Starting phenix.real_space_refine on Sun Mar 17 06:47:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/03_2024/5zya_6915_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/03_2024/5zya_6915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/03_2024/5zya_6915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/03_2024/5zya_6915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/03_2024/5zya_6915_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/03_2024/5zya_6915_updated.pdb" } resolution = 3.95 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 ------------------------------------------------------------------------------- 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 1 8.98 5 Zn 3 6.06 5 S 102 5.16 5 C 10800 2.51 5 N 2895 2.21 5 O 3156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 495": "NH1" <-> "NH2" Residue "C ARG 558": "NH1" <-> "NH2" Residue "C ARG 590": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 736": "NH1" <-> "NH2" Residue "C ARG 822": "NH1" <-> "NH2" Residue "C ARG 827": "NH1" <-> "NH2" Residue "C ARG 831": "NH1" <-> "NH2" Residue "C ARG 939": "NH1" <-> "NH2" Residue "C ARG 948": "NH1" <-> "NH2" Residue "C ARG 1027": "NH1" <-> "NH2" Residue "C ARG 1045": "NH1" <-> "NH2" Residue "C ARG 1057": "NH1" <-> "NH2" Residue "C ARG 1075": "NH1" <-> "NH2" Residue "C ARG 1106": "NH1" <-> "NH2" Residue "C ARG 1245": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 718": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 895": "NH1" <-> "NH2" Residue "A ARG 1013": "NH1" <-> "NH2" Residue "A PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16957 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 539 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "C" Number of atoms: 6438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6438 Classifications: {'peptide': 809} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 774} Chain breaks: 1 Chain: "D" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 645 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "A" Number of atoms: 9280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9280 Classifications: {'peptide': 1183} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1122} Chain breaks: 5 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'9B0': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7105 SG CYS D 23 30.112 90.456 66.528 1.00 68.38 S ATOM 7376 SG CYS D 58 33.151 91.184 64.701 1.00 63.42 S ATOM 7397 SG CYS D 61 29.986 92.741 63.750 1.00 65.46 S ATOM 7018 SG CYS D 11 43.982 98.304 55.595 1.00 71.87 S ATOM 7281 SG CYS D 46 46.263 97.192 59.934 1.00 62.04 S ATOM 7575 SG CYS D 85 45.777 95.371 56.868 1.00 67.32 S ATOM 7156 SG CYS D 30 38.525 81.746 57.804 1.00 52.14 S ATOM 7177 SG CYS D 33 37.070 80.142 54.160 1.00 47.74 S ATOM 7472 SG CYS D 72 39.458 78.230 56.015 1.00 44.18 S ATOM 7496 SG CYS D 75 40.699 80.609 53.666 1.00 43.95 S Time building chain proxies: 9.55, per 1000 atoms: 0.56 Number of scatterers: 16957 At special positions: 0 Unit cell: (132.2, 145.42, 125.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 K 1 19.00 S 102 16.00 O 3156 8.00 N 2895 7.00 C 10800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.72 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 61 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 23 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 58 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 46 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 11 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 33 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 30 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 75 " Number of angles added : 6 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 25 sheets defined 31.3% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'B' and resid 28 through 45 Processing helix chain 'B' and resid 49 through 56 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'C' and resid 492 through 505 removed outlier: 4.834A pdb=" N LEU C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU C 501 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU C 502 " --> pdb=" O MET C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 521 Processing helix chain 'C' and resid 523 through 526 No H-bonds generated for 'chain 'C' and resid 523 through 526' Processing helix chain 'C' and resid 529 through 540 Proline residue: C 537 - end of helix Processing helix chain 'C' and resid 546 through 559 removed outlier: 3.516A pdb=" N LYS C 554 " --> pdb=" O HIS C 550 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 579 Processing helix chain 'C' and resid 587 through 603 Processing helix chain 'C' and resid 606 through 612 Processing helix chain 'C' and resid 622 through 639 Processing helix chain 'C' and resid 642 through 652 Proline residue: C 646 - end of helix Processing helix chain 'C' and resid 658 through 675 Processing helix chain 'C' and resid 683 through 693 removed outlier: 5.598A pdb=" N HIS C 692 " --> pdb=" O GLU C 688 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLY C 693 " --> pdb=" O ILE C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 716 removed outlier: 4.306A pdb=" N ALA C 715 " --> pdb=" O ALA C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 737 removed outlier: 3.896A pdb=" N LEU C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG C 736 " --> pdb=" O TRP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 751 removed outlier: 3.767A pdb=" N ALA C 749 " --> pdb=" O ALA C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 775 removed outlier: 4.192A pdb=" N LEU C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C 772 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 795 Processing helix chain 'C' and resid 803 through 809 Processing helix chain 'C' and resid 811 through 817 Processing helix chain 'C' and resid 827 through 844 removed outlier: 4.139A pdb=" N LYS C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 852 Processing helix chain 'C' and resid 855 through 857 No H-bonds generated for 'chain 'C' and resid 855 through 857' Processing helix chain 'C' and resid 862 through 878 Processing helix chain 'C' and resid 889 through 901 Processing helix chain 'C' and resid 911 through 924 removed outlier: 7.469A pdb=" N LYS C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG C 924 " --> pdb=" O ALA C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 940 Processing helix chain 'C' and resid 943 through 945 No H-bonds generated for 'chain 'C' and resid 943 through 945' Processing helix chain 'C' and resid 948 through 956 Processing helix chain 'C' and resid 959 through 963 Processing helix chain 'C' and resid 970 through 980 Processing helix chain 'C' and resid 987 through 1003 removed outlier: 3.923A pdb=" N SER C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1025 Proline residue: C1018 - end of helix Proline residue: C1022 - end of helix removed outlier: 4.871A pdb=" N LYS C1025 " --> pdb=" O THR C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1045 Processing helix chain 'C' and resid 1052 through 1067 removed outlier: 4.369A pdb=" N GLU C1064 " --> pdb=" O PHE C1060 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C1065 " --> pdb=" O GLU C1061 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU C1066 " --> pdb=" O LEU C1062 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LYS C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 1071 through 1087 Processing helix chain 'C' and resid 1110 through 1122 Processing helix chain 'C' and resid 1128 through 1136 Processing helix chain 'C' and resid 1144 through 1158 Processing helix chain 'C' and resid 1160 through 1162 No H-bonds generated for 'chain 'C' and resid 1160 through 1162' Processing helix chain 'C' and resid 1167 through 1177 Proline residue: C1171 - end of helix Processing helix chain 'C' and resid 1182 through 1198 Processing helix chain 'C' and resid 1206 through 1219 removed outlier: 3.866A pdb=" N TYR C1214 " --> pdb=" O HIS C1210 " (cutoff:3.500A) Proline residue: C1217 - end of helix Processing helix chain 'C' and resid 1224 through 1241 Processing helix chain 'C' and resid 1243 through 1248 Processing helix chain 'C' and resid 1251 through 1253 No H-bonds generated for 'chain 'C' and resid 1251 through 1253' Processing helix chain 'C' and resid 1259 through 1274 removed outlier: 3.646A pdb=" N VAL C1264 " --> pdb=" O LYS C1260 " (cutoff:3.500A) Processing helix chain 'C' and resid 1277 through 1280 Processing helix chain 'C' and resid 1298 through 1300 No H-bonds generated for 'chain 'C' and resid 1298 through 1300' Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 809 through 824 Processing helix chain 'A' and resid 839 through 842 No H-bonds generated for 'chain 'A' and resid 839 through 842' Processing helix chain 'A' and resid 1135 through 1151 removed outlier: 4.528A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1164 No H-bonds generated for 'chain 'A' and resid 1161 through 1164' Processing helix chain 'A' and resid 1187 through 1194 Processing helix chain 'A' and resid 1201 through 1214 removed outlier: 3.860A pdb=" N ILE A1211 " --> pdb=" O LYS A1207 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 39 through 42 removed outlier: 3.743A pdb=" N CYS D 40 " --> pdb=" O TYR D 71 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR D 71 " --> pdb=" O CYS D 40 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.791A pdb=" N GLU A 39 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 54 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.225A pdb=" N SER A 64 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A 66 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE A 78 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 87 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 120 through 123 Processing sheet with id= E, first strand: chain 'A' and resid 165 through 167 removed outlier: 3.648A pdb=" N THR A 207 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 224 " --> pdb=" O PHE A 210 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLU A 212 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ARG A 222 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP A 214 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL A 220 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 235 through 237 removed outlier: 3.989A pdb=" N ILE A 236 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 249 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 248 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 292 through 294 removed outlier: 3.594A pdb=" N HIS A 293 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 300 " --> pdb=" O HIS A 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 775 through 780 removed outlier: 3.543A pdb=" N CYS A 427 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 409 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 473 through 477 Processing sheet with id= J, first strand: chain 'A' and resid 533 through 537 removed outlier: 3.836A pdb=" N ARG A 525 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 518 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 507 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 574 through 576 removed outlier: 3.748A pdb=" N VAL A 564 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 554 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 546 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 640 through 643 removed outlier: 4.155A pdb=" N CYS A 641 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 666 " --> pdb=" O CYS A 641 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 664 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 677 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 667 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 675 " --> pdb=" O ILE A 667 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.673A pdb=" N PHE A 702 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 712 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 722 " --> pdb=" O VAL A 712 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 754 through 756 removed outlier: 6.453A pdb=" N ALA A 766 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU A 446 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 785 through 790 removed outlier: 7.587A pdb=" N ILE A 800 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE A 788 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 798 " --> pdb=" O PHE A 788 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 803 " --> pdb=" O ALA A 863 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 878 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 943 through 945 removed outlier: 4.156A pdb=" N SER A 890 " --> pdb=" O GLY A 908 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA A 910 " --> pdb=" O ALA A 888 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA A 888 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 953 through 955 Processing sheet with id= R, first strand: chain 'A' and resid 990 through 994 removed outlier: 6.927A pdb=" N SER A1003 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE A 993 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A1001 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A1025 " --> pdb=" O TRP A1011 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG A1013 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE A1023 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS A1015 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU A1021 " --> pdb=" O LYS A1015 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 1043 through 1045 removed outlier: 3.745A pdb=" N VAL A1055 " --> pdb=" O MET A1093 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET A1093 " --> pdb=" O VAL A1055 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG A1057 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL A1091 " --> pdb=" O ARG A1057 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 1104 through 1107 Processing sheet with id= U, first strand: chain 'A' and resid 6 through 9 removed outlier: 6.743A pdb=" N ILE A1126 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 314 through 317 removed outlier: 3.981A pdb=" N ARG A 326 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 336 through 342 removed outlier: 7.973A pdb=" N ALA A 350 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N MET A 339 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE A 348 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A 341 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE A 346 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 356 through 360 removed outlier: 3.815A pdb=" N LEU A 358 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP A 399 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN A 360 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A 397 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 613 through 617 removed outlier: 3.864A pdb=" N SER A 629 " --> pdb=" O ILE A 616 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1536 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: 6.27 Time building geometry restraints manager: 7.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4284 1.33 - 1.45: 3717 1.45 - 1.58: 9125 1.58 - 1.70: 6 1.70 - 1.83: 158 Bond restraints: 17290 Sorted by residual: bond pdb=" C17 9B0 C1401 " pdb=" C18 9B0 C1401 " ideal model delta sigma weight residual 1.337 1.516 -0.179 2.00e-02 2.50e+03 7.97e+01 bond pdb=" C6 9B0 C1401 " pdb=" C8 9B0 C1401 " ideal model delta sigma weight residual 1.542 1.720 -0.178 2.00e-02 2.50e+03 7.91e+01 bond pdb=" C14 9B0 C1401 " pdb=" C16 9B0 C1401 " ideal model delta sigma weight residual 1.344 1.518 -0.174 2.00e-02 2.50e+03 7.57e+01 bond pdb=" C11 9B0 C1401 " pdb=" C13 9B0 C1401 " ideal model delta sigma weight residual 1.540 1.693 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C34 9B0 C1401 " pdb=" C40 9B0 C1401 " ideal model delta sigma weight residual 1.542 1.654 -0.112 2.00e-02 2.50e+03 3.11e+01 ... (remaining 17285 not shown) Histogram of bond angle deviations from ideal: 58.60 - 75.54: 3 75.54 - 92.49: 1 92.49 - 109.44: 2357 109.44 - 126.39: 20844 126.39 - 143.34: 224 Bond angle restraints: 23429 Sorted by residual: angle pdb=" C35 9B0 C1401 " pdb=" C34 9B0 C1401 " pdb=" N2 9B0 C1401 " ideal model delta sigma weight residual 110.42 138.11 -27.69 3.00e+00 1.11e-01 8.52e+01 angle pdb=" C36 9B0 C1401 " pdb=" C37 9B0 C1401 " pdb=" C38 9B0 C1401 " ideal model delta sigma weight residual 115.94 143.34 -27.40 3.00e+00 1.11e-01 8.34e+01 angle pdb=" C37 9B0 C1401 " pdb=" C38 9B0 C1401 " pdb=" C39 9B0 C1401 " ideal model delta sigma weight residual 113.37 87.02 26.35 3.00e+00 1.11e-01 7.71e+01 angle pdb=" C34 9B0 C1401 " pdb=" C40 9B0 C1401 " pdb=" C39 9B0 C1401 " ideal model delta sigma weight residual 116.42 141.00 -24.58 3.00e+00 1.11e-01 6.71e+01 angle pdb=" N GLY C 740 " pdb=" CA GLY C 740 " pdb=" C GLY C 740 " ideal model delta sigma weight residual 110.29 119.21 -8.92 1.28e+00 6.10e-01 4.85e+01 ... (remaining 23424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 10252 24.14 - 48.29: 263 48.29 - 72.43: 15 72.43 - 96.57: 6 96.57 - 120.72: 6 Dihedral angle restraints: 10542 sinusoidal: 4315 harmonic: 6227 Sorted by residual: dihedral pdb=" CA GLN B 74 " pdb=" C GLN B 74 " pdb=" N PRO B 75 " pdb=" CA PRO B 75 " ideal model delta harmonic sigma weight residual -180.00 -143.25 -36.75 0 5.00e+00 4.00e-02 5.40e+01 dihedral pdb=" CA TYR C 719 " pdb=" C TYR C 719 " pdb=" N GLY C 720 " pdb=" CA GLY C 720 " ideal model delta harmonic sigma weight residual -180.00 -145.04 -34.96 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" CA ILE C 754 " pdb=" C ILE C 754 " pdb=" N PRO C 755 " pdb=" CA PRO C 755 " ideal model delta harmonic sigma weight residual 180.00 145.63 34.37 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 10539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2503 0.123 - 0.246: 147 0.246 - 0.369: 8 0.369 - 0.492: 2 0.492 - 0.615: 2 Chirality restraints: 2662 Sorted by residual: chirality pdb=" C8 9B0 C1401 " pdb=" C6 9B0 C1401 " pdb=" C9 9B0 C1401 " pdb=" O5 9B0 C1401 " both_signs ideal model delta sigma weight residual False 2.50 1.88 0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" C13 9B0 C1401 " pdb=" C11 9B0 C1401 " pdb=" C14 9B0 C1401 " pdb=" O1 9B0 C1401 " both_signs ideal model delta sigma weight residual False -2.57 -3.08 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" C3 9B0 C1401 " pdb=" C2 9B0 C1401 " pdb=" C4 9B0 C1401 " pdb=" O3 9B0 C1401 " both_signs ideal model delta sigma weight residual False -2.37 -2.76 0.39 2.00e-01 2.50e+01 3.90e+00 ... (remaining 2659 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 9B0 C1401 " -0.130 2.00e-02 2.50e+03 7.49e-02 5.61e+01 pdb=" C2 9B0 C1401 " 0.041 2.00e-02 2.50e+03 pdb=" O1 9B0 C1401 " 0.041 2.00e-02 2.50e+03 pdb=" O2 9B0 C1401 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 9B0 C1401 " 0.012 2.00e-02 2.50e+03 3.72e-02 1.73e+01 pdb=" C14 9B0 C1401 " -0.065 2.00e-02 2.50e+03 pdb=" C15 9B0 C1401 " 0.027 2.00e-02 2.50e+03 pdb=" C16 9B0 C1401 " 0.041 2.00e-02 2.50e+03 pdb=" C17 9B0 C1401 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 754 " -0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO C 755 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 755 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 755 " -0.049 5.00e-02 4.00e+02 ... (remaining 3019 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.37: 31 2.37 - 3.06: 10323 3.06 - 3.75: 29151 3.75 - 4.45: 43767 4.45 - 5.14: 71160 Nonbonded interactions: 154432 Sorted by model distance: nonbonded pdb=" O LEU C1251 " pdb=" CD1 LEU C1254 " model vdw 1.673 3.460 nonbonded pdb=" O ALA C 762 " pdb=" OG1 THR C 766 " model vdw 2.226 2.440 nonbonded pdb=" O GLN B 35 " pdb=" OG SER B 39 " model vdw 2.244 2.440 nonbonded pdb=" OG SER C 657 " pdb=" OE1 GLN C 659 " model vdw 2.249 2.440 nonbonded pdb=" O TYR C1167 " pdb=" OG1 THR C1170 " model vdw 2.252 2.440 ... (remaining 154427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.550 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: 0.010 Extract box with map and model: 2.800 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 51.560 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5313 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 : 0.009 0.179 17290 Z= 0.558 Angle : 1.272 27.693 23429 Z= 0.662 Chirality : 0.066 0.615 2662 Planarity : 0.009 0.089 3022 Dihedral : 11.428 120.717 6530 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 0.32 % Allowed : 3.46 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.10 % 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: -4.57 (0.15), residues: 2123 helix: -2.81 (0.14), residues: 682 sheet: -2.76 (0.21), residues: 445 loop : -3.28 (0.16), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C1055 HIS 0.014 0.003 HIS A 440 PHE 0.047 0.004 PHE A 261 TYR 0.030 0.004 TYR C 623 ARG 0.018 0.001 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 562 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 LEU cc_start: 0.8025 (tp) cc_final: 0.7737 (tt) REVERT: B 38 ASP cc_start: 0.7279 (p0) cc_final: 0.7032 (p0) REVERT: B 64 VAL cc_start: 0.7069 (t) cc_final: 0.6705 (t) REVERT: C 773 LEU cc_start: 0.6651 (tp) cc_final: 0.6337 (mp) REVERT: C 933 CYS cc_start: 0.6350 (m) cc_final: 0.4998 (t) REVERT: C 1262 ARG cc_start: 0.6319 (mtm110) cc_final: 0.6057 (mtp-110) REVERT: A 222 ARG cc_start: 0.5751 (mtt180) cc_final: 0.5482 (ttm110) REVERT: A 891 VAL cc_start: 0.3520 (p) cc_final: 0.2027 (t) outliers start: 6 outliers final: 2 residues processed: 566 average time/residue: 0.3489 time to fit residues: 283.3398 Evaluate side-chains 326 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 324 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain A residue 948 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 192 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 67 ASN C 619 ASN C 662 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 HIS C 821 HIS ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 ASN ** C1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN A 161 HIS A 194 ASN A 206 GLN A 231 HIS A 293 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN A 518 GLN A 636 GLN A 760 ASN A 775 ASN A 916 ASN A1052 ASN A1061 ASN A1160 HIS ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17290 Z= 0.224 Angle : 0.770 11.228 23429 Z= 0.383 Chirality : 0.047 0.220 2662 Planarity : 0.006 0.066 3022 Dihedral : 7.127 51.912 2420 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.73 % Allowed : 12.48 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -3.35 (0.16), residues: 2123 helix: -1.27 (0.17), residues: 690 sheet: -2.21 (0.22), residues: 442 loop : -2.91 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 536 HIS 0.008 0.001 HIS A 804 PHE 0.033 0.002 PHE C 777 TYR 0.030 0.002 TYR C 830 ARG 0.010 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 378 time to evaluate : 2.079 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: C 721 ILE cc_start: 0.5355 (OUTLIER) cc_final: 0.4855 (mt) REVERT: C 1006 MET cc_start: 0.0712 (mmm) cc_final: 0.0422 (mmm) REVERT: C 1027 ARG cc_start: 0.6397 (mpt90) cc_final: 0.6063 (mmt180) REVERT: A 120 PHE cc_start: 0.5384 (m-80) cc_final: 0.5131 (m-80) REVERT: A 320 ASP cc_start: 0.7712 (p0) cc_final: 0.7453 (p0) REVERT: A 321 MET cc_start: 0.6215 (mmt) cc_final: 0.5905 (mmt) REVERT: A 414 ASP cc_start: 0.7569 (t0) cc_final: 0.7318 (t0) REVERT: A 447 MET cc_start: 0.2133 (mmm) cc_final: 0.1755 (mmm) REVERT: A 1173 VAL cc_start: 0.7707 (t) cc_final: 0.7340 (t) REVERT: A 1210 ASP cc_start: 0.6939 (m-30) cc_final: 0.6631 (t70) outliers start: 69 outliers final: 30 residues processed: 422 average time/residue: 0.2948 time to fit residues: 186.4612 Evaluate side-chains 309 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 278 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 912 ASN Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1112 THR Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1189 SER Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1138 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 208 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 154 optimal weight: 50.0000 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1283 HIS ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 HIS A 666 ASN A 760 ASN A 791 HIS A 804 HIS A 818 GLN A 885 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17290 Z= 0.260 Angle : 0.766 10.856 23429 Z= 0.384 Chirality : 0.047 0.236 2662 Planarity : 0.006 0.064 3022 Dihedral : 6.231 58.032 2418 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.92 % Favored : 93.03 % Rotamer: Outliers : 3.94 % Allowed : 15.67 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.17), residues: 2123 helix: -0.47 (0.19), residues: 686 sheet: -1.98 (0.23), residues: 431 loop : -2.64 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 536 HIS 0.050 0.002 HIS C 692 PHE 0.043 0.002 PHE C 632 TYR 0.020 0.002 TYR C 864 ARG 0.011 0.001 ARG C 614 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 305 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 498 MET cc_start: 0.0879 (OUTLIER) cc_final: 0.0302 (mpp) REVERT: C 511 MET cc_start: 0.6687 (mtt) cc_final: 0.5697 (mmt) REVERT: C 721 ILE cc_start: 0.5437 (OUTLIER) cc_final: 0.4908 (mt) REVERT: C 932 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8631 (tp) REVERT: C 1009 MET cc_start: 0.6685 (tpp) cc_final: 0.4801 (mmm) REVERT: A 447 MET cc_start: 0.2347 (mmm) cc_final: 0.2099 (mmm) REVERT: A 583 MET cc_start: -0.1431 (mmt) cc_final: -0.3033 (pmm) REVERT: A 1128 ILE cc_start: 0.7293 (pt) cc_final: 0.7071 (pt) REVERT: A 1185 MET cc_start: 0.6995 (mmm) cc_final: 0.6762 (tpp) outliers start: 73 outliers final: 48 residues processed: 352 average time/residue: 0.2650 time to fit residues: 144.2146 Evaluate side-chains 317 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 266 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 875 ILE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 978 LEU Chi-restraints excluded: chain C residue 1069 HIS Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1112 THR Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain C residue 1226 VAL Chi-restraints excluded: chain C residue 1271 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1138 HIS Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 92 optimal weight: 0.0870 chunk 129 optimal weight: 0.6980 chunk 193 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 692 HIS ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 886 HIS ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17290 Z= 0.231 Angle : 0.698 10.147 23429 Z= 0.350 Chirality : 0.045 0.199 2662 Planarity : 0.005 0.054 3022 Dihedral : 5.696 46.652 2418 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.38 % Allowed : 17.07 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.17), residues: 2123 helix: -0.18 (0.19), residues: 690 sheet: -1.82 (0.23), residues: 456 loop : -2.52 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 31 HIS 0.006 0.001 HIS B 46 PHE 0.017 0.001 PHE A 788 TYR 0.023 0.001 TYR C 587 ARG 0.006 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 284 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 511 MET cc_start: 0.6753 (mtt) cc_final: 0.5684 (mmt) REVERT: C 721 ILE cc_start: 0.5718 (OUTLIER) cc_final: 0.5131 (mt) REVERT: C 752 TYR cc_start: 0.6818 (m-10) cc_final: 0.6504 (m-80) REVERT: C 932 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8725 (tp) REVERT: C 1041 ARG cc_start: 0.5763 (mmm160) cc_final: 0.5490 (tpt90) REVERT: A 39 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 135 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7781 (mt) REVERT: A 321 MET cc_start: 0.6442 (mmt) cc_final: 0.5939 (mmm) REVERT: A 325 ILE cc_start: 0.8019 (mm) cc_final: 0.7679 (mt) REVERT: A 447 MET cc_start: 0.2339 (mmm) cc_final: 0.2092 (mmm) REVERT: A 1185 MET cc_start: 0.7292 (mmm) cc_final: 0.6757 (tpp) outliers start: 81 outliers final: 53 residues processed: 335 average time/residue: 0.2819 time to fit residues: 145.6019 Evaluate side-chains 314 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 258 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 556 ILE Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 875 ILE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 978 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1069 HIS Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1145 ASN Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain C residue 1226 VAL Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1138 HIS Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 141 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 36 HIS C 547 GLN C 692 HIS ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 760 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1183 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.8349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 17290 Z= 0.339 Angle : 0.776 9.724 23429 Z= 0.400 Chirality : 0.048 0.179 2662 Planarity : 0.006 0.079 3022 Dihedral : 5.934 37.437 2418 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 5.13 % Allowed : 17.23 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.17), residues: 2123 helix: -0.37 (0.19), residues: 708 sheet: -1.79 (0.23), residues: 432 loop : -2.59 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C1266 HIS 0.013 0.002 HIS C 692 PHE 0.019 0.002 PHE A 788 TYR 0.030 0.002 TYR C 752 ARG 0.014 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 274 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 LEU cc_start: 0.8609 (tp) cc_final: 0.8276 (tt) REVERT: C 511 MET cc_start: 0.5640 (mtt) cc_final: 0.5228 (mmt) REVERT: C 612 THR cc_start: 0.6714 (m) cc_final: 0.6496 (p) REVERT: C 770 MET cc_start: 0.5843 (ppp) cc_final: 0.5619 (ptt) REVERT: C 898 TYR cc_start: 0.5607 (OUTLIER) cc_final: 0.4637 (t80) REVERT: C 1037 ASP cc_start: 0.7270 (m-30) cc_final: 0.6935 (m-30) REVERT: C 1155 PHE cc_start: 0.7328 (m-80) cc_final: 0.7116 (m-80) REVERT: A 1 MET cc_start: 0.5869 (ttt) cc_final: 0.4742 (tpt) REVERT: A 199 GLU cc_start: 0.6232 (tp30) cc_final: 0.5884 (pm20) REVERT: A 321 MET cc_start: 0.6528 (mmt) cc_final: 0.6082 (mmm) REVERT: A 447 MET cc_start: 0.2390 (mmm) cc_final: 0.2172 (mmm) REVERT: A 706 MET cc_start: -0.1795 (tpt) cc_final: -0.2164 (tpt) REVERT: A 889 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7022 (m-10) REVERT: A 1166 TYR cc_start: 0.7274 (t80) cc_final: 0.6858 (t80) outliers start: 95 outliers final: 63 residues processed: 335 average time/residue: 0.2892 time to fit residues: 148.5974 Evaluate side-chains 298 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 233 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 556 ILE Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 898 TYR Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 978 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1069 HIS Chi-restraints excluded: chain C residue 1091 HIS Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1145 ASN Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain C residue 1172 LEU Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 SER Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain C residue 1271 SER Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1138 HIS Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 205 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 67 ASN C 692 HIS ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1277 GLN ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.8622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17290 Z= 0.175 Angle : 0.687 9.384 23429 Z= 0.338 Chirality : 0.045 0.280 2662 Planarity : 0.004 0.048 3022 Dihedral : 5.312 30.028 2418 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.13 % Allowed : 20.15 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.18), residues: 2123 helix: -0.07 (0.20), residues: 708 sheet: -1.56 (0.24), residues: 435 loop : -2.45 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C1216 HIS 0.006 0.001 HIS C 692 PHE 0.019 0.001 PHE C1155 TYR 0.015 0.001 TYR A 224 ARG 0.007 0.000 ARG C 549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 277 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 511 MET cc_start: 0.5682 (mtt) cc_final: 0.5370 (mmt) REVERT: C 692 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.7199 (t70) REVERT: C 867 MET cc_start: 0.8001 (ptp) cc_final: 0.7677 (ttt) REVERT: C 898 TYR cc_start: 0.5405 (OUTLIER) cc_final: 0.4521 (t80) REVERT: C 933 CYS cc_start: 0.6676 (m) cc_final: 0.5381 (t) REVERT: C 1246 MET cc_start: 0.6383 (mtp) cc_final: 0.6075 (mtm) REVERT: A 1 MET cc_start: 0.5894 (ttt) cc_final: 0.4869 (tpt) REVERT: A 321 MET cc_start: 0.6374 (mmt) cc_final: 0.5886 (mmm) REVERT: A 706 MET cc_start: -0.1846 (tpt) cc_final: -0.2068 (tpt) REVERT: A 889 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.6754 (m-10) REVERT: A 1185 MET cc_start: 0.7979 (tpp) cc_final: 0.7364 (mmm) outliers start: 58 outliers final: 42 residues processed: 316 average time/residue: 0.2512 time to fit residues: 124.1194 Evaluate side-chains 293 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 248 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 556 ILE Chi-restraints excluded: chain C residue 613 MET Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 898 TYR Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1145 ASN Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1138 HIS Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 116 optimal weight: 0.3980 chunk 149 optimal weight: 50.0000 chunk 172 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 692 HIS ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS A 760 ASN A 941 HIS ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.9102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17290 Z= 0.233 Angle : 0.707 12.470 23429 Z= 0.349 Chirality : 0.045 0.208 2662 Planarity : 0.005 0.047 3022 Dihedral : 5.322 31.487 2418 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.73 % Allowed : 20.15 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.18), residues: 2123 helix: -0.12 (0.20), residues: 706 sheet: -1.45 (0.24), residues: 437 loop : -2.52 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C1216 HIS 0.011 0.001 HIS C 692 PHE 0.029 0.002 PHE A 59 TYR 0.018 0.002 TYR A1014 ARG 0.006 0.001 ARG C 957 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 254 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6243 (pm20) REVERT: C 692 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7261 (t70) REVERT: C 784 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6309 (mmt) REVERT: C 823 MET cc_start: 0.3522 (OUTLIER) cc_final: 0.2498 (mmm) REVERT: C 898 TYR cc_start: 0.5554 (OUTLIER) cc_final: 0.4615 (t80) REVERT: C 933 CYS cc_start: 0.6625 (m) cc_final: 0.5502 (t) REVERT: C 1246 MET cc_start: 0.6474 (mtp) cc_final: 0.6172 (mtm) REVERT: A 1 MET cc_start: 0.5968 (ttt) cc_final: 0.5134 (tpt) REVERT: A 199 GLU cc_start: 0.6927 (tp30) cc_final: 0.6183 (pp20) REVERT: A 706 MET cc_start: -0.1695 (tpt) cc_final: -0.1905 (tpt) REVERT: A 889 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.6874 (m-10) REVERT: A 1093 MET cc_start: 0.6981 (mmm) cc_final: 0.6717 (tpp) REVERT: A 1146 MET cc_start: 0.8306 (ppp) cc_final: 0.7912 (ppp) outliers start: 69 outliers final: 48 residues processed: 297 average time/residue: 0.2658 time to fit residues: 123.6322 Evaluate side-chains 290 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 236 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 556 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 613 MET Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 898 TYR Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1145 ASN Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1138 HIS Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 692 HIS ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.9605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17290 Z= 0.258 Angle : 0.737 12.145 23429 Z= 0.362 Chirality : 0.046 0.175 2662 Planarity : 0.005 0.047 3022 Dihedral : 5.443 32.554 2418 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.27 % Allowed : 19.72 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.18), residues: 2123 helix: -0.19 (0.20), residues: 698 sheet: -1.42 (0.24), residues: 431 loop : -2.50 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C1216 HIS 0.016 0.001 HIS C 692 PHE 0.021 0.002 PHE B 47 TYR 0.014 0.002 TYR C1269 ARG 0.012 0.001 ARG C 524 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 243 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 559 ILE cc_start: 0.5553 (OUTLIER) cc_final: 0.5113 (tp) REVERT: C 575 LEU cc_start: 0.6031 (pp) cc_final: 0.5785 (pp) REVERT: C 623 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: C 692 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7226 (t70) REVERT: C 757 MET cc_start: 0.8358 (tmm) cc_final: 0.8087 (tmm) REVERT: C 784 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6695 (mmt) REVERT: C 823 MET cc_start: 0.3630 (OUTLIER) cc_final: 0.2751 (mmm) REVERT: C 933 CYS cc_start: 0.6716 (m) cc_final: 0.5531 (t) REVERT: C 962 MET cc_start: 0.4940 (ttt) cc_final: 0.4634 (ttt) REVERT: C 1246 MET cc_start: 0.6383 (mtp) cc_final: 0.6134 (mtt) REVERT: D 79 GLU cc_start: 0.8484 (tp30) cc_final: 0.8158 (tp30) REVERT: A 1 MET cc_start: 0.5897 (ttt) cc_final: 0.5126 (tpt) REVERT: A 186 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6607 (tp30) REVERT: A 199 GLU cc_start: 0.7001 (tp30) cc_final: 0.6648 (pt0) REVERT: A 889 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.6857 (m-10) outliers start: 79 outliers final: 60 residues processed: 295 average time/residue: 0.2611 time to fit residues: 120.5184 Evaluate side-chains 301 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 235 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 556 ILE Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 613 MET Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 978 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1091 HIS Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1145 ASN Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain C residue 1276 SER Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1138 HIS Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 149 optimal weight: 50.0000 chunk 58 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 189 optimal weight: 0.0870 chunk 125 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 692 HIS ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1007 HIS ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.9732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17290 Z= 0.181 Angle : 0.722 15.695 23429 Z= 0.347 Chirality : 0.045 0.291 2662 Planarity : 0.004 0.053 3022 Dihedral : 5.112 32.309 2418 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.70 % Allowed : 21.72 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.18), residues: 2123 helix: 0.05 (0.20), residues: 690 sheet: -1.16 (0.25), residues: 435 loop : -2.35 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C1216 HIS 0.009 0.001 HIS C 692 PHE 0.032 0.001 PHE A 59 TYR 0.017 0.001 TYR C 830 ARG 0.005 0.000 ARG C1259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 264 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 511 MET cc_start: 0.5604 (ptp) cc_final: 0.4069 (mtt) REVERT: C 545 GLU cc_start: 0.8421 (tp30) cc_final: 0.8187 (tp30) REVERT: C 559 ILE cc_start: 0.5625 (OUTLIER) cc_final: 0.5311 (tt) REVERT: C 623 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: C 692 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.6951 (t70) REVERT: C 757 MET cc_start: 0.8004 (tmm) cc_final: 0.7751 (tmm) REVERT: C 823 MET cc_start: 0.3685 (OUTLIER) cc_final: 0.2832 (mmm) REVERT: C 933 CYS cc_start: 0.6607 (m) cc_final: 0.5454 (t) REVERT: C 1246 MET cc_start: 0.6429 (mtp) cc_final: 0.6180 (mtm) REVERT: A 1 MET cc_start: 0.6109 (ttt) cc_final: 0.5087 (tpt) REVERT: A 447 MET cc_start: 0.1442 (mmm) cc_final: 0.0869 (mmp) REVERT: A 818 GLN cc_start: 0.8237 (tt0) cc_final: 0.8027 (tm-30) REVERT: A 889 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6441 (m-10) REVERT: A 1146 MET cc_start: 0.8368 (ppp) cc_final: 0.7942 (ppp) outliers start: 50 outliers final: 34 residues processed: 292 average time/residue: 0.2710 time to fit residues: 122.0203 Evaluate side-chains 278 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 239 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1145 ASN Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1138 HIS Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 5.9990 chunk 122 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 211 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 692 HIS ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1194 HIS ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN A 988 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.9987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17290 Z= 0.211 Angle : 0.725 13.934 23429 Z= 0.350 Chirality : 0.045 0.160 2662 Planarity : 0.004 0.067 3022 Dihedral : 5.138 32.992 2418 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.43 % Allowed : 21.88 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.18), residues: 2123 helix: 0.16 (0.20), residues: 676 sheet: -1.08 (0.24), residues: 438 loop : -2.33 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C1216 HIS 0.010 0.001 HIS C 692 PHE 0.020 0.001 PHE B 47 TYR 0.025 0.001 TYR C 752 ARG 0.006 0.000 ARG A 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 235 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.6739 (pm20) cc_final: 0.6456 (pm20) REVERT: C 511 MET cc_start: 0.5613 (ptp) cc_final: 0.4100 (mtt) REVERT: C 559 ILE cc_start: 0.5775 (OUTLIER) cc_final: 0.5464 (tt) REVERT: C 623 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: C 692 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.6827 (t70) REVERT: C 757 MET cc_start: 0.8041 (tmm) cc_final: 0.7804 (tmm) REVERT: C 823 MET cc_start: 0.3804 (OUTLIER) cc_final: 0.2850 (mmm) REVERT: C 1197 LEU cc_start: 0.6651 (pt) cc_final: 0.6246 (pp) REVERT: C 1246 MET cc_start: 0.6508 (mtp) cc_final: 0.6243 (mtm) REVERT: D 79 GLU cc_start: 0.8418 (tp30) cc_final: 0.8104 (tp30) REVERT: A 1 MET cc_start: 0.6208 (ttt) cc_final: 0.5130 (tpt) REVERT: A 447 MET cc_start: 0.1337 (mmm) cc_final: 0.0753 (mmp) REVERT: A 889 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.6837 (m-10) REVERT: A 1017 ASN cc_start: 0.8622 (p0) cc_final: 0.8305 (p0) REVERT: A 1093 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6646 (tpp) outliers start: 45 outliers final: 38 residues processed: 264 average time/residue: 0.2559 time to fit residues: 107.2736 Evaluate side-chains 276 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 232 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain C residue 632 PHE Chi-restraints excluded: chain C residue 682 HIS Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1145 ASN Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1225 HIS Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 736 TYR Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 889 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1138 HIS Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 6.9990 chunk 51 optimal weight: 0.0570 chunk 155 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 147 optimal weight: 50.0000 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN A 988 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.140960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.111101 restraints weight = 47564.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.111348 restraints weight = 29721.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.111893 restraints weight = 23687.201| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 1.0369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17290 Z= 0.264 Angle : 0.748 12.313 23429 Z= 0.368 Chirality : 0.046 0.182 2662 Planarity : 0.005 0.072 3022 Dihedral : 5.335 36.075 2418 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.81 % Allowed : 21.66 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.18), residues: 2123 helix: -0.13 (0.20), residues: 687 sheet: -1.14 (0.24), residues: 439 loop : -2.46 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C1216 HIS 0.017 0.001 HIS C 692 PHE 0.024 0.002 PHE C 900 TYR 0.027 0.002 TYR C 752 ARG 0.007 0.001 ARG A 815 =============================================================================== Job complete usr+sys time: 3596.81 seconds wall clock time: 65 minutes 42.74 seconds (3942.74 seconds total)