: 0.8206 (m-30) cc_final: 0.7575 (t0) REVERT: E 20 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8778 (tp) REVERT: G 27 ILE cc_start: 0.9232 (mt) cc_final: 0.8952 (mt) REVERT: G 108 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8179 (tt0) REVERT: G 133 MET cc_start: 0.8098 (tpt) cc_final: 0.7729 (tpt) REVERT: I 1 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6202 (ttm) REVERT: I 157 ASP cc_start: 0.7666 (p0) cc_final: 0.7447 (p0) REVERT: J 68 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8940 (tp) REVERT: J 124 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.7989 (mmm-85) REVERT: K 68 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9141 (tp) REVERT: K 144 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8895 (tp) REVERT: M 68 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9193 (tp) REVERT: O 68 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9246 (tp) REVERT: R 326 ASN cc_start: 0.7919 (p0) cc_final: 0.7098 (p0) REVERT: R 486 TYR cc_start: 0.8543 (m-80) cc_final: 0.8172 (m-80) outliers start: 88 outliers final: 50 residues processed: 431 average time/residue: 0.3964 time to fit residues: 268.3907 Evaluate side-chains 397 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 338 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 190 PHE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 125 ASP Chi-restraints excluded: chain R residue 318 VAL Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 454 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 284 optimal weight: 0.6980 chunk 193 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 499 HIS ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 28171 Z= 0.365 Angle : 0.671 18.611 38231 Z= 0.336 Chirality : 0.044 0.249 4514 Planarity : 0.004 0.045 4807 Dihedral : 4.574 24.369 3902 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.52 % Favored : 94.45 % Rotamer: Outliers : 3.33 % Allowed : 12.53 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.59 (0.14), residues: 3620 helix: 1.54 (0.11), residues: 2421 sheet: -0.92 (0.58), residues: 78 loop : -2.15 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 77 HIS 0.005 0.001 HIS A 232 PHE 0.033 0.002 PHE D 133 TYR 0.023 0.002 TYR D 345 ARG 0.006 0.001 ARG J 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 343 time to evaluate : 2.859 Fit side-chains revert: symmetry clash REVERT: A 344 ASP cc_start: 0.7341 (p0) cc_final: 0.6903 (p0) REVERT: A 453 GLU cc_start: 0.6471 (tp30) cc_final: 0.6143 (tp30) REVERT: A 556 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8973 (tp) REVERT: B 246 ASN cc_start: 0.8733 (m110) cc_final: 0.8507 (m-40) REVERT: D 150 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: D 236 ASP cc_start: 0.8209 (m-30) cc_final: 0.7542 (t0) REVERT: E 20 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8786 (tp) REVERT: E 68 ARG cc_start: 0.7468 (mtt-85) cc_final: 0.7211 (mtt180) REVERT: G 27 ILE cc_start: 0.9279 (mt) cc_final: 0.9013 (mt) REVERT: G 108 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8225 (tt0) REVERT: G 133 MET cc_start: 0.8319 (tpt) cc_final: 0.7993 (tpt) REVERT: I 1 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.6198 (ttm) REVERT: O 68 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9284 (tp) REVERT: P 137 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: R 111 LEU cc_start: 0.8196 (mp) cc_final: 0.7792 (mp) REVERT: R 326 ASN cc_start: 0.7875 (p0) cc_final: 0.6965 (p0) outliers start: 97 outliers final: 67 residues processed: 419 average time/residue: 0.3873 time to fit residues: 256.3195 Evaluate side-chains 400 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 327 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 125 ASP Chi-restraints excluded: chain R residue 318 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 114 optimal weight: 7.9990 chunk 307 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 341 optimal weight: 7.9990 chunk 283 optimal weight: 30.0000 chunk 158 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN E 55 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 481 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 28171 Z= 0.561 Angle : 0.770 19.797 38231 Z= 0.387 Chirality : 0.048 0.281 4514 Planarity : 0.005 0.050 4807 Dihedral : 4.933 29.053 3902 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.52 % Favored : 94.42 % Rotamer: Outliers : 4.09 % Allowed : 12.53 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.24 (0.14), residues: 3620 helix: 1.26 (0.10), residues: 2412 sheet: -0.68 (0.60), residues: 74 loop : -2.26 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 77 HIS 0.006 0.001 HIS E 57 PHE 0.037 0.002 PHE G 80 TYR 0.035 0.002 TYR D 345 ARG 0.005 0.001 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 335 time to evaluate : 3.093 Fit side-chains REVERT: A 112 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7356 (ptp90) REVERT: A 453 GLU cc_start: 0.6388 (tp30) cc_final: 0.6057 (tp30) REVERT: A 556 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8939 (tp) REVERT: B 246 ASN cc_start: 0.8807 (m110) cc_final: 0.8601 (m-40) REVERT: D 150 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: D 236 ASP cc_start: 0.8221 (m-30) cc_final: 0.7627 (t0) REVERT: E 20 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8762 (tp) REVERT: E 54 CYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8213 (p) REVERT: E 68 ARG cc_start: 0.7586 (mtt-85) cc_final: 0.7223 (mtt180) REVERT: G 27 ILE cc_start: 0.9270 (mt) cc_final: 0.9001 (mt) REVERT: G 108 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8311 (tt0) REVERT: I 1 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6152 (ttm) REVERT: N 77 SER cc_start: 0.9159 (t) cc_final: 0.8852 (p) REVERT: O 68 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9265 (tp) REVERT: P 137 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7248 (mm-30) outliers start: 119 outliers final: 83 residues processed: 428 average time/residue: 0.4400 time to fit residues: 300.7699 Evaluate side-chains 418 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 327 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain I residue 157 ASP Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 125 ASP Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 318 VAL Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 440 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 329 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 340 optimal weight: 6.9990 chunk 212 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS A 745 GLN D 81 ASN G 132 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28171 Z= 0.165 Angle : 0.561 19.823 38231 Z= 0.284 Chirality : 0.039 0.182 4514 Planarity : 0.004 0.049 4807 Dihedral : 4.316 25.287 3902 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.27 % Allowed : 14.35 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.02 (0.14), residues: 3620 helix: 1.91 (0.11), residues: 2418 sheet: -0.49 (0.59), residues: 79 loop : -2.12 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 33 HIS 0.004 0.001 HIS A 796 PHE 0.032 0.001 PHE D 133 TYR 0.016 0.001 TYR F 56 ARG 0.005 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 362 time to evaluate : 3.006 Fit side-chains REVERT: A 85 GLU cc_start: 0.7713 (pp20) cc_final: 0.7471 (pp20) REVERT: A 112 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7339 (ptp90) REVERT: A 344 ASP cc_start: 0.7358 (p0) cc_final: 0.7022 (p0) REVERT: A 453 GLU cc_start: 0.6272 (tp30) cc_final: 0.5888 (tp30) REVERT: D 150 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: D 236 ASP cc_start: 0.8149 (m-30) cc_final: 0.7571 (t0) REVERT: E 68 ARG cc_start: 0.7401 (mtt-85) cc_final: 0.7159 (mtt180) REVERT: F 32 ASN cc_start: 0.8542 (t0) cc_final: 0.8283 (t0) REVERT: G 27 ILE cc_start: 0.9232 (mt) cc_final: 0.8916 (mt) REVERT: G 108 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8149 (tt0) REVERT: I 1 MET cc_start: 0.6347 (OUTLIER) cc_final: 0.6055 (ttm) REVERT: I 81 LYS cc_start: 0.8967 (mttp) cc_final: 0.8488 (mtpp) REVERT: J 68 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8966 (tp) REVERT: J 124 ARG cc_start: 0.8354 (mmm-85) cc_final: 0.8112 (mmm-85) REVERT: K 68 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9187 (tp) REVERT: L 68 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9161 (tp) REVERT: M 68 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9180 (tp) REVERT: N 46 ARG cc_start: 0.8342 (mtt90) cc_final: 0.8124 (mtp180) REVERT: Q 121 LYS cc_start: 0.5261 (mptt) cc_final: 0.4199 (mptt) REVERT: R 311 LYS cc_start: 0.6573 (mmtm) cc_final: 0.6286 (pttt) outliers start: 66 outliers final: 40 residues processed: 405 average time/residue: 0.4033 time to fit residues: 256.1532 Evaluate side-chains 385 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 338 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 157 ASP Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain R residue 125 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 210 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 168 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 267 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 745 GLN G 132 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28171 Z= 0.332 Angle : 0.642 19.129 38231 Z= 0.322 Chirality : 0.042 0.228 4514 Planarity : 0.004 0.047 4807 Dihedral : 4.446 24.896 3902 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.59 % Rotamer: Outliers : 2.85 % Allowed : 14.35 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.91 (0.14), residues: 3620 helix: 1.81 (0.11), residues: 2410 sheet: -0.65 (0.61), residues: 74 loop : -2.08 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 77 HIS 0.004 0.001 HIS A 232 PHE 0.031 0.002 PHE D 133 TYR 0.022 0.001 TYR D 345 ARG 0.005 0.000 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 334 time to evaluate : 3.159 Fit side-chains REVERT: A 85 GLU cc_start: 0.7810 (pp20) cc_final: 0.7574 (pp20) REVERT: A 112 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7340 (ptp90) REVERT: A 344 ASP cc_start: 0.7407 (p0) cc_final: 0.7063 (p0) REVERT: A 453 GLU cc_start: 0.6367 (tp30) cc_final: 0.5981 (tp30) REVERT: B 246 ASN cc_start: 0.8782 (m110) cc_final: 0.8497 (m-40) REVERT: D 150 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: D 236 ASP cc_start: 0.8171 (m-30) cc_final: 0.7541 (t0) REVERT: D 266 ARG cc_start: 0.8264 (tpp80) cc_final: 0.8029 (ttt180) REVERT: E 20 LEU cc_start: 0.9102 (tp) cc_final: 0.8861 (tt) REVERT: E 54 CYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8322 (p) REVERT: E 68 ARG cc_start: 0.7525 (mtt-85) cc_final: 0.7280 (mtt180) REVERT: F 32 ASN cc_start: 0.8690 (t0) cc_final: 0.8454 (t0) REVERT: G 27 ILE cc_start: 0.9272 (mt) cc_final: 0.8984 (mt) REVERT: G 108 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8228 (tt0) REVERT: I 1 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.5890 (ttm) REVERT: J 124 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.8117 (mmm-85) REVERT: N 46 ARG cc_start: 0.8399 (mtt90) cc_final: 0.8177 (mtp180) REVERT: Q 121 LYS cc_start: 0.5289 (mptt) cc_final: 0.4140 (mptt) REVERT: Q 315 MET cc_start: 0.6127 (ppp) cc_final: 0.4569 (ptp) REVERT: R 311 LYS cc_start: 0.6558 (mmtm) cc_final: 0.6257 (pttt) outliers start: 83 outliers final: 65 residues processed: 394 average time/residue: 0.3869 time to fit residues: 242.0808 Evaluate side-chains 398 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 329 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 125 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 309 optimal weight: 5.9990 chunk 325 optimal weight: 9.9990 chunk 297 optimal weight: 1.9990 chunk 317 optimal weight: 40.0000 chunk 190 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 chunk 299 optimal weight: 9.9990 chunk 315 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 384 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN P 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28171 Z= 0.202 Angle : 0.578 19.244 38231 Z= 0.290 Chirality : 0.040 0.197 4514 Planarity : 0.004 0.048 4807 Dihedral : 4.282 24.583 3902 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.30 % Allowed : 14.73 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.17 (0.14), residues: 3620 helix: 2.02 (0.11), residues: 2416 sheet: -0.56 (0.61), residues: 74 loop : -2.03 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 33 HIS 0.004 0.001 HIS A 796 PHE 0.032 0.001 PHE D 133 TYR 0.012 0.001 TYR D 345 ARG 0.006 0.000 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 344 time to evaluate : 3.440 Fit side-chains REVERT: A 85 GLU cc_start: 0.7715 (pp20) cc_final: 0.7486 (pp20) REVERT: A 112 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7348 (ptp90) REVERT: A 344 ASP cc_start: 0.7417 (p0) cc_final: 0.7075 (p0) REVERT: A 453 GLU cc_start: 0.6342 (tp30) cc_final: 0.5969 (tp30) REVERT: A 764 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6506 (t80) REVERT: D 150 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: D 236 ASP cc_start: 0.8127 (m-30) cc_final: 0.7580 (t0) REVERT: D 266 ARG cc_start: 0.8239 (tpp80) cc_final: 0.8006 (ttt180) REVERT: E 20 LEU cc_start: 0.9083 (tp) cc_final: 0.8857 (tt) REVERT: E 54 CYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8194 (p) REVERT: E 68 ARG cc_start: 0.7429 (mtt-85) cc_final: 0.7218 (mtt180) REVERT: F 32 ASN cc_start: 0.8595 (t0) cc_final: 0.8377 (t0) REVERT: G 27 ILE cc_start: 0.9255 (mt) cc_final: 0.8950 (mt) REVERT: G 108 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8144 (tt0) REVERT: I 1 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5903 (ttm) REVERT: J 68 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8915 (tp) REVERT: J 124 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.8126 (mmm-85) REVERT: K 68 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9141 (tp) REVERT: M 68 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9154 (tp) REVERT: N 46 ARG cc_start: 0.8363 (mtt90) cc_final: 0.8157 (mtp180) REVERT: Q 121 LYS cc_start: 0.5182 (mptt) cc_final: 0.4342 (mptt) REVERT: Q 315 MET cc_start: 0.5968 (ppp) cc_final: 0.4433 (ptp) REVERT: R 311 LYS cc_start: 0.6490 (mmtm) cc_final: 0.6227 (pttt) outliers start: 67 outliers final: 52 residues processed: 390 average time/residue: 0.3869 time to fit residues: 239.0192 Evaluate side-chains 398 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 338 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain R residue 125 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 208 optimal weight: 7.9990 chunk 335 optimal weight: 0.0020 chunk 204 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 351 optimal weight: 0.9990 chunk 323 optimal weight: 5.9990 chunk 280 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 216 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28171 Z= 0.218 Angle : 0.582 19.012 38231 Z= 0.291 Chirality : 0.040 0.200 4514 Planarity : 0.004 0.048 4807 Dihedral : 4.242 23.831 3902 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.44 % Allowed : 14.66 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.24 (0.14), residues: 3620 helix: 2.07 (0.11), residues: 2416 sheet: -0.62 (0.61), residues: 74 loop : -1.99 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 77 HIS 0.004 0.001 HIS A 796 PHE 0.031 0.001 PHE D 133 TYR 0.021 0.001 TYR F 56 ARG 0.006 0.000 ARG J 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 341 time to evaluate : 3.370 Fit side-chains REVERT: A 112 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7364 (ptp90) REVERT: A 344 ASP cc_start: 0.7423 (p0) cc_final: 0.7019 (p0) REVERT: A 453 GLU cc_start: 0.6311 (tp30) cc_final: 0.5945 (tp30) REVERT: A 764 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6594 (t80) REVERT: D 150 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7537 (mt-10) REVERT: D 236 ASP cc_start: 0.8130 (m-30) cc_final: 0.7526 (t0) REVERT: D 266 ARG cc_start: 0.8238 (tpp80) cc_final: 0.8006 (ttt180) REVERT: E 20 LEU cc_start: 0.9064 (tp) cc_final: 0.8832 (tt) REVERT: E 54 CYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8208 (p) REVERT: F 32 ASN cc_start: 0.8607 (t0) cc_final: 0.8389 (t0) REVERT: G 27 ILE cc_start: 0.9257 (mt) cc_final: 0.8950 (mt) REVERT: G 108 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8182 (tt0) REVERT: I 1 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5765 (ttm) REVERT: J 68 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8904 (tp) REVERT: J 124 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8117 (mmm-85) REVERT: N 46 ARG cc_start: 0.8335 (mtt90) cc_final: 0.8076 (mtp180) REVERT: Q 121 LYS cc_start: 0.5144 (mptt) cc_final: 0.4243 (mptt) REVERT: Q 315 MET cc_start: 0.5836 (ppp) cc_final: 0.4297 (ptp) REVERT: R 311 LYS cc_start: 0.6536 (mmtm) cc_final: 0.6250 (pttt) outliers start: 71 outliers final: 59 residues processed: 391 average time/residue: 0.3903 time to fit residues: 242.9272 Evaluate side-chains 402 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 337 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 138 VAL Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain R residue 125 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 222 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 41 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 280 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 288 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN P 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.087047 restraints weight = 33972.128| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.29 r_work: 0.2693 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28171 Z= 0.303 Angle : 0.627 19.178 38231 Z= 0.313 Chirality : 0.042 0.220 4514 Planarity : 0.004 0.048 4807 Dihedral : 4.344 24.288 3902 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.70 % Rotamer: Outliers : 2.40 % Allowed : 14.80 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.09 (0.14), residues: 3620 helix: 1.94 (0.11), residues: 2418 sheet: -0.61 (0.61), residues: 74 loop : -2.01 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 77 HIS 0.004 0.001 HIS A 232 PHE 0.030 0.002 PHE D 133 TYR 0.020 0.001 TYR D 345 ARG 0.005 0.000 ARG J 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6088.21 seconds wall clock time: 110 minutes 3.44 seconds (6603.44 seconds total)