Starting phenix.real_space_refine on Sun Jul 28 00:18:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5w_13203/07_2024/7p5w_13203.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5w_13203/07_2024/7p5w_13203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5w_13203/07_2024/7p5w_13203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5w_13203/07_2024/7p5w_13203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5w_13203/07_2024/7p5w_13203.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5w_13203/07_2024/7p5w_13203.cif" } resolution = 3.5 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= 0.003 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 174 5.16 5 C 26730 2.51 5 N 6960 2.21 5 O 7386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 41250 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "B" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "C" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "D" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "E" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "F" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "K" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "G" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "I" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "J" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Time building chain proxies: 20.04, per 1000 atoms: 0.49 Number of scatterers: 41250 At special positions: 0 Unit cell: (187.488, 180.978, 188.79, 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 174 16.00 O 7386 8.00 N 6960 7.00 C 26730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 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: 15.43 Conformation dependent library (CDL) restraints added in 7.3 seconds 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9648 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 40 sheets defined 44.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 4.285A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 146 Proline residue: A 126 - end of helix removed outlier: 5.270A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.027A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.506A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 287 removed outlier: 4.563A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 344 Processing helix chain 'A' and resid 353 through 360 removed outlier: 4.397A pdb=" N ARG A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.111A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.696A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 504 through 508 removed outlier: 3.518A pdb=" N GLU A 507 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 534 through 543 removed outlier: 4.947A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.553A pdb=" N ILE A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 635 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.503A pdb=" N ILE A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY A 705 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.846A pdb=" N VAL A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 751 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 806 removed outlier: 3.873A pdb=" N LYS A 799 " --> pdb=" O PRO A 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 4.051A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 5.285A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.993A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 344 Processing helix chain 'B' and resid 353 through 360 removed outlier: 3.980A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.038A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.908A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 629 through 636 removed outlier: 3.752A pdb=" N ILE B 632 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 633 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 636 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.650A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 659 " --> pdb=" O ILE B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 655 through 659' Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.854A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 726 through 730 removed outlier: 3.501A pdb=" N CYS B 730 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 753 removed outlier: 3.617A pdb=" N GLU B 752 " --> pdb=" O ARG B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 775 Processing helix chain 'B' and resid 787 through 792 removed outlier: 3.639A pdb=" N SER B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 795 No H-bonds generated for 'chain 'B' and resid 793 through 795' Processing helix chain 'B' and resid 796 through 805 removed outlier: 3.502A pdb=" N GLU B 800 " --> pdb=" O PRO B 796 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG B 801 " --> pdb=" O GLU B 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.530A pdb=" N LYS C 21 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 5.284A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 4.098A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 166 " --> pdb=" O LYS C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 287 removed outlier: 4.623A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 344 Processing helix chain 'C' and resid 353 through 360 removed outlier: 4.358A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.114A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.520A pdb=" N PHE C 443 " --> pdb=" O ASP C 440 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 495 Processing helix chain 'C' and resid 504 through 508 removed outlier: 3.543A pdb=" N GLU C 507 " --> pdb=" O ASP C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 534 through 543 removed outlier: 5.027A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 608 through 613 Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.515A pdb=" N ILE C 632 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 679 through 684 removed outlier: 3.510A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.517A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 705 " --> pdb=" O ALA C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 removed outlier: 4.050A pdb=" N CYS C 730 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.825A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 806 removed outlier: 3.863A pdb=" N LYS C 799 " --> pdb=" O PRO C 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 21 removed outlier: 4.089A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.502A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.301A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.026A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 166 " --> pdb=" O LYS D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 344 Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.904A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.053A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 411 Processing helix chain 'D' and resid 412 through 420 Processing helix chain 'D' and resid 441 through 445 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 535 through 542 removed outlier: 3.945A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 566 Processing helix chain 'D' and resid 567 through 569 No H-bonds generated for 'chain 'D' and resid 567 through 569' Processing helix chain 'D' and resid 629 through 636 removed outlier: 3.642A pdb=" N ILE D 632 " --> pdb=" O ILE D 629 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE D 633 " --> pdb=" O GLU D 630 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN D 636 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 660 removed outlier: 3.670A pdb=" N ILE D 658 " --> pdb=" O PRO D 655 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY D 659 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.862A pdb=" N CYS D 684 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 707 Processing helix chain 'D' and resid 726 through 730 Processing helix chain 'D' and resid 747 through 753 removed outlier: 3.759A pdb=" N VAL D 750 " --> pdb=" O PRO D 747 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 751 " --> pdb=" O SER D 748 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU D 752 " --> pdb=" O ARG D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 775 Processing helix chain 'D' and resid 787 through 792 removed outlier: 3.614A pdb=" N SER D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 805 removed outlier: 4.211A pdb=" N LYS D 799 " --> pdb=" O PRO D 795 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 801 " --> pdb=" O GLU D 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 removed outlier: 4.219A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 5.257A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 4.053A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 287 removed outlier: 4.612A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 344 Processing helix chain 'E' and resid 353 through 360 removed outlier: 4.368A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.135A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 418 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.571A pdb=" N PHE E 443 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU E 445 " --> pdb=" O VAL E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 484 through 495 Processing helix chain 'E' and resid 504 through 508 removed outlier: 3.504A pdb=" N GLU E 507 " --> pdb=" O ASP E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 534 through 543 removed outlier: 4.979A pdb=" N GLY E 539 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 Processing helix chain 'E' and resid 567 through 569 No H-bonds generated for 'chain 'E' and resid 567 through 569' Processing helix chain 'E' and resid 608 through 613 Processing helix chain 'E' and resid 629 through 638 removed outlier: 3.506A pdb=" N ILE E 632 " --> pdb=" O ILE E 629 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 Processing helix chain 'E' and resid 679 through 684 Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.505A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY E 705 " --> pdb=" O ALA E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 729 Processing helix chain 'E' and resid 747 through 753 removed outlier: 3.938A pdb=" N VAL E 750 " --> pdb=" O PRO E 747 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY E 751 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 806 removed outlier: 3.835A pdb=" N LYS E 799 " --> pdb=" O PRO E 795 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 removed outlier: 4.039A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS F 21 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 117 Processing helix chain 'F' and resid 119 through 146 Proline residue: F 126 - end of helix removed outlier: 5.299A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 4.032A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 176 Processing helix chain 'F' and resid 233 through 255 Processing helix chain 'F' and resid 259 through 286 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 314 through 344 Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.943A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 391 removed outlier: 4.043A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 395 through 411 Processing helix chain 'F' and resid 412 through 420 Processing helix chain 'F' and resid 441 through 445 Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 484 through 494 Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 535 through 542 removed outlier: 3.821A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG F 541 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 566 Processing helix chain 'F' and resid 567 through 569 No H-bonds generated for 'chain 'F' and resid 567 through 569' Processing helix chain 'F' and resid 629 through 636 removed outlier: 3.745A pdb=" N ILE F 632 " --> pdb=" O ILE F 629 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE F 633 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN F 636 " --> pdb=" O ILE F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 659 removed outlier: 3.659A pdb=" N ILE F 658 " --> pdb=" O PRO F 655 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 655 through 659' Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.878A pdb=" N CYS F 684 " --> pdb=" O LEU F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 707 Processing helix chain 'F' and resid 726 through 730 Processing helix chain 'F' and resid 749 through 753 removed outlier: 3.560A pdb=" N GLU F 752 " --> pdb=" O ARG F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 775 removed outlier: 3.531A pdb=" N GLU F 775 " --> pdb=" O GLU F 772 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 792 removed outlier: 3.582A pdb=" N SER F 792 " --> pdb=" O GLU F 788 " (cutoff:3.500A) Processing helix chain 'F' and resid 793 through 795 No H-bonds generated for 'chain 'F' and resid 793 through 795' Processing helix chain 'F' and resid 796 through 806 removed outlier: 4.152A pdb=" N ARG F 801 " --> pdb=" O GLU F 797 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.902A pdb=" N LYS K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.632A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.847A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.583A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.502A pdb=" N THR J 91 " --> pdb=" O PRO J 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 3.521A pdb=" N LEU A 498 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 549 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 461 removed outlier: 6.792A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 618 through 620 removed outlier: 5.844A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 712 through 714 removed outlier: 7.001A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.610A pdb=" N LEU B 428 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LYS B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 430 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLU B 454 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 432 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU B 549 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN B 575 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU B 551 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP B 620 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 619 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AA9, first strand: chain 'B' and resid 712 through 714 removed outlier: 6.900A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB2, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.268A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU C 549 " --> pdb=" O SER C 573 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 459 through 461 removed outlier: 6.744A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 618 through 620 removed outlier: 5.947A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 712 through 714 removed outlier: 7.055A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB7, first strand: chain 'D' and resid 421 through 422 removed outlier: 6.662A pdb=" N LEU D 428 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LYS D 452 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU D 430 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU D 454 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU D 432 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU D 549 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN D 575 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 620 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 459 through 461 Processing sheet with id=AB9, first strand: chain 'D' and resid 712 through 714 removed outlier: 7.047A pdb=" N LEU D 736 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AC2, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.280A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU E 549 " --> pdb=" O SER E 573 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 459 through 461 removed outlier: 6.738A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 618 through 620 removed outlier: 5.865A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 712 through 714 removed outlier: 7.227A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AC7, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.593A pdb=" N LEU F 428 " --> pdb=" O VAL F 450 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU F 430 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLU F 454 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU F 432 " --> pdb=" O GLU F 454 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TYR F 477 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU F 453 " --> pdb=" O TYR F 477 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU F 549 " --> pdb=" O SER F 573 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASN F 575 " --> pdb=" O LEU F 549 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU F 551 " --> pdb=" O ASN F 575 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP F 620 " --> pdb=" O LEU F 596 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE F 619 " --> pdb=" O LYS F 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 459 through 461 Processing sheet with id=AC9, first strand: chain 'F' and resid 712 through 714 removed outlier: 7.038A pdb=" N LEU F 736 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.601A pdb=" N VAL K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 11 through 13 removed outlier: 3.660A pdb=" N SER K 120 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.558A pdb=" N VAL L 79 " --> pdb=" O CYS L 22 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.602A pdb=" N SER L 120 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.527A pdb=" N VAL G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.634A pdb=" N SER G 120 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.590A pdb=" N VAL H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.556A pdb=" N SER H 120 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.556A pdb=" N SER H 120 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 98 " --> pdb=" O TYR H 110 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR H 110 " --> pdb=" O VAL H 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AE2, first strand: chain 'I' and resid 11 through 13 removed outlier: 3.579A pdb=" N SER I 120 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.585A pdb=" N VAL J 79 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 11 through 13 removed outlier: 3.622A pdb=" N SER J 120 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) 1753 hydrogen bonds defined for protein. 4521 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: 16.66 Time building geometry restraints manager: 17.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13065 1.34 - 1.46: 9636 1.46 - 1.58: 19263 1.58 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 42204 Sorted by residual: bond pdb=" C ALA C 485 " pdb=" N PRO C 486 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.71e+00 bond pdb=" C ALA E 485 " pdb=" N PRO E 486 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.52e+00 bond pdb=" C ALA A 485 " pdb=" N PRO A 486 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.20e-02 6.94e+03 2.12e+00 bond pdb=" CA VAL B 742 " pdb=" CB VAL B 742 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.05e+00 bond pdb=" C GLN L 39 " pdb=" N ALA L 40 " ideal model delta sigma weight residual 1.331 1.310 0.021 2.07e-02 2.33e+03 1.04e+00 ... (remaining 42199 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.09: 1096 107.09 - 113.83: 24044 113.83 - 120.58: 16443 120.58 - 127.32: 15140 127.32 - 134.06: 517 Bond angle restraints: 57240 Sorted by residual: angle pdb=" N VAL B 591 " pdb=" CA VAL B 591 " pdb=" C VAL B 591 " ideal model delta sigma weight residual 113.71 110.68 3.03 9.50e-01 1.11e+00 1.02e+01 angle pdb=" C THR H 104 " pdb=" N THR H 105 " pdb=" CA THR H 105 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.77e+00 angle pdb=" C THR K 104 " pdb=" N THR K 105 " pdb=" CA THR K 105 " ideal model delta sigma weight residual 121.54 127.13 -5.59 1.91e+00 2.74e-01 8.55e+00 angle pdb=" C THR G 104 " pdb=" N THR G 105 " pdb=" CA THR G 105 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.51e+00 angle pdb=" C THR L 104 " pdb=" N THR L 105 " pdb=" CA THR L 105 " ideal model delta sigma weight residual 121.54 127.02 -5.48 1.91e+00 2.74e-01 8.23e+00 ... (remaining 57235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 23495 16.76 - 33.51: 1391 33.51 - 50.27: 397 50.27 - 67.03: 76 67.03 - 83.79: 3 Dihedral angle restraints: 25362 sinusoidal: 10476 harmonic: 14886 Sorted by residual: dihedral pdb=" CA TRP L 33 " pdb=" C TRP L 33 " pdb=" N MET L 34 " pdb=" CA MET L 34 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TRP J 33 " pdb=" C TRP J 33 " pdb=" N MET J 34 " pdb=" CA MET J 34 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TRP H 33 " pdb=" C TRP H 33 " pdb=" N MET H 34 " pdb=" CA MET H 34 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 25359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3668 0.027 - 0.054: 1873 0.054 - 0.081: 649 0.081 - 0.108: 222 0.108 - 0.135: 86 Chirality restraints: 6498 Sorted by residual: chirality pdb=" CA ILE F 438 " pdb=" N ILE F 438 " pdb=" C ILE F 438 " pdb=" CB ILE F 438 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA VAL L 93 " pdb=" N VAL L 93 " pdb=" C VAL L 93 " pdb=" CB VAL L 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE F 674 " pdb=" N ILE F 674 " pdb=" C ILE F 674 " pdb=" CB ILE F 674 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 6495 not shown) Planarity restraints: 7122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 795 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO B 796 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 796 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 796 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 795 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO D 796 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 796 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 796 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 795 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.58e+00 pdb=" N PRO F 796 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO F 796 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 796 " 0.017 5.00e-02 4.00e+02 ... (remaining 7119 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 791 2.68 - 3.24: 41445 3.24 - 3.79: 67004 3.79 - 4.35: 90060 4.35 - 4.90: 146018 Nonbonded interactions: 345318 Sorted by model distance: nonbonded pdb=" OH TYR B 513 " pdb=" O VAL B 536 " model vdw 2.131 2.440 nonbonded pdb=" OG1 THR H 101 " pdb=" O GLN H 107 " model vdw 2.146 2.440 nonbonded pdb=" OG1 THR L 101 " pdb=" O GLN L 107 " model vdw 2.152 2.440 nonbonded pdb=" OG1 THR J 101 " pdb=" O GLN J 107 " model vdw 2.152 2.440 nonbonded pdb=" OH TYR D 513 " pdb=" O VAL D 536 " model vdw 2.153 2.440 ... (remaining 345313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.050 Extract box with map and model: 1.510 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 104.840 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 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 : 0.002 0.044 42204 Z= 0.150 Angle : 0.487 7.016 57240 Z= 0.276 Chirality : 0.039 0.135 6498 Planarity : 0.003 0.033 7122 Dihedral : 11.731 83.787 15642 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.75 % Allowed : 7.44 % Favored : 88.81 % 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: -0.37 (0.12), residues: 4980 helix: 0.24 (0.12), residues: 2007 sheet: -0.64 (0.19), residues: 879 loop : -0.36 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 33 HIS 0.003 0.001 HIS A 312 PHE 0.010 0.001 PHE D 146 TYR 0.011 0.001 TYR C 332 ARG 0.002 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 768 time to evaluate : 4.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7331 (t0) cc_final: 0.6983 (t0) REVERT: A 238 GLU cc_start: 0.7627 (tt0) cc_final: 0.7226 (tm-30) REVERT: A 288 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8406 (t0) REVERT: A 415 LYS cc_start: 0.5880 (tttt) cc_final: 0.5613 (tptt) REVERT: A 471 LEU cc_start: 0.7565 (tp) cc_final: 0.7116 (pt) REVERT: A 495 LEU cc_start: 0.4085 (tp) cc_final: 0.3767 (tp) REVERT: A 562 VAL cc_start: 0.7636 (t) cc_final: 0.7418 (t) REVERT: A 603 LEU cc_start: 0.5794 (mt) cc_final: 0.5347 (mt) REVERT: A 700 LEU cc_start: 0.5468 (OUTLIER) cc_final: 0.4941 (mp) REVERT: A 744 GLN cc_start: 0.4746 (mp10) cc_final: 0.4467 (pm20) REVERT: B 104 HIS cc_start: 0.9025 (OUTLIER) cc_final: 0.8736 (t70) REVERT: B 160 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6817 (mm) REVERT: B 238 GLU cc_start: 0.6119 (tt0) cc_final: 0.5716 (pp20) REVERT: B 250 PHE cc_start: 0.5013 (t80) cc_final: 0.4635 (t80) REVERT: B 472 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7474 (tttp) REVERT: B 545 ARG cc_start: 0.6288 (mmm160) cc_final: 0.5925 (mmm160) REVERT: B 687 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5786 (mt) REVERT: B 706 LEU cc_start: 0.8130 (mt) cc_final: 0.7827 (mm) REVERT: B 715 VAL cc_start: 0.6141 (OUTLIER) cc_final: 0.5889 (t) REVERT: C 235 LYS cc_start: 0.7340 (mptt) cc_final: 0.6785 (tptp) REVERT: C 253 HIS cc_start: 0.5367 (OUTLIER) cc_final: 0.4986 (t-90) REVERT: C 473 GLU cc_start: 0.5388 (mt-10) cc_final: 0.5091 (mp0) REVERT: C 755 ASN cc_start: 0.6566 (t0) cc_final: 0.5342 (m110) REVERT: D 19 ILE cc_start: 0.8490 (pt) cc_final: 0.7974 (mp) REVERT: D 250 PHE cc_start: 0.4833 (t80) cc_final: 0.4358 (t80) REVERT: D 321 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7891 (mt) REVERT: D 354 GLU cc_start: 0.4781 (OUTLIER) cc_final: 0.4146 (tp30) REVERT: D 545 ARG cc_start: 0.6254 (mmm160) cc_final: 0.5797 (mmm160) REVERT: D 706 LEU cc_start: 0.7343 (mt) cc_final: 0.6921 (mp) REVERT: D 711 GLN cc_start: 0.4251 (mt0) cc_final: 0.4049 (mm-40) REVERT: D 715 VAL cc_start: 0.6913 (OUTLIER) cc_final: 0.6643 (t) REVERT: D 794 LEU cc_start: 0.1294 (OUTLIER) cc_final: 0.1090 (pp) REVERT: E 243 LEU cc_start: 0.8041 (tp) cc_final: 0.7828 (tp) REVERT: E 344 LEU cc_start: 0.7019 (mt) cc_final: 0.6413 (pp) REVERT: E 468 LEU cc_start: 0.4897 (mt) cc_final: 0.4682 (mp) REVERT: E 473 GLU cc_start: 0.5592 (mt-10) cc_final: 0.5327 (mp0) REVERT: E 540 LEU cc_start: 0.7185 (tp) cc_final: 0.6956 (tp) REVERT: E 592 ASN cc_start: 0.5740 (m-40) cc_final: 0.5468 (p0) REVERT: E 603 LEU cc_start: 0.5623 (mt) cc_final: 0.5364 (mt) REVERT: E 755 ASN cc_start: 0.4595 (t0) cc_final: 0.4300 (m-40) REVERT: E 761 LEU cc_start: 0.1846 (OUTLIER) cc_final: 0.1516 (mp) REVERT: F 29 ASP cc_start: 0.7493 (t0) cc_final: 0.7146 (m-30) REVERT: F 160 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7037 (mm) REVERT: F 250 PHE cc_start: 0.4981 (t80) cc_final: 0.4614 (t80) REVERT: F 275 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7183 (t80) REVERT: F 321 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7958 (mt) REVERT: F 423 ASN cc_start: 0.4965 (p0) cc_final: 0.4082 (p0) REVERT: F 450 VAL cc_start: 0.6550 (t) cc_final: 0.6043 (t) REVERT: F 468 LEU cc_start: 0.5098 (mt) cc_final: 0.4872 (mt) REVERT: F 546 LEU cc_start: 0.6094 (tp) cc_final: 0.5757 (mt) REVERT: F 548 VAL cc_start: 0.5496 (t) cc_final: 0.5077 (t) REVERT: F 673 LYS cc_start: 0.5136 (mptt) cc_final: 0.4778 (pttt) REVERT: F 701 PRO cc_start: 0.4088 (Cg_exo) cc_final: 0.3829 (Cg_endo) REVERT: F 706 LEU cc_start: 0.8317 (mt) cc_final: 0.8068 (mm) REVERT: F 708 GLN cc_start: 0.4462 (OUTLIER) cc_final: 0.4146 (mm110) REVERT: K 33 TRP cc_start: 0.2383 (OUTLIER) cc_final: 0.0796 (m100) REVERT: K 34 MET cc_start: 0.6861 (tpp) cc_final: 0.6494 (mmp) REVERT: K 36 TRP cc_start: 0.3327 (m100) cc_final: 0.3054 (m100) REVERT: K 37 TYR cc_start: 0.3590 (OUTLIER) cc_final: 0.3260 (m-80) REVERT: K 73 ASP cc_start: 0.5837 (m-30) cc_final: 0.4868 (m-30) REVERT: K 86 LEU cc_start: -0.2610 (OUTLIER) cc_final: -0.3203 (mt) REVERT: K 95 TYR cc_start: 0.4890 (m-10) cc_final: 0.4600 (m-80) REVERT: K 96 CYS cc_start: -0.0159 (OUTLIER) cc_final: -0.0539 (p) REVERT: K 98 VAL cc_start: 0.4399 (OUTLIER) cc_final: 0.3732 (p) REVERT: K 107 GLN cc_start: 0.6729 (tt0) cc_final: 0.6479 (tp40) REVERT: L 3 GLN cc_start: 0.6653 (pp30) cc_final: 0.5812 (mp-120) REVERT: L 5 VAL cc_start: 0.6520 (t) cc_final: 0.6271 (m) REVERT: L 29 VAL cc_start: 0.4267 (OUTLIER) cc_final: 0.3919 (p) REVERT: L 89 GLU cc_start: 0.3378 (pp20) cc_final: 0.2995 (pt0) REVERT: L 113 GLN cc_start: 0.5765 (mm-40) cc_final: 0.4701 (mt0) REVERT: L 116 GLN cc_start: 0.6034 (mt0) cc_final: 0.5613 (tm-30) REVERT: G 33 TRP cc_start: 0.1637 (OUTLIER) cc_final: 0.0079 (m100) REVERT: G 34 MET cc_start: 0.6877 (tpp) cc_final: 0.6469 (mmp) REVERT: G 35 TRP cc_start: 0.4909 (OUTLIER) cc_final: 0.4673 (m-10) REVERT: G 59 TRP cc_start: 0.4977 (m100) cc_final: 0.4777 (m100) REVERT: G 95 TYR cc_start: 0.4787 (m-80) cc_final: 0.4311 (m-80) REVERT: G 96 CYS cc_start: 0.0140 (OUTLIER) cc_final: -0.0179 (p) REVERT: H 4 LEU cc_start: -0.0818 (mp) cc_final: -0.1139 (mm) REVERT: H 29 VAL cc_start: 0.3099 (OUTLIER) cc_final: 0.2813 (p) REVERT: H 37 TYR cc_start: 0.4830 (OUTLIER) cc_final: 0.1881 (t80) REVERT: H 101 THR cc_start: 0.5294 (OUTLIER) cc_final: 0.5077 (m) REVERT: H 113 GLN cc_start: 0.6920 (mm-40) cc_final: 0.6176 (mm-40) REVERT: I 33 TRP cc_start: 0.2158 (OUTLIER) cc_final: 0.0694 (m100) REVERT: I 34 MET cc_start: 0.6521 (tpp) cc_final: 0.6298 (mmp) REVERT: I 35 TRP cc_start: 0.5426 (OUTLIER) cc_final: 0.4713 (m-10) REVERT: I 86 LEU cc_start: -0.5362 (OUTLIER) cc_final: -0.5819 (mt) REVERT: I 96 CYS cc_start: -0.0340 (OUTLIER) cc_final: -0.0881 (p) REVERT: I 98 VAL cc_start: 0.4783 (OUTLIER) cc_final: 0.4212 (p) outliers start: 172 outliers final: 40 residues processed: 919 average time/residue: 0.5514 time to fit residues: 804.3509 Evaluate side-chains 451 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 378 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 673 LYS Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 708 GLN Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 96 CYS Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 101 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 0.7980 chunk 377 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 254 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 390 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 452 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN B 377 HIS B 425 GLN ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 755 ASN D 404 GLN D 617 GLN D 696 ASN E 253 HIS E 288 ASN E 649 ASN ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN F 650 HIS ** F 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN K 82 GLN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN G 107 GLN ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 ASN I 84 ASN ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 42204 Z= 0.284 Angle : 0.596 8.288 57240 Z= 0.309 Chirality : 0.043 0.238 6498 Planarity : 0.004 0.038 7122 Dihedral : 6.603 59.420 5631 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.75 % Allowed : 12.19 % Favored : 84.05 % 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 (0.12), residues: 4980 helix: -0.05 (0.12), residues: 2055 sheet: -0.61 (0.19), residues: 879 loop : -0.55 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 33 HIS 0.012 0.001 HIS E 253 PHE 0.027 0.002 PHE B 443 TYR 0.020 0.002 TYR E 106 ARG 0.011 0.001 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 404 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.6803 (m-10) cc_final: 0.6415 (m-10) REVERT: A 29 ASP cc_start: 0.7390 (t0) cc_final: 0.7048 (t0) REVERT: A 238 GLU cc_start: 0.7628 (tt0) cc_final: 0.7226 (tm-30) REVERT: A 288 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8407 (t0) REVERT: A 353 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.4506 (t80) REVERT: A 375 MET cc_start: 0.8010 (mtt) cc_final: 0.7765 (mtm) REVERT: A 434 MET cc_start: 0.7178 (mmm) cc_final: 0.6903 (mmm) REVERT: A 465 ILE cc_start: 0.5558 (tt) cc_final: 0.5315 (tt) REVERT: A 471 LEU cc_start: 0.7329 (tp) cc_final: 0.7074 (pt) REVERT: A 475 TRP cc_start: 0.7225 (m-10) cc_final: 0.6293 (m-10) REVERT: A 495 LEU cc_start: 0.4110 (tp) cc_final: 0.3892 (tp) REVERT: A 592 ASN cc_start: 0.5718 (m-40) cc_final: 0.5506 (p0) REVERT: A 658 ILE cc_start: 0.5091 (mm) cc_final: 0.4858 (mm) REVERT: A 800 GLU cc_start: 0.2885 (OUTLIER) cc_final: 0.2279 (tp30) REVERT: B 160 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6746 (mm) REVERT: B 238 GLU cc_start: 0.6624 (tt0) cc_final: 0.6162 (pp20) REVERT: B 250 PHE cc_start: 0.5055 (t80) cc_final: 0.4658 (t80) REVERT: B 548 VAL cc_start: 0.5984 (t) cc_final: 0.5590 (t) REVERT: B 580 LYS cc_start: 0.5272 (tptt) cc_final: 0.4965 (tppt) REVERT: B 673 LYS cc_start: 0.6617 (mptt) cc_final: 0.5690 (ttmm) REVERT: B 687 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5717 (mt) REVERT: B 758 GLN cc_start: 0.5575 (pt0) cc_final: 0.5044 (mp10) REVERT: B 784 LEU cc_start: 0.4995 (mp) cc_final: 0.4721 (tt) REVERT: C 234 LYS cc_start: 0.6056 (tptt) cc_final: 0.5720 (tmtt) REVERT: C 238 GLU cc_start: 0.6525 (pt0) cc_final: 0.6302 (tm-30) REVERT: C 353 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.3820 (t80) REVERT: C 443 PHE cc_start: 0.5310 (m-80) cc_final: 0.5057 (m-80) REVERT: C 475 TRP cc_start: 0.6777 (m-10) cc_final: 0.6439 (m-10) REVERT: C 676 LYS cc_start: 0.7090 (mmtt) cc_final: 0.6700 (tppt) REVERT: C 755 ASN cc_start: 0.6637 (t0) cc_final: 0.5321 (m110) REVERT: D 19 ILE cc_start: 0.8658 (pt) cc_final: 0.8185 (mp) REVERT: D 250 PHE cc_start: 0.4764 (t80) cc_final: 0.4249 (t80) REVERT: D 321 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7783 (mt) REVERT: D 354 GLU cc_start: 0.5168 (OUTLIER) cc_final: 0.4627 (tp30) REVERT: D 488 LEU cc_start: 0.6787 (tp) cc_final: 0.6469 (pp) REVERT: D 522 HIS cc_start: 0.7250 (m90) cc_final: 0.6934 (m90) REVERT: D 546 LEU cc_start: 0.5838 (tp) cc_final: 0.5323 (mt) REVERT: D 673 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.5403 (pttp) REVERT: D 711 GLN cc_start: 0.4545 (mt0) cc_final: 0.4152 (mm-40) REVERT: D 715 VAL cc_start: 0.6969 (OUTLIER) cc_final: 0.6712 (t) REVERT: E 243 LEU cc_start: 0.8107 (tp) cc_final: 0.7864 (tp) REVERT: E 321 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7837 (mt) REVERT: E 344 LEU cc_start: 0.6939 (mt) cc_final: 0.6260 (pp) REVERT: E 353 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.4224 (t80) REVERT: E 465 ILE cc_start: 0.6742 (tt) cc_final: 0.6325 (tp) REVERT: E 587 LEU cc_start: 0.4936 (mt) cc_final: 0.4539 (tp) REVERT: E 592 ASN cc_start: 0.5738 (m-40) cc_final: 0.5394 (p0) REVERT: E 699 PHE cc_start: 0.5881 (t80) cc_final: 0.5528 (t80) REVERT: E 755 ASN cc_start: 0.5037 (t0) cc_final: 0.4635 (m-40) REVERT: E 761 LEU cc_start: 0.1706 (OUTLIER) cc_final: 0.1463 (mp) REVERT: F 29 ASP cc_start: 0.7622 (t0) cc_final: 0.7187 (m-30) REVERT: F 160 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6926 (mm) REVERT: F 250 PHE cc_start: 0.4965 (t80) cc_final: 0.4505 (t80) REVERT: F 321 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7923 (mt) REVERT: F 468 LEU cc_start: 0.5319 (mt) cc_final: 0.5087 (mt) REVERT: F 706 LEU cc_start: 0.8339 (mt) cc_final: 0.8033 (mm) REVERT: K 33 TRP cc_start: 0.2452 (OUTLIER) cc_final: 0.0975 (m100) REVERT: K 34 MET cc_start: 0.6887 (tpp) cc_final: 0.6577 (mmp) REVERT: K 86 LEU cc_start: -0.2602 (OUTLIER) cc_final: -0.3099 (mt) REVERT: K 98 VAL cc_start: 0.4034 (OUTLIER) cc_final: 0.3343 (p) REVERT: L 5 VAL cc_start: 0.6226 (t) cc_final: 0.5968 (t) REVERT: L 89 GLU cc_start: 0.3414 (pp20) cc_final: 0.3150 (pt0) REVERT: L 113 GLN cc_start: 0.6055 (mm-40) cc_final: 0.5085 (mt0) REVERT: G 33 TRP cc_start: 0.1584 (OUTLIER) cc_final: 0.0258 (m100) REVERT: G 34 MET cc_start: 0.6389 (tpp) cc_final: 0.6105 (mmp) REVERT: G 82 GLN cc_start: 0.4887 (tp40) cc_final: 0.3944 (tm-30) REVERT: G 95 TYR cc_start: 0.4607 (m-80) cc_final: 0.4104 (m-80) REVERT: H 113 GLN cc_start: 0.6934 (mm-40) cc_final: 0.6263 (mm-40) REVERT: I 33 TRP cc_start: 0.2111 (OUTLIER) cc_final: 0.0690 (m100) REVERT: I 34 MET cc_start: 0.6437 (tpp) cc_final: 0.6221 (mmp) REVERT: I 86 LEU cc_start: -0.5618 (OUTLIER) cc_final: -0.5913 (mt) REVERT: I 98 VAL cc_start: 0.5182 (OUTLIER) cc_final: 0.4391 (p) REVERT: J 83 MET cc_start: 0.0710 (OUTLIER) cc_final: -0.0322 (pmm) REVERT: J 113 GLN cc_start: 0.6964 (mm110) cc_final: 0.5828 (pt0) outliers start: 172 outliers final: 88 residues processed: 559 average time/residue: 0.5084 time to fit residues: 473.6178 Evaluate side-chains 416 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 305 time to evaluate : 4.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 745 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 673 LYS Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain J residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 376 optimal weight: 0.6980 chunk 307 optimal weight: 0.5980 chunk 124 optimal weight: 8.9990 chunk 453 optimal weight: 10.0000 chunk 489 optimal weight: 7.9990 chunk 403 optimal weight: 5.9990 chunk 449 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 363 optimal weight: 0.6980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 478 HIS ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS B 718 ASN C 755 ASN ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 ASN K 82 GLN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN H 103 HIS ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 42204 Z= 0.248 Angle : 0.562 9.152 57240 Z= 0.291 Chirality : 0.042 0.225 6498 Planarity : 0.003 0.032 7122 Dihedral : 6.077 59.583 5593 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.12 % Allowed : 13.26 % Favored : 82.61 % 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: -0.70 (0.12), residues: 4980 helix: -0.11 (0.12), residues: 2052 sheet: -0.69 (0.19), residues: 909 loop : -0.51 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 47 HIS 0.005 0.001 HIS B 104 PHE 0.023 0.002 PHE C 699 TYR 0.017 0.002 TYR I 80 ARG 0.005 0.000 ARG D 545 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 351 time to evaluate : 4.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.6739 (m-10) cc_final: 0.6395 (m-10) REVERT: A 29 ASP cc_start: 0.7386 (t0) cc_final: 0.7027 (t0) REVERT: A 238 GLU cc_start: 0.7380 (tt0) cc_final: 0.7110 (tm-30) REVERT: A 288 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8358 (t0) REVERT: A 353 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.4938 (t80) REVERT: A 375 MET cc_start: 0.8019 (mtt) cc_final: 0.7759 (mtm) REVERT: A 471 LEU cc_start: 0.7211 (tp) cc_final: 0.6882 (pt) REVERT: A 475 TRP cc_start: 0.7254 (m-10) cc_final: 0.6298 (m-10) REVERT: A 592 ASN cc_start: 0.5820 (m-40) cc_final: 0.5355 (p0) REVERT: A 658 ILE cc_start: 0.5029 (mm) cc_final: 0.4794 (mm) REVERT: A 761 LEU cc_start: 0.2267 (OUTLIER) cc_final: 0.1937 (mp) REVERT: B 160 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6672 (mt) REVERT: B 234 LYS cc_start: 0.5587 (OUTLIER) cc_final: 0.5085 (ttmm) REVERT: B 250 PHE cc_start: 0.4917 (t80) cc_final: 0.4548 (t80) REVERT: B 468 LEU cc_start: 0.5723 (mt) cc_final: 0.5516 (mt) REVERT: B 478 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7267 (m-70) REVERT: B 580 LYS cc_start: 0.4946 (tptt) cc_final: 0.4561 (tppt) REVERT: B 673 LYS cc_start: 0.6626 (mptt) cc_final: 0.5677 (ttmm) REVERT: B 784 LEU cc_start: 0.5022 (mp) cc_final: 0.4703 (tt) REVERT: C 234 LYS cc_start: 0.6010 (tptt) cc_final: 0.5735 (tmtt) REVERT: C 353 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.4393 (t80) REVERT: C 443 PHE cc_start: 0.5429 (m-80) cc_final: 0.4783 (m-80) REVERT: C 465 ILE cc_start: 0.5613 (tt) cc_final: 0.5139 (tt) REVERT: C 475 TRP cc_start: 0.6897 (m-10) cc_final: 0.6085 (m-10) REVERT: C 587 LEU cc_start: 0.4268 (mt) cc_final: 0.4050 (tp) REVERT: C 676 LYS cc_start: 0.7111 (mmtt) cc_final: 0.6707 (tppt) REVERT: C 755 ASN cc_start: 0.6621 (t0) cc_final: 0.5267 (m110) REVERT: D 19 ILE cc_start: 0.8731 (pt) cc_final: 0.8249 (mp) REVERT: D 250 PHE cc_start: 0.5035 (t80) cc_final: 0.4402 (t80) REVERT: D 321 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7844 (mt) REVERT: D 354 GLU cc_start: 0.5506 (OUTLIER) cc_final: 0.4729 (tp30) REVERT: D 448 LEU cc_start: 0.7567 (tp) cc_final: 0.7228 (tp) REVERT: D 488 LEU cc_start: 0.6785 (tp) cc_final: 0.6454 (pp) REVERT: D 522 HIS cc_start: 0.7282 (m90) cc_final: 0.6882 (m90) REVERT: D 549 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5871 (mm) REVERT: D 602 ASP cc_start: 0.6562 (t0) cc_final: 0.6120 (t0) REVERT: D 625 ASN cc_start: 0.6386 (OUTLIER) cc_final: 0.5901 (t0) REVERT: D 673 LYS cc_start: 0.6445 (OUTLIER) cc_final: 0.5479 (pttp) REVERT: D 711 GLN cc_start: 0.4548 (mt0) cc_final: 0.4194 (mm-40) REVERT: D 715 VAL cc_start: 0.6964 (OUTLIER) cc_final: 0.6728 (t) REVERT: E 344 LEU cc_start: 0.6930 (mt) cc_final: 0.6351 (pp) REVERT: E 353 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.5026 (t80) REVERT: E 592 ASN cc_start: 0.5844 (m-40) cc_final: 0.5460 (p0) REVERT: E 699 PHE cc_start: 0.6027 (t80) cc_final: 0.5535 (t80) REVERT: E 755 ASN cc_start: 0.4947 (t0) cc_final: 0.4511 (m-40) REVERT: E 761 LEU cc_start: 0.1825 (OUTLIER) cc_final: 0.1564 (mp) REVERT: E 800 GLU cc_start: 0.3194 (OUTLIER) cc_final: 0.2889 (tp30) REVERT: F 29 ASP cc_start: 0.7583 (t0) cc_final: 0.7208 (m-30) REVERT: F 160 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6988 (mm) REVERT: F 378 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7099 (mp) REVERT: F 468 LEU cc_start: 0.5224 (mt) cc_final: 0.4966 (mt) REVERT: F 549 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6508 (tp) REVERT: F 587 LEU cc_start: 0.5712 (mt) cc_final: 0.5379 (tp) REVERT: K 33 TRP cc_start: 0.2114 (OUTLIER) cc_final: 0.0321 (m100) REVERT: K 34 MET cc_start: 0.6652 (tpp) cc_final: 0.6347 (mmp) REVERT: K 86 LEU cc_start: -0.2818 (OUTLIER) cc_final: -0.3263 (mt) REVERT: K 98 VAL cc_start: 0.4417 (OUTLIER) cc_final: 0.3568 (p) REVERT: L 3 GLN cc_start: 0.6776 (tm-30) cc_final: 0.6206 (mp10) REVERT: L 44 GLU cc_start: 0.2800 (tp30) cc_final: 0.2480 (mm-30) REVERT: L 89 GLU cc_start: 0.3673 (pp20) cc_final: 0.3427 (pt0) REVERT: L 113 GLN cc_start: 0.6409 (mm-40) cc_final: 0.5544 (mm-40) REVERT: G 33 TRP cc_start: 0.1176 (OUTLIER) cc_final: 0.0013 (m100) REVERT: G 34 MET cc_start: 0.6678 (tpp) cc_final: 0.6136 (mmp) REVERT: G 82 GLN cc_start: 0.4745 (tp40) cc_final: 0.3793 (tm-30) REVERT: G 107 GLN cc_start: 0.7194 (tt0) cc_final: 0.6789 (tt0) REVERT: H 37 TYR cc_start: 0.4139 (OUTLIER) cc_final: 0.1926 (t80) REVERT: H 113 GLN cc_start: 0.6965 (mm-40) cc_final: 0.6711 (mm-40) REVERT: I 33 TRP cc_start: 0.1102 (OUTLIER) cc_final: 0.0249 (m100) REVERT: I 34 MET cc_start: 0.6327 (tpp) cc_final: 0.6107 (mmp) REVERT: I 86 LEU cc_start: -0.5594 (OUTLIER) cc_final: -0.5947 (mt) REVERT: I 87 LYS cc_start: 0.3242 (mttt) cc_final: 0.2883 (mtpp) REVERT: I 98 VAL cc_start: 0.5378 (OUTLIER) cc_final: 0.4620 (p) REVERT: I 108 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.6098 (t80) REVERT: J 113 GLN cc_start: 0.6967 (mm110) cc_final: 0.5847 (pt0) outliers start: 189 outliers final: 105 residues processed: 513 average time/residue: 0.4878 time to fit residues: 424.6537 Evaluate side-chains 422 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 289 time to evaluate : 4.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 673 LYS Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 800 GLU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 108 TYR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain J residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 447 optimal weight: 5.9990 chunk 340 optimal weight: 0.0970 chunk 235 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 216 optimal weight: 0.8980 chunk 304 optimal weight: 3.9990 chunk 454 optimal weight: 0.9990 chunk 481 optimal weight: 0.0270 chunk 237 optimal weight: 1.9990 chunk 430 optimal weight: 0.0980 chunk 129 optimal weight: 0.3980 overall best weight: 0.2436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 42204 Z= 0.136 Angle : 0.513 8.448 57240 Z= 0.264 Chirality : 0.040 0.203 6498 Planarity : 0.003 0.030 7122 Dihedral : 5.814 59.369 5589 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.38 % Allowed : 15.12 % Favored : 81.50 % 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: -0.48 (0.12), residues: 4980 helix: 0.14 (0.12), residues: 2028 sheet: -0.66 (0.19), residues: 909 loop : -0.43 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 47 HIS 0.015 0.001 HIS A 478 PHE 0.019 0.001 PHE E 393 TYR 0.024 0.001 TYR K 110 ARG 0.007 0.000 ARG F 762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 334 time to evaluate : 4.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7395 (t0) cc_final: 0.6964 (t0) REVERT: A 238 GLU cc_start: 0.7611 (tt0) cc_final: 0.7219 (tm-30) REVERT: A 288 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8293 (t0) REVERT: A 353 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.5432 (t80) REVERT: A 375 MET cc_start: 0.7965 (mtt) cc_final: 0.7717 (mtm) REVERT: A 443 PHE cc_start: 0.4954 (m-80) cc_final: 0.4573 (m-80) REVERT: A 471 LEU cc_start: 0.7074 (tp) cc_final: 0.6869 (pt) REVERT: A 592 ASN cc_start: 0.5850 (m-40) cc_final: 0.5429 (p0) REVERT: A 658 ILE cc_start: 0.5073 (mm) cc_final: 0.4839 (mm) REVERT: A 749 ARG cc_start: 0.4319 (ptp90) cc_final: 0.3580 (mtm110) REVERT: A 761 LEU cc_start: 0.2172 (OUTLIER) cc_final: 0.1888 (mp) REVERT: A 800 GLU cc_start: 0.2675 (OUTLIER) cc_final: 0.2176 (tp30) REVERT: B 160 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6492 (mt) REVERT: B 234 LYS cc_start: 0.5740 (OUTLIER) cc_final: 0.5316 (ttmm) REVERT: B 250 PHE cc_start: 0.5113 (t80) cc_final: 0.4704 (t80) REVERT: B 580 LYS cc_start: 0.4965 (tptt) cc_final: 0.4659 (tppt) REVERT: B 673 LYS cc_start: 0.6580 (mptt) cc_final: 0.5667 (ttmm) REVERT: B 686 LYS cc_start: 0.5558 (ptpp) cc_final: 0.5127 (tmtt) REVERT: C 353 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.4409 (t80) REVERT: C 443 PHE cc_start: 0.5237 (m-80) cc_final: 0.4265 (m-10) REVERT: C 465 ILE cc_start: 0.5571 (tt) cc_final: 0.5061 (tt) REVERT: C 475 TRP cc_start: 0.6837 (m-10) cc_final: 0.6058 (m-10) REVERT: C 658 ILE cc_start: 0.5024 (mm) cc_final: 0.4793 (mm) REVERT: C 676 LYS cc_start: 0.7081 (mmtt) cc_final: 0.6693 (tppt) REVERT: C 755 ASN cc_start: 0.6275 (t0) cc_final: 0.5286 (m-40) REVERT: D 19 ILE cc_start: 0.8714 (pt) cc_final: 0.8236 (mp) REVERT: D 250 PHE cc_start: 0.4923 (t80) cc_final: 0.4281 (t80) REVERT: D 354 GLU cc_start: 0.5143 (OUTLIER) cc_final: 0.4572 (tp30) REVERT: D 448 LEU cc_start: 0.7673 (tp) cc_final: 0.7281 (tp) REVERT: D 488 LEU cc_start: 0.6829 (tp) cc_final: 0.6426 (pp) REVERT: D 522 HIS cc_start: 0.7219 (m90) cc_final: 0.6885 (m90) REVERT: D 673 LYS cc_start: 0.6387 (mptt) cc_final: 0.5540 (pttp) REVERT: D 715 VAL cc_start: 0.6936 (OUTLIER) cc_final: 0.6683 (t) REVERT: E 344 LEU cc_start: 0.7128 (mt) cc_final: 0.6537 (pp) REVERT: E 353 PHE cc_start: 0.6244 (OUTLIER) cc_final: 0.4917 (t80) REVERT: E 592 ASN cc_start: 0.5838 (m-40) cc_final: 0.5436 (p0) REVERT: E 699 PHE cc_start: 0.5972 (t80) cc_final: 0.5489 (t80) REVERT: E 755 ASN cc_start: 0.4694 (t0) cc_final: 0.4331 (m-40) REVERT: E 761 LEU cc_start: 0.2236 (OUTLIER) cc_final: 0.1948 (mp) REVERT: E 800 GLU cc_start: 0.3364 (OUTLIER) cc_final: 0.3053 (tp30) REVERT: F 29 ASP cc_start: 0.7535 (t0) cc_final: 0.7116 (m-30) REVERT: F 160 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6900 (mm) REVERT: F 468 LEU cc_start: 0.4836 (mt) cc_final: 0.4574 (mt) REVERT: F 549 LEU cc_start: 0.6996 (tp) cc_final: 0.6352 (tp) REVERT: F 733 LEU cc_start: 0.5589 (mm) cc_final: 0.4585 (mp) REVERT: F 737 HIS cc_start: 0.6212 (m90) cc_final: 0.5928 (m-70) REVERT: F 794 LEU cc_start: 0.1294 (OUTLIER) cc_final: 0.0797 (tp) REVERT: K 33 TRP cc_start: 0.0351 (OUTLIER) cc_final: -0.0386 (m100) REVERT: K 34 MET cc_start: 0.6497 (tpp) cc_final: 0.5952 (mmp) REVERT: K 36 TRP cc_start: 0.3965 (m100) cc_final: 0.3759 (m100) REVERT: K 86 LEU cc_start: -0.2903 (OUTLIER) cc_final: -0.3318 (mt) REVERT: K 98 VAL cc_start: 0.4873 (OUTLIER) cc_final: 0.4206 (p) REVERT: L 3 GLN cc_start: 0.6749 (tm-30) cc_final: 0.6271 (mp-120) REVERT: L 89 GLU cc_start: 0.3650 (pp20) cc_final: 0.3397 (pt0) REVERT: L 113 GLN cc_start: 0.6356 (mm-40) cc_final: 0.5394 (mp10) REVERT: G 33 TRP cc_start: 0.1130 (OUTLIER) cc_final: -0.0063 (m100) REVERT: G 34 MET cc_start: 0.6390 (tpp) cc_final: 0.5936 (mmp) REVERT: G 82 GLN cc_start: 0.4785 (tp40) cc_final: 0.3841 (tm-30) REVERT: H 113 GLN cc_start: 0.7455 (mm-40) cc_final: 0.6976 (mm-40) REVERT: I 33 TRP cc_start: 0.1204 (OUTLIER) cc_final: 0.0280 (m100) REVERT: I 34 MET cc_start: 0.6209 (tpp) cc_final: 0.5918 (mmp) REVERT: I 86 LEU cc_start: -0.5606 (OUTLIER) cc_final: -0.5944 (mt) REVERT: I 87 LYS cc_start: 0.3318 (mttt) cc_final: 0.2961 (mtpp) REVERT: I 98 VAL cc_start: 0.5538 (OUTLIER) cc_final: 0.4798 (p) REVERT: I 108 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.5786 (t80) REVERT: J 83 MET cc_start: 0.0713 (OUTLIER) cc_final: -0.0295 (pmm) REVERT: J 113 GLN cc_start: 0.6969 (mm110) cc_final: 0.5855 (pt0) outliers start: 155 outliers final: 89 residues processed: 469 average time/residue: 0.5007 time to fit residues: 400.9282 Evaluate side-chains 402 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 290 time to evaluate : 4.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 800 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 794 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 108 TYR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain J residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 1.9990 chunk 273 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 358 optimal weight: 0.7980 chunk 198 optimal weight: 10.0000 chunk 410 optimal weight: 0.2980 chunk 332 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 432 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 478 HIS B 478 HIS ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 HIS C 758 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42204 Z= 0.178 Angle : 0.524 8.606 57240 Z= 0.270 Chirality : 0.041 0.184 6498 Planarity : 0.003 0.030 7122 Dihedral : 5.679 59.270 5579 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.49 % Allowed : 15.42 % Favored : 81.09 % 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: -0.54 (0.12), residues: 4980 helix: 0.07 (0.12), residues: 2049 sheet: -0.64 (0.19), residues: 909 loop : -0.46 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 647 HIS 0.016 0.001 HIS A 478 PHE 0.027 0.001 PHE E 443 TYR 0.023 0.001 TYR K 110 ARG 0.006 0.000 ARG C 685 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 325 time to evaluate : 4.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7432 (t0) cc_final: 0.6980 (t0) REVERT: A 238 GLU cc_start: 0.7393 (tt0) cc_final: 0.7107 (tm-30) REVERT: A 288 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8326 (t0) REVERT: A 353 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.5684 (t80) REVERT: A 375 MET cc_start: 0.7975 (mtt) cc_final: 0.7746 (mtm) REVERT: A 414 ASP cc_start: 0.6112 (OUTLIER) cc_final: 0.5302 (t70) REVERT: A 471 LEU cc_start: 0.7160 (tp) cc_final: 0.6894 (pt) REVERT: A 592 ASN cc_start: 0.5877 (m-40) cc_final: 0.5390 (p0) REVERT: A 658 ILE cc_start: 0.5092 (mm) cc_final: 0.4844 (mm) REVERT: A 749 ARG cc_start: 0.4368 (ptp90) cc_final: 0.3648 (mtm110) REVERT: A 761 LEU cc_start: 0.2229 (OUTLIER) cc_final: 0.1906 (mp) REVERT: A 800 GLU cc_start: 0.3299 (OUTLIER) cc_final: 0.2700 (tp30) REVERT: B 160 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6500 (mt) REVERT: B 234 LYS cc_start: 0.5811 (OUTLIER) cc_final: 0.5365 (ttmm) REVERT: B 250 PHE cc_start: 0.4958 (t80) cc_final: 0.4594 (t80) REVERT: B 478 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7361 (m-70) REVERT: B 580 LYS cc_start: 0.4973 (tptt) cc_final: 0.4663 (tppt) REVERT: B 673 LYS cc_start: 0.6502 (mptt) cc_final: 0.5608 (ttmm) REVERT: C 353 PHE cc_start: 0.6250 (OUTLIER) cc_final: 0.4582 (t80) REVERT: C 434 MET cc_start: 0.6262 (mmm) cc_final: 0.5732 (mmm) REVERT: C 475 TRP cc_start: 0.6821 (m-10) cc_final: 0.6076 (m-10) REVERT: C 658 ILE cc_start: 0.5349 (mm) cc_final: 0.5086 (mm) REVERT: C 676 LYS cc_start: 0.7021 (mmtt) cc_final: 0.6693 (tppt) REVERT: C 755 ASN cc_start: 0.6270 (t0) cc_final: 0.5280 (m-40) REVERT: D 19 ILE cc_start: 0.8749 (pt) cc_final: 0.8280 (mp) REVERT: D 250 PHE cc_start: 0.5183 (t80) cc_final: 0.4653 (t80) REVERT: D 354 GLU cc_start: 0.5435 (OUTLIER) cc_final: 0.4686 (tp30) REVERT: D 448 LEU cc_start: 0.7668 (tp) cc_final: 0.7252 (tp) REVERT: D 488 LEU cc_start: 0.6930 (tp) cc_final: 0.6511 (pp) REVERT: D 522 HIS cc_start: 0.7280 (m90) cc_final: 0.6943 (m90) REVERT: D 602 ASP cc_start: 0.6109 (t0) cc_final: 0.5643 (t0) REVERT: D 673 LYS cc_start: 0.6448 (mptt) cc_final: 0.5633 (pttp) REVERT: D 715 VAL cc_start: 0.6939 (OUTLIER) cc_final: 0.6692 (t) REVERT: E 344 LEU cc_start: 0.7031 (mt) cc_final: 0.6409 (pp) REVERT: E 353 PHE cc_start: 0.6265 (OUTLIER) cc_final: 0.5004 (t80) REVERT: E 501 LYS cc_start: 0.6747 (ptpt) cc_final: 0.6514 (tttm) REVERT: E 520 GLU cc_start: 0.4651 (OUTLIER) cc_final: 0.4313 (pt0) REVERT: E 540 LEU cc_start: 0.7350 (mt) cc_final: 0.7131 (pp) REVERT: E 592 ASN cc_start: 0.5860 (m-40) cc_final: 0.5451 (p0) REVERT: E 699 PHE cc_start: 0.6005 (t80) cc_final: 0.5499 (t80) REVERT: E 755 ASN cc_start: 0.4720 (t0) cc_final: 0.4345 (m-40) REVERT: E 761 LEU cc_start: 0.2233 (OUTLIER) cc_final: 0.1951 (mp) REVERT: E 800 GLU cc_start: 0.3306 (OUTLIER) cc_final: 0.3070 (tp30) REVERT: F 29 ASP cc_start: 0.7562 (t0) cc_final: 0.7162 (m-30) REVERT: F 160 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6878 (mm) REVERT: F 378 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7086 (mp) REVERT: F 468 LEU cc_start: 0.4827 (mt) cc_final: 0.4554 (mt) REVERT: F 549 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6255 (mm) REVERT: F 585 ASN cc_start: 0.5890 (t0) cc_final: 0.4661 (p0) REVERT: F 733 LEU cc_start: 0.5482 (mm) cc_final: 0.4363 (mp) REVERT: F 794 LEU cc_start: 0.1337 (OUTLIER) cc_final: 0.0835 (tp) REVERT: K 33 TRP cc_start: 0.0997 (OUTLIER) cc_final: 0.0043 (m100) REVERT: K 34 MET cc_start: 0.6626 (tpp) cc_final: 0.6103 (mmp) REVERT: K 86 LEU cc_start: -0.3039 (OUTLIER) cc_final: -0.3475 (mt) REVERT: K 98 VAL cc_start: 0.5033 (OUTLIER) cc_final: 0.4433 (p) REVERT: L 89 GLU cc_start: 0.3662 (pp20) cc_final: 0.3431 (pt0) REVERT: L 113 GLN cc_start: 0.6404 (mm-40) cc_final: 0.5890 (mm110) REVERT: G 33 TRP cc_start: 0.1131 (OUTLIER) cc_final: 0.0016 (m100) REVERT: G 34 MET cc_start: 0.6236 (tpp) cc_final: 0.5891 (mmp) REVERT: G 82 GLN cc_start: 0.4795 (tp40) cc_final: 0.3842 (tm-30) REVERT: G 108 TYR cc_start: 0.5933 (OUTLIER) cc_final: 0.5713 (t80) REVERT: H 113 GLN cc_start: 0.7058 (mm-40) cc_final: 0.6621 (mm-40) REVERT: I 33 TRP cc_start: 0.1002 (OUTLIER) cc_final: 0.0244 (m100) REVERT: I 34 MET cc_start: 0.6115 (tpp) cc_final: 0.5796 (mmp) REVERT: I 87 LYS cc_start: 0.3242 (mttt) cc_final: 0.2922 (mtpp) REVERT: I 98 VAL cc_start: 0.5579 (OUTLIER) cc_final: 0.4844 (p) REVERT: I 108 TYR cc_start: 0.6181 (OUTLIER) cc_final: 0.5907 (t80) REVERT: J 83 MET cc_start: 0.0714 (OUTLIER) cc_final: -0.0289 (pmm) REVERT: J 89 GLU cc_start: 0.3366 (OUTLIER) cc_final: 0.2945 (pm20) REVERT: J 113 GLN cc_start: 0.6909 (mm110) cc_final: 0.5789 (pt0) outliers start: 160 outliers final: 102 residues processed: 459 average time/residue: 0.5092 time to fit residues: 392.5472 Evaluate side-chains 420 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 289 time to evaluate : 4.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 800 GLU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 794 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 108 TYR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain J residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 161 optimal weight: 1.9990 chunk 433 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 282 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 481 optimal weight: 4.9990 chunk 399 optimal weight: 20.0000 chunk 223 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS C 615 ASN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 HIS ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 GLN K 82 GLN L 84 ASN G 97 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42204 Z= 0.214 Angle : 0.531 7.791 57240 Z= 0.276 Chirality : 0.041 0.192 6498 Planarity : 0.003 0.031 7122 Dihedral : 5.619 59.496 5573 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.58 % Allowed : 16.30 % Favored : 80.13 % 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: -0.60 (0.12), residues: 4980 helix: -0.05 (0.12), residues: 2061 sheet: -0.59 (0.19), residues: 909 loop : -0.47 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I 59 HIS 0.025 0.001 HIS B 478 PHE 0.015 0.001 PHE E 244 TYR 0.024 0.001 TYR K 110 ARG 0.004 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 309 time to evaluate : 4.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7355 (t0) cc_final: 0.6997 (t0) REVERT: A 238 GLU cc_start: 0.7438 (tt0) cc_final: 0.7122 (tm-30) REVERT: A 288 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8336 (t0) REVERT: A 353 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.5810 (t80) REVERT: A 375 MET cc_start: 0.8043 (mtt) cc_final: 0.7828 (mtm) REVERT: A 414 ASP cc_start: 0.5937 (OUTLIER) cc_final: 0.5224 (t70) REVERT: A 592 ASN cc_start: 0.5805 (m-40) cc_final: 0.5271 (p0) REVERT: A 658 ILE cc_start: 0.5142 (mm) cc_final: 0.4878 (mm) REVERT: A 749 ARG cc_start: 0.4399 (ptp90) cc_final: 0.3849 (mtm110) REVERT: A 761 LEU cc_start: 0.2326 (OUTLIER) cc_final: 0.1999 (mp) REVERT: A 800 GLU cc_start: 0.3343 (OUTLIER) cc_final: 0.2701 (tp30) REVERT: B 160 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6510 (mt) REVERT: B 234 LYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5286 (ttmm) REVERT: B 250 PHE cc_start: 0.4969 (t80) cc_final: 0.4592 (t80) REVERT: B 580 LYS cc_start: 0.4965 (tptt) cc_final: 0.4631 (tppt) REVERT: B 673 LYS cc_start: 0.6413 (mptt) cc_final: 0.5540 (ttmm) REVERT: C 353 PHE cc_start: 0.6324 (OUTLIER) cc_final: 0.4696 (t80) REVERT: C 443 PHE cc_start: 0.5312 (m-80) cc_final: 0.4843 (m-10) REVERT: C 465 ILE cc_start: 0.5799 (tp) cc_final: 0.5154 (tp) REVERT: C 475 TRP cc_start: 0.6805 (m-10) cc_final: 0.6112 (m-10) REVERT: C 658 ILE cc_start: 0.5347 (mm) cc_final: 0.5071 (mm) REVERT: C 664 LEU cc_start: 0.3094 (OUTLIER) cc_final: 0.2794 (mm) REVERT: C 676 LYS cc_start: 0.7032 (mmtt) cc_final: 0.6707 (tppt) REVERT: C 755 ASN cc_start: 0.6151 (t0) cc_final: 0.5292 (m-40) REVERT: D 19 ILE cc_start: 0.8788 (pt) cc_final: 0.8324 (mp) REVERT: D 160 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6914 (mm) REVERT: D 250 PHE cc_start: 0.5175 (t80) cc_final: 0.4692 (t80) REVERT: D 345 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5794 (mmm160) REVERT: D 354 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.4986 (tp30) REVERT: D 448 LEU cc_start: 0.7824 (tp) cc_final: 0.7405 (tp) REVERT: D 488 LEU cc_start: 0.6930 (tp) cc_final: 0.6516 (pp) REVERT: D 522 HIS cc_start: 0.7223 (m90) cc_final: 0.6839 (m90) REVERT: D 673 LYS cc_start: 0.6417 (mptt) cc_final: 0.5472 (pttp) REVERT: D 715 VAL cc_start: 0.6942 (OUTLIER) cc_final: 0.6681 (t) REVERT: E 344 LEU cc_start: 0.7036 (mt) cc_final: 0.6399 (pp) REVERT: E 353 PHE cc_start: 0.6353 (OUTLIER) cc_final: 0.5129 (t80) REVERT: E 520 GLU cc_start: 0.4636 (OUTLIER) cc_final: 0.4320 (pt0) REVERT: E 592 ASN cc_start: 0.5853 (m-40) cc_final: 0.5443 (p0) REVERT: E 699 PHE cc_start: 0.6013 (t80) cc_final: 0.5473 (t80) REVERT: E 755 ASN cc_start: 0.4891 (t0) cc_final: 0.4470 (m-40) REVERT: E 761 LEU cc_start: 0.2325 (OUTLIER) cc_final: 0.2034 (mp) REVERT: E 800 GLU cc_start: 0.3560 (OUTLIER) cc_final: 0.3288 (tp30) REVERT: F 29 ASP cc_start: 0.7605 (t0) cc_final: 0.7169 (m-30) REVERT: F 160 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6842 (mt) REVERT: F 378 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7117 (mp) REVERT: F 468 LEU cc_start: 0.4865 (mt) cc_final: 0.4581 (mt) REVERT: F 549 LEU cc_start: 0.7006 (tp) cc_final: 0.6366 (mm) REVERT: F 733 LEU cc_start: 0.5472 (mm) cc_final: 0.4295 (mp) REVERT: F 794 LEU cc_start: 0.1393 (OUTLIER) cc_final: 0.0874 (tp) REVERT: K 33 TRP cc_start: 0.1016 (OUTLIER) cc_final: 0.0074 (m100) REVERT: K 34 MET cc_start: 0.6642 (tpp) cc_final: 0.6133 (mmp) REVERT: K 86 LEU cc_start: -0.3032 (OUTLIER) cc_final: -0.3452 (mt) REVERT: K 98 VAL cc_start: 0.5094 (OUTLIER) cc_final: 0.4443 (p) REVERT: L 89 GLU cc_start: 0.3525 (pp20) cc_final: 0.3201 (pt0) REVERT: L 113 GLN cc_start: 0.6308 (mm-40) cc_final: 0.5792 (mm110) REVERT: G 33 TRP cc_start: 0.1075 (OUTLIER) cc_final: -0.0088 (m100) REVERT: G 34 MET cc_start: 0.6090 (tpp) cc_final: 0.5781 (mmp) REVERT: G 82 GLN cc_start: 0.4792 (tp40) cc_final: 0.3837 (tm-30) REVERT: H 108 TYR cc_start: 0.5726 (m-80) cc_final: 0.5324 (m-10) REVERT: H 113 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6621 (mm-40) REVERT: I 33 TRP cc_start: 0.1060 (OUTLIER) cc_final: 0.0236 (m100) REVERT: I 34 MET cc_start: 0.5972 (tpp) cc_final: 0.5720 (mmp) REVERT: I 87 LYS cc_start: 0.3319 (mttt) cc_final: 0.2972 (mtpp) REVERT: J 83 MET cc_start: 0.0740 (OUTLIER) cc_final: -0.0275 (pmm) REVERT: J 113 GLN cc_start: 0.6913 (mm110) cc_final: 0.5799 (pt0) outliers start: 164 outliers final: 113 residues processed: 446 average time/residue: 0.4913 time to fit residues: 370.0048 Evaluate side-chains 414 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 275 time to evaluate : 4.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 427 LYS Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 800 GLU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain F residue 794 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 59 TRP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain J residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 351 optimal weight: 0.8980 chunk 272 optimal weight: 8.9990 chunk 405 optimal weight: 10.0000 chunk 269 optimal weight: 1.9990 chunk 479 optimal weight: 2.9990 chunk 300 optimal weight: 0.7980 chunk 292 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 478 HIS A 636 GLN A 649 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 HIS F 155 HIS ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN L 84 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42204 Z= 0.196 Angle : 0.524 7.753 57240 Z= 0.272 Chirality : 0.041 0.255 6498 Planarity : 0.003 0.032 7122 Dihedral : 5.595 59.956 5572 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.60 % Allowed : 16.62 % Favored : 79.78 % 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: -0.62 (0.12), residues: 4980 helix: -0.07 (0.12), residues: 2061 sheet: -0.54 (0.19), residues: 894 loop : -0.51 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 647 HIS 0.015 0.001 HIS A 637 PHE 0.029 0.001 PHE A 443 TYR 0.023 0.001 TYR K 110 ARG 0.004 0.000 ARG E 541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 307 time to evaluate : 4.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7348 (t0) cc_final: 0.6974 (t0) REVERT: A 238 GLU cc_start: 0.7505 (tt0) cc_final: 0.7249 (pt0) REVERT: A 288 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8322 (t0) REVERT: A 353 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.6039 (t80) REVERT: A 375 MET cc_start: 0.8070 (mtt) cc_final: 0.7853 (mtm) REVERT: A 414 ASP cc_start: 0.5929 (OUTLIER) cc_final: 0.5213 (t70) REVERT: A 592 ASN cc_start: 0.5627 (m-40) cc_final: 0.5122 (p0) REVERT: A 658 ILE cc_start: 0.5203 (mm) cc_final: 0.4934 (mm) REVERT: A 749 ARG cc_start: 0.4337 (ptp90) cc_final: 0.3764 (mtm110) REVERT: A 761 LEU cc_start: 0.2389 (OUTLIER) cc_final: 0.2045 (mp) REVERT: A 800 GLU cc_start: 0.3391 (OUTLIER) cc_final: 0.2858 (tp30) REVERT: B 160 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6271 (mt) REVERT: B 234 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.5337 (ttmm) REVERT: B 250 PHE cc_start: 0.4956 (t80) cc_final: 0.4590 (t80) REVERT: B 580 LYS cc_start: 0.4993 (tptt) cc_final: 0.4668 (tppt) REVERT: B 673 LYS cc_start: 0.6590 (mptt) cc_final: 0.5795 (ttmm) REVERT: C 353 PHE cc_start: 0.6304 (OUTLIER) cc_final: 0.4783 (t80) REVERT: C 433 PHE cc_start: 0.5691 (t80) cc_final: 0.5039 (t80) REVERT: C 434 MET cc_start: 0.6296 (mmm) cc_final: 0.5709 (mmm) REVERT: C 475 TRP cc_start: 0.6818 (m-10) cc_final: 0.6152 (m-10) REVERT: C 658 ILE cc_start: 0.5189 (mm) cc_final: 0.4909 (mm) REVERT: C 664 LEU cc_start: 0.2875 (OUTLIER) cc_final: 0.2570 (mm) REVERT: C 676 LYS cc_start: 0.7036 (mmtt) cc_final: 0.6710 (tppt) REVERT: C 755 ASN cc_start: 0.6156 (t0) cc_final: 0.5265 (m-40) REVERT: D 19 ILE cc_start: 0.8812 (pt) cc_final: 0.8368 (mp) REVERT: D 160 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6917 (mm) REVERT: D 250 PHE cc_start: 0.5168 (t80) cc_final: 0.4664 (t80) REVERT: D 345 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5870 (mmm160) REVERT: D 354 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.4991 (tp30) REVERT: D 448 LEU cc_start: 0.7817 (tp) cc_final: 0.7402 (tp) REVERT: D 488 LEU cc_start: 0.6926 (tp) cc_final: 0.6511 (pp) REVERT: D 522 HIS cc_start: 0.7238 (m90) cc_final: 0.6850 (m90) REVERT: D 673 LYS cc_start: 0.6417 (mptt) cc_final: 0.5471 (pttp) REVERT: D 715 VAL cc_start: 0.7063 (OUTLIER) cc_final: 0.6809 (t) REVERT: E 344 LEU cc_start: 0.7203 (mt) cc_final: 0.6617 (pp) REVERT: E 353 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.5233 (t80) REVERT: E 520 GLU cc_start: 0.4903 (OUTLIER) cc_final: 0.4602 (pt0) REVERT: E 592 ASN cc_start: 0.5856 (m-40) cc_final: 0.5432 (p0) REVERT: E 699 PHE cc_start: 0.5855 (t80) cc_final: 0.5336 (t80) REVERT: E 755 ASN cc_start: 0.4905 (t0) cc_final: 0.4470 (m-40) REVERT: E 761 LEU cc_start: 0.2618 (OUTLIER) cc_final: 0.2325 (mp) REVERT: E 800 GLU cc_start: 0.3828 (OUTLIER) cc_final: 0.3358 (tp30) REVERT: F 29 ASP cc_start: 0.7581 (t0) cc_final: 0.7129 (m-30) REVERT: F 160 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.7014 (mt) REVERT: F 468 LEU cc_start: 0.5160 (mt) cc_final: 0.4834 (mt) REVERT: F 521 LEU cc_start: 0.7369 (tp) cc_final: 0.7145 (tp) REVERT: F 549 LEU cc_start: 0.7172 (tp) cc_final: 0.6306 (mm) REVERT: F 794 LEU cc_start: 0.1378 (OUTLIER) cc_final: 0.0854 (tp) REVERT: K 33 TRP cc_start: 0.1037 (OUTLIER) cc_final: 0.0054 (m100) REVERT: K 34 MET cc_start: 0.6583 (tpp) cc_final: 0.6083 (mmp) REVERT: K 86 LEU cc_start: -0.2952 (OUTLIER) cc_final: -0.3336 (mt) REVERT: K 98 VAL cc_start: 0.5127 (OUTLIER) cc_final: 0.4462 (p) REVERT: L 89 GLU cc_start: 0.3525 (pp20) cc_final: 0.3139 (pt0) REVERT: L 113 GLN cc_start: 0.6473 (mm-40) cc_final: 0.5977 (mm110) REVERT: G 33 TRP cc_start: 0.1140 (OUTLIER) cc_final: -0.0044 (m100) REVERT: G 34 MET cc_start: 0.6121 (tpp) cc_final: 0.5819 (mmp) REVERT: G 82 GLN cc_start: 0.4792 (tp40) cc_final: 0.3872 (tm-30) REVERT: H 108 TYR cc_start: 0.5737 (m-80) cc_final: 0.5374 (m-10) REVERT: I 33 TRP cc_start: 0.1131 (OUTLIER) cc_final: 0.0396 (m100) REVERT: I 34 MET cc_start: 0.6070 (tpp) cc_final: 0.5704 (mmp) REVERT: I 87 LYS cc_start: 0.3514 (mttt) cc_final: 0.3183 (mtpp) REVERT: J 83 MET cc_start: 0.0764 (OUTLIER) cc_final: -0.0257 (pmm) REVERT: J 113 GLN cc_start: 0.6798 (mm110) cc_final: 0.5681 (pt0) outliers start: 165 outliers final: 119 residues processed: 452 average time/residue: 0.5002 time to fit residues: 381.9483 Evaluate side-chains 428 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 284 time to evaluate : 4.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 660 ASN Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 427 LYS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 478 HIS Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 800 GLU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 794 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain J residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 296 optimal weight: 0.0970 chunk 191 optimal weight: 6.9990 chunk 286 optimal weight: 0.0770 chunk 144 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 305 optimal weight: 0.7980 chunk 327 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 377 optimal weight: 0.8980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 478 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 HIS ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 42204 Z= 0.146 Angle : 0.513 8.096 57240 Z= 0.265 Chirality : 0.040 0.225 6498 Planarity : 0.003 0.044 7122 Dihedral : 5.454 59.673 5570 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.12 % Allowed : 17.32 % Favored : 79.56 % 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: -0.51 (0.12), residues: 4980 helix: 0.06 (0.12), residues: 2043 sheet: -0.54 (0.19), residues: 888 loop : -0.47 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP I 59 HIS 0.019 0.001 HIS E 478 PHE 0.037 0.001 PHE A 443 TYR 0.025 0.001 TYR K 110 ARG 0.011 0.000 ARG F 666 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 310 time to evaluate : 4.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7405 (t0) cc_final: 0.6945 (t0) REVERT: A 238 GLU cc_start: 0.7493 (tt0) cc_final: 0.7246 (pt0) REVERT: A 288 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8298 (t0) REVERT: A 353 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.5994 (t80) REVERT: A 592 ASN cc_start: 0.5671 (m-40) cc_final: 0.5211 (p0) REVERT: A 658 ILE cc_start: 0.5239 (mm) cc_final: 0.4965 (mm) REVERT: A 749 ARG cc_start: 0.4410 (ptp90) cc_final: 0.3826 (mtm110) REVERT: A 761 LEU cc_start: 0.2378 (OUTLIER) cc_final: 0.2037 (mp) REVERT: A 800 GLU cc_start: 0.3246 (OUTLIER) cc_final: 0.2746 (tp30) REVERT: B 160 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6247 (mt) REVERT: B 234 LYS cc_start: 0.5873 (OUTLIER) cc_final: 0.5471 (ttmm) REVERT: B 250 PHE cc_start: 0.4938 (t80) cc_final: 0.4592 (t80) REVERT: B 580 LYS cc_start: 0.5093 (tptt) cc_final: 0.4755 (tppt) REVERT: B 673 LYS cc_start: 0.6569 (mptt) cc_final: 0.5764 (ttmm) REVERT: C 353 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.4743 (t80) REVERT: C 443 PHE cc_start: 0.5165 (m-80) cc_final: 0.4609 (m-10) REVERT: C 475 TRP cc_start: 0.7012 (m-10) cc_final: 0.6308 (m-10) REVERT: C 658 ILE cc_start: 0.5103 (mm) cc_final: 0.4835 (mm) REVERT: C 676 LYS cc_start: 0.7021 (mmtt) cc_final: 0.6705 (tppt) REVERT: C 755 ASN cc_start: 0.6151 (t0) cc_final: 0.5265 (m-40) REVERT: D 19 ILE cc_start: 0.8810 (pt) cc_final: 0.8371 (mp) REVERT: D 160 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6868 (mm) REVERT: D 250 PHE cc_start: 0.5153 (t80) cc_final: 0.4656 (t80) REVERT: D 354 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5058 (tp30) REVERT: D 448 LEU cc_start: 0.7626 (tp) cc_final: 0.7231 (tp) REVERT: D 488 LEU cc_start: 0.6921 (tp) cc_final: 0.6513 (pp) REVERT: D 522 HIS cc_start: 0.7214 (m90) cc_final: 0.6841 (m90) REVERT: D 673 LYS cc_start: 0.6533 (mptt) cc_final: 0.5584 (pttp) REVERT: D 715 VAL cc_start: 0.7045 (OUTLIER) cc_final: 0.6795 (t) REVERT: E 344 LEU cc_start: 0.7231 (mt) cc_final: 0.6660 (pp) REVERT: E 353 PHE cc_start: 0.6068 (OUTLIER) cc_final: 0.5039 (t80) REVERT: E 520 GLU cc_start: 0.5232 (OUTLIER) cc_final: 0.4755 (pt0) REVERT: E 592 ASN cc_start: 0.5794 (m-40) cc_final: 0.5366 (p0) REVERT: E 699 PHE cc_start: 0.6019 (t80) cc_final: 0.5505 (t80) REVERT: E 755 ASN cc_start: 0.4851 (t0) cc_final: 0.4454 (m-40) REVERT: E 761 LEU cc_start: 0.2610 (OUTLIER) cc_final: 0.2331 (mp) REVERT: E 800 GLU cc_start: 0.3799 (OUTLIER) cc_final: 0.3359 (tp30) REVERT: F 29 ASP cc_start: 0.7513 (t0) cc_final: 0.7096 (m-30) REVERT: F 160 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6959 (mt) REVERT: F 378 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7112 (mp) REVERT: F 468 LEU cc_start: 0.5070 (mt) cc_final: 0.4813 (mt) REVERT: F 521 LEU cc_start: 0.7258 (tp) cc_final: 0.7040 (tp) REVERT: F 549 LEU cc_start: 0.7142 (tp) cc_final: 0.6275 (mm) REVERT: F 733 LEU cc_start: 0.5534 (mm) cc_final: 0.4379 (mp) REVERT: F 794 LEU cc_start: 0.1344 (OUTLIER) cc_final: 0.0827 (tp) REVERT: K 33 TRP cc_start: 0.0996 (OUTLIER) cc_final: 0.0081 (m100) REVERT: K 34 MET cc_start: 0.6525 (tpp) cc_final: 0.6009 (mmp) REVERT: K 86 LEU cc_start: -0.2964 (OUTLIER) cc_final: -0.3338 (mt) REVERT: K 98 VAL cc_start: 0.5495 (OUTLIER) cc_final: 0.4658 (p) REVERT: L 113 GLN cc_start: 0.6456 (mm-40) cc_final: 0.5946 (mm110) REVERT: G 33 TRP cc_start: 0.1015 (OUTLIER) cc_final: -0.0123 (m100) REVERT: G 34 MET cc_start: 0.6123 (tpp) cc_final: 0.5825 (mmp) REVERT: H 108 TYR cc_start: 0.5788 (m-80) cc_final: 0.5505 (m-10) REVERT: I 33 TRP cc_start: 0.0978 (OUTLIER) cc_final: 0.0378 (m100) REVERT: I 34 MET cc_start: 0.5922 (tpp) cc_final: 0.5512 (mmp) REVERT: I 51 ILE cc_start: 0.5850 (tp) cc_final: 0.5553 (tt) REVERT: I 87 LYS cc_start: 0.3493 (mttt) cc_final: 0.3175 (mtpp) REVERT: I 95 TYR cc_start: 0.4778 (m-10) cc_final: 0.4284 (m-10) REVERT: I 98 VAL cc_start: 0.5515 (OUTLIER) cc_final: 0.4716 (p) REVERT: J 83 MET cc_start: 0.0761 (OUTLIER) cc_final: -0.0254 (pmm) REVERT: J 113 GLN cc_start: 0.6912 (mm110) cc_final: 0.5798 (pt0) outliers start: 143 outliers final: 98 residues processed: 436 average time/residue: 0.5001 time to fit residues: 367.4634 Evaluate side-chains 405 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 283 time to evaluate : 4.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 427 LYS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 478 HIS Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 800 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain F residue 794 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain J residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 436 optimal weight: 9.9990 chunk 459 optimal weight: 5.9990 chunk 419 optimal weight: 20.0000 chunk 447 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 351 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 404 optimal weight: 0.0020 chunk 423 optimal weight: 6.9990 chunk 445 optimal weight: 3.9990 overall best weight: 3.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 ASN B 737 HIS ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 HIS ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN I 107 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 42204 Z= 0.592 Angle : 0.815 13.487 57240 Z= 0.419 Chirality : 0.051 0.308 6498 Planarity : 0.006 0.074 7122 Dihedral : 6.346 59.686 5568 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.51 % Allowed : 17.43 % Favored : 79.06 % 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: -1.43 (0.12), residues: 4980 helix: -0.94 (0.11), residues: 2001 sheet: -0.85 (0.18), residues: 903 loop : -0.76 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP A 647 HIS 0.014 0.002 HIS E 478 PHE 0.037 0.003 PHE D 374 TYR 0.052 0.003 TYR C 477 ARG 0.008 0.001 ARG F 762 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 305 time to evaluate : 4.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7358 (t0) cc_final: 0.7041 (t0) REVERT: A 238 GLU cc_start: 0.7531 (tt0) cc_final: 0.7195 (pt0) REVERT: A 288 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8313 (t0) REVERT: A 321 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7418 (mp) REVERT: A 353 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6081 (t80) REVERT: A 375 MET cc_start: 0.7963 (mtt) cc_final: 0.7732 (mtt) REVERT: A 414 ASP cc_start: 0.6087 (OUTLIER) cc_final: 0.5001 (t0) REVERT: A 592 ASN cc_start: 0.5705 (m-40) cc_final: 0.5066 (p0) REVERT: B 160 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6967 (mm) REVERT: B 234 LYS cc_start: 0.5916 (OUTLIER) cc_final: 0.5315 (ttmm) REVERT: B 238 GLU cc_start: 0.6947 (tt0) cc_final: 0.6190 (pp20) REVERT: B 250 PHE cc_start: 0.4814 (t80) cc_final: 0.4361 (t80) REVERT: B 673 LYS cc_start: 0.6491 (mptt) cc_final: 0.5700 (ttmm) REVERT: B 784 LEU cc_start: 0.4841 (mp) cc_final: 0.4411 (tp) REVERT: C 353 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.5634 (t80) REVERT: C 647 TRP cc_start: 0.4829 (OUTLIER) cc_final: 0.4080 (p90) REVERT: C 676 LYS cc_start: 0.7145 (mmtt) cc_final: 0.6640 (tppt) REVERT: C 755 ASN cc_start: 0.6606 (t0) cc_final: 0.5364 (m-40) REVERT: D 250 PHE cc_start: 0.5081 (t80) cc_final: 0.4674 (t80) REVERT: D 354 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.5734 (tp30) REVERT: D 448 LEU cc_start: 0.7803 (tp) cc_final: 0.7432 (tp) REVERT: D 522 HIS cc_start: 0.7308 (m90) cc_final: 0.6822 (m90) REVERT: D 673 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.5254 (pttp) REVERT: D 715 VAL cc_start: 0.7046 (OUTLIER) cc_final: 0.6805 (t) REVERT: E 353 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.5596 (t80) REVERT: E 520 GLU cc_start: 0.4861 (OUTLIER) cc_final: 0.4557 (pm20) REVERT: E 645 LYS cc_start: 0.5139 (mttt) cc_final: 0.4904 (mtmm) REVERT: E 755 ASN cc_start: 0.5301 (t0) cc_final: 0.4666 (m-40) REVERT: E 800 GLU cc_start: 0.4010 (OUTLIER) cc_final: 0.3177 (tp30) REVERT: F 29 ASP cc_start: 0.7692 (t0) cc_final: 0.7311 (m-30) REVERT: F 378 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7221 (mp) REVERT: F 478 HIS cc_start: 0.7605 (OUTLIER) cc_final: 0.6781 (m-70) REVERT: F 736 LEU cc_start: 0.5580 (OUTLIER) cc_final: 0.5199 (mm) REVERT: F 758 GLN cc_start: 0.5867 (pt0) cc_final: 0.5562 (mp10) REVERT: K 33 TRP cc_start: 0.1602 (OUTLIER) cc_final: 0.0203 (m100) REVERT: K 34 MET cc_start: 0.6696 (tpp) cc_final: 0.6302 (mmp) REVERT: K 59 TRP cc_start: 0.5165 (m-10) cc_final: 0.4940 (m-10) REVERT: K 86 LEU cc_start: -0.3596 (OUTLIER) cc_final: -0.3818 (pp) REVERT: L 113 GLN cc_start: 0.6136 (mm-40) cc_final: 0.5598 (mm110) REVERT: G 33 TRP cc_start: 0.1360 (OUTLIER) cc_final: 0.0072 (m100) REVERT: G 59 TRP cc_start: 0.4391 (m100) cc_final: 0.4167 (m100) REVERT: G 95 TYR cc_start: 0.4847 (m-80) cc_final: 0.4408 (m-80) REVERT: H 108 TYR cc_start: 0.6049 (m-80) cc_final: 0.5799 (m-10) REVERT: I 33 TRP cc_start: 0.1961 (OUTLIER) cc_final: 0.0857 (m100) REVERT: I 34 MET cc_start: 0.6063 (tpp) cc_final: 0.5839 (mmp) REVERT: I 59 TRP cc_start: 0.5917 (m100) cc_final: 0.5574 (m100) REVERT: I 87 LYS cc_start: 0.3439 (mttt) cc_final: 0.3133 (mtpp) REVERT: J 83 MET cc_start: 0.1182 (OUTLIER) cc_final: 0.0154 (pmm) REVERT: J 113 GLN cc_start: 0.6888 (mm110) cc_final: 0.5808 (pt0) outliers start: 161 outliers final: 107 residues processed: 445 average time/residue: 0.5006 time to fit residues: 377.8618 Evaluate side-chains 395 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 266 time to evaluate : 4.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 673 LYS Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 478 HIS Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain E residue 800 GLU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 478 HIS Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 590 MET Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain J residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 293 optimal weight: 0.5980 chunk 472 optimal weight: 5.9990 chunk 288 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 chunk 328 optimal weight: 7.9990 chunk 496 optimal weight: 6.9990 chunk 456 optimal weight: 0.9980 chunk 395 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 305 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 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 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 HIS ** E 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42204 Z= 0.197 Angle : 0.587 10.171 57240 Z= 0.300 Chirality : 0.042 0.314 6498 Planarity : 0.003 0.035 7122 Dihedral : 5.731 59.924 5559 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.55 % Allowed : 18.59 % Favored : 78.86 % 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: -0.88 (0.12), residues: 4980 helix: -0.30 (0.12), residues: 1977 sheet: -0.77 (0.18), residues: 903 loop : -0.58 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP E 647 HIS 0.007 0.001 HIS E 478 PHE 0.021 0.001 PHE E 393 TYR 0.045 0.002 TYR L 37 ARG 0.008 0.000 ARG E 685 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 288 time to evaluate : 4.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7199 (t0) cc_final: 0.6899 (t0) REVERT: A 238 GLU cc_start: 0.7650 (tt0) cc_final: 0.7175 (pt0) REVERT: A 288 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8250 (t0) REVERT: A 321 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7270 (mp) REVERT: A 353 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6389 (t80) REVERT: A 414 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.4910 (t70) REVERT: A 592 ASN cc_start: 0.5662 (m-40) cc_final: 0.5060 (p0) REVERT: B 19 ILE cc_start: 0.8578 (pt) cc_final: 0.8092 (mp) REVERT: B 160 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6478 (mt) REVERT: B 234 LYS cc_start: 0.5961 (OUTLIER) cc_final: 0.5428 (ttmm) REVERT: B 238 GLU cc_start: 0.6735 (tt0) cc_final: 0.6153 (pp20) REVERT: B 250 PHE cc_start: 0.4866 (t80) cc_final: 0.4523 (t80) REVERT: B 580 LYS cc_start: 0.4550 (tptt) cc_final: 0.4100 (tppt) REVERT: B 673 LYS cc_start: 0.6440 (mptt) cc_final: 0.5666 (ttmm) REVERT: B 784 LEU cc_start: 0.4967 (mp) cc_final: 0.4394 (tt) REVERT: C 353 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.5924 (t80) REVERT: C 443 PHE cc_start: 0.5310 (m-10) cc_final: 0.5061 (m-80) REVERT: C 475 TRP cc_start: 0.6879 (m-10) cc_final: 0.6155 (m-10) REVERT: C 676 LYS cc_start: 0.7183 (mmtt) cc_final: 0.6753 (tppt) REVERT: C 755 ASN cc_start: 0.6114 (t0) cc_final: 0.5166 (m-40) REVERT: D 29 ASP cc_start: 0.7954 (t0) cc_final: 0.7315 (m-30) REVERT: D 250 PHE cc_start: 0.5071 (t80) cc_final: 0.4752 (t80) REVERT: D 448 LEU cc_start: 0.7868 (tp) cc_final: 0.7489 (tp) REVERT: D 478 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.6718 (m-70) REVERT: D 488 LEU cc_start: 0.6893 (tp) cc_final: 0.6675 (pp) REVERT: D 522 HIS cc_start: 0.7299 (m90) cc_final: 0.6834 (m90) REVERT: D 673 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.5621 (pttp) REVERT: D 715 VAL cc_start: 0.7135 (OUTLIER) cc_final: 0.6882 (t) REVERT: E 234 LYS cc_start: 0.6446 (tmtt) cc_final: 0.6239 (tttp) REVERT: E 344 LEU cc_start: 0.7008 (mt) cc_final: 0.6498 (pp) REVERT: E 353 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.6354 (t80) REVERT: E 520 GLU cc_start: 0.5453 (OUTLIER) cc_final: 0.5192 (pm20) REVERT: E 755 ASN cc_start: 0.5100 (t0) cc_final: 0.4544 (m-40) REVERT: F 29 ASP cc_start: 0.7646 (t0) cc_final: 0.7185 (m-30) REVERT: F 160 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6507 (mt) REVERT: K 33 TRP cc_start: 0.1229 (OUTLIER) cc_final: 0.0043 (m100) REVERT: K 34 MET cc_start: 0.6594 (tpp) cc_final: 0.6170 (mmp) REVERT: K 86 LEU cc_start: -0.3065 (OUTLIER) cc_final: -0.3316 (pp) REVERT: L 113 GLN cc_start: 0.6136 (mm-40) cc_final: 0.5270 (pp30) REVERT: G 33 TRP cc_start: 0.1457 (OUTLIER) cc_final: -0.0349 (m100) REVERT: G 95 TYR cc_start: 0.4560 (m-80) cc_final: 0.4149 (m-80) REVERT: G 107 GLN cc_start: 0.6150 (tt0) cc_final: 0.5574 (mp10) REVERT: H 108 TYR cc_start: 0.5919 (m-80) cc_final: 0.5656 (m-10) REVERT: I 33 TRP cc_start: 0.1366 (OUTLIER) cc_final: 0.0421 (m100) REVERT: I 34 MET cc_start: 0.6067 (tpp) cc_final: 0.5856 (mmp) REVERT: I 59 TRP cc_start: 0.6094 (m100) cc_final: 0.5686 (m100) REVERT: I 87 LYS cc_start: 0.3196 (mttt) cc_final: 0.2913 (mtpp) REVERT: J 83 MET cc_start: 0.1163 (OUTLIER) cc_final: 0.0157 (pmm) REVERT: J 113 GLN cc_start: 0.6808 (mm110) cc_final: 0.5698 (pt0) outliers start: 117 outliers final: 86 residues processed: 389 average time/residue: 0.5026 time to fit residues: 330.5448 Evaluate side-chains 375 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 271 time to evaluate : 4.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 673 LYS Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 478 HIS Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 590 MET Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain J residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 313 optimal weight: 0.9980 chunk 420 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 364 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 395 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 chunk 406 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS C 478 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 HIS ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.177744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.150942 restraints weight = 82844.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.147531 restraints weight = 121734.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.144455 restraints weight = 81439.331| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42204 Z= 0.191 Angle : 0.573 10.200 57240 Z= 0.292 Chirality : 0.042 0.307 6498 Planarity : 0.003 0.058 7122 Dihedral : 5.588 58.629 5559 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.47 % Allowed : 18.85 % Favored : 78.69 % 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: -0.79 (0.12), residues: 4980 helix: -0.14 (0.12), residues: 1977 sheet: -0.74 (0.18), residues: 915 loop : -0.60 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 647 HIS 0.025 0.001 HIS E 478 PHE 0.021 0.001 PHE E 433 TYR 0.032 0.001 TYR L 37 ARG 0.007 0.000 ARG F 666 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8428.12 seconds wall clock time: 152 minutes 17.51 seconds (9137.51 seconds total)