Starting phenix.real_space_refine on Fri Feb 16 22:10:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1h_8955/02_2024/6e1h_8955_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1h_8955/02_2024/6e1h_8955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1h_8955/02_2024/6e1h_8955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1h_8955/02_2024/6e1h_8955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1h_8955/02_2024/6e1h_8955_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1h_8955/02_2024/6e1h_8955_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.089 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 Ca 2 9.91 5 Zn 1 6.06 5 S 90 5.16 5 C 10834 2.51 5 N 2762 2.21 5 O 2978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 135": "NH1" <-> "NH2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 530": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 772": "NH1" <-> "NH2" Residue "A ARG 824": "NH1" <-> "NH2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 982": "NH1" <-> "NH2" Residue "A ARG 1150": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 530": "NH1" <-> "NH2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 772": "NH1" <-> "NH2" Residue "B ARG 786": "NH1" <-> "NH2" Residue "B ARG 942": "NH1" <-> "NH2" Residue "B TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 982": "NH1" <-> "NH2" Residue "B TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1025": "NH1" <-> "NH2" Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1150": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16667 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7667 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 40, 'TRANS': 937} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1313 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "B" Number of atoms: 7667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7667 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 40, 'TRANS': 937} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Unusual residues: {' CA': 2, ' ZN': 1, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 9.28, per 1000 atoms: 0.56 Number of scatterers: 16667 At special positions: 0 Unit cell: (154, 100, 148, 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 1 29.99 Ca 2 19.99 S 90 16.00 O 2978 8.00 N 2762 7.00 C 10834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.02 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 327 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.54 Conformation dependent library (CDL) restraints added in 3.2 seconds 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 5 sheets defined 52.4% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 removed outlier: 4.364A pdb=" N LEU A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 102 through 116 removed outlier: 4.307A pdb=" N PHE A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 276 through 282 removed outlier: 4.006A pdb=" N MET A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 389 through 410 Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 439 through 456 removed outlier: 3.507A pdb=" N TYR A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 490 Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 503 through 524 removed outlier: 4.299A pdb=" N LEU A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 517 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 562 removed outlier: 5.002A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 603 Proline residue: A 593 - end of helix removed outlier: 3.724A pdb=" N MET A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 742 through 744 No H-bonds generated for 'chain 'A' and resid 742 through 744' Processing helix chain 'A' and resid 747 through 769 Processing helix chain 'A' and resid 777 through 780 No H-bonds generated for 'chain 'A' and resid 777 through 780' Processing helix chain 'A' and resid 786 through 796 Processing helix chain 'A' and resid 817 through 826 removed outlier: 4.263A pdb=" N PHE A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 844 through 865 removed outlier: 3.878A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 888 Processing helix chain 'A' and resid 898 through 900 No H-bonds generated for 'chain 'A' and resid 898 through 900' Processing helix chain 'A' and resid 919 through 929 removed outlier: 3.807A pdb=" N SER A 928 " --> pdb=" O THR A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 937 Processing helix chain 'A' and resid 986 through 1004 Processing helix chain 'A' and resid 1013 through 1018 Processing helix chain 'A' and resid 1020 through 1022 No H-bonds generated for 'chain 'A' and resid 1020 through 1022' Processing helix chain 'A' and resid 1024 through 1047 Processing helix chain 'A' and resid 1050 through 1074 removed outlier: 3.665A pdb=" N GLY A1072 " --> pdb=" O PHE A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1103 removed outlier: 3.676A pdb=" N VAL A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY A1091 " --> pdb=" O ILE A1087 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A1103 " --> pdb=" O HIS A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1121 Processing helix chain 'A' and resid 1124 through 1140 removed outlier: 4.207A pdb=" N MET A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU A1140 " --> pdb=" O GLY A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1174 removed outlier: 4.978A pdb=" N LEU A1171 " --> pdb=" O GLY A1167 " (cutoff:3.500A) Proline residue: A1172 - end of helix Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 100 through 116 removed outlier: 3.553A pdb=" N SER C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 158 through 168 removed outlier: 3.729A pdb=" N VAL C 166 " --> pdb=" O ALA C 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 94 removed outlier: 3.985A pdb=" N LYS B 82 " --> pdb=" O TRP B 78 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS B 92 " --> pdb=" O PHE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 117 removed outlier: 4.958A pdb=" N GLY B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 276 through 284 removed outlier: 3.671A pdb=" N GLU B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 322 No H-bonds generated for 'chain 'B' and resid 319 through 322' Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 369 through 375 removed outlier: 3.789A pdb=" N GLU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 389 through 408 Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 439 through 456 removed outlier: 3.599A pdb=" N GLY B 445 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 490 Processing helix chain 'B' and resid 497 through 527 removed outlier: 4.279A pdb=" N GLN B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Proline residue: B 504 - end of helix removed outlier: 3.823A pdb=" N LEU B 518 " --> pdb=" O ASP B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 562 removed outlier: 4.234A pdb=" N ARG B 543 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU B 550 " --> pdb=" O ALA B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 605 Proline residue: B 593 - end of helix removed outlier: 3.771A pdb=" N TYR B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 602 " --> pdb=" O MET B 598 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP B 605 " --> pdb=" O TYR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 743 removed outlier: 3.797A pdb=" N ALA B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Proline residue: B 742 - end of helix Processing helix chain 'B' and resid 747 through 769 removed outlier: 3.548A pdb=" N TYR B 766 " --> pdb=" O GLY B 762 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 767 " --> pdb=" O VAL B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 779 No H-bonds generated for 'chain 'B' and resid 777 through 779' Processing helix chain 'B' and resid 786 through 796 removed outlier: 3.808A pdb=" N PHE B 790 " --> pdb=" O ARG B 786 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE B 791 " --> pdb=" O GLU B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 814 No H-bonds generated for 'chain 'B' and resid 812 through 814' Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.786A pdb=" N TYR B 820 " --> pdb=" O GLN B 816 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B 821 " --> pdb=" O HIS B 817 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER B 827 " --> pdb=" O HIS B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 837 No H-bonds generated for 'chain 'B' and resid 835 through 837' Processing helix chain 'B' and resid 844 through 863 Processing helix chain 'B' and resid 878 through 887 Processing helix chain 'B' and resid 916 through 929 removed outlier: 6.375A pdb=" N TYR B 920 " --> pdb=" O SER B 917 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 924 " --> pdb=" O ILE B 921 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 927 " --> pdb=" O THR B 924 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN B 929 " --> pdb=" O TRP B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 936 Processing helix chain 'B' and resid 986 through 1003 removed outlier: 3.535A pdb=" N THR B1002 " --> pdb=" O CYS B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1017 No H-bonds generated for 'chain 'B' and resid 1014 through 1017' Processing helix chain 'B' and resid 1024 through 1046 removed outlier: 4.299A pdb=" N SER B1033 " --> pdb=" O LEU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1074 Processing helix chain 'B' and resid 1080 through 1103 removed outlier: 3.902A pdb=" N GLY B1091 " --> pdb=" O ILE B1087 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B1100 " --> pdb=" O PHE B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1121 Processing helix chain 'B' and resid 1123 through 1142 removed outlier: 4.327A pdb=" N GLY B1142 " --> pdb=" O LEU B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1168 Processing helix chain 'B' and resid 1171 through 1174 No H-bonds generated for 'chain 'B' and resid 1171 through 1174' Processing sheet with id= A, first strand: chain 'A' and resid 417 through 422 Processing sheet with id= B, first strand: chain 'A' and resid 972 through 979 removed outlier: 3.800A pdb=" N ASN A1011 " --> pdb=" O TYR A 804 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 84 through 86 removed outlier: 6.875A pdb=" N LEU C 122 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP C 147 " --> pdb=" O THR C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 359 through 363 Processing sheet with id= E, first strand: chain 'B' and resid 972 through 979 removed outlier: 3.530A pdb=" N ILE B 805 " --> pdb=" O PHE B 974 " (cutoff:3.500A) 773 hydrogen bonds defined for protein. 2271 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: 5.00 Time building geometry restraints manager: 7.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2903 1.32 - 1.45: 4542 1.45 - 1.57: 9476 1.57 - 1.70: 1 1.70 - 1.82: 147 Bond restraints: 17069 Sorted by residual: bond pdb=" N LEU B1048 " pdb=" CA LEU B1048 " ideal model delta sigma weight residual 1.457 1.513 -0.056 1.29e-02 6.01e+03 1.88e+01 bond pdb=" N CYS C 24 " pdb=" CA CYS C 24 " ideal model delta sigma weight residual 1.458 1.532 -0.074 1.90e-02 2.77e+03 1.51e+01 bond pdb=" CA PLM C 204 " pdb=" CB PLM C 204 " ideal model delta sigma weight residual 1.524 1.600 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" N LEU A 297 " pdb=" CA LEU A 297 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.15e-02 7.56e+03 1.13e+01 bond pdb=" C CYS B 304 " pdb=" N PRO B 305 " ideal model delta sigma weight residual 1.334 1.362 -0.028 8.40e-03 1.42e+04 1.11e+01 ... (remaining 17064 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.79: 411 105.79 - 112.96: 8788 112.96 - 120.13: 7027 120.13 - 127.30: 6798 127.30 - 134.46: 172 Bond angle restraints: 23196 Sorted by residual: angle pdb=" N PRO A 896 " pdb=" CA PRO A 896 " pdb=" CB PRO A 896 " ideal model delta sigma weight residual 103.25 110.79 -7.54 1.05e+00 9.07e-01 5.16e+01 angle pdb=" N PRO B 896 " pdb=" CA PRO B 896 " pdb=" CB PRO B 896 " ideal model delta sigma weight residual 103.25 110.52 -7.27 1.05e+00 9.07e-01 4.80e+01 angle pdb=" N PRO A 225 " pdb=" CA PRO A 225 " pdb=" C PRO A 225 " ideal model delta sigma weight residual 112.47 123.89 -11.42 2.06e+00 2.36e-01 3.07e+01 angle pdb=" C PHE A 101 " pdb=" N LEU A 102 " pdb=" CA LEU A 102 " ideal model delta sigma weight residual 120.44 126.73 -6.29 1.30e+00 5.92e-01 2.34e+01 angle pdb=" N PRO B 225 " pdb=" CA PRO B 225 " pdb=" C PRO B 225 " ideal model delta sigma weight residual 113.84 119.99 -6.15 1.30e+00 5.92e-01 2.24e+01 ... (remaining 23191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 9273 16.82 - 33.65: 665 33.65 - 50.47: 125 50.47 - 67.29: 11 67.29 - 84.11: 9 Dihedral angle restraints: 10083 sinusoidal: 3909 harmonic: 6174 Sorted by residual: dihedral pdb=" CB CYS A 203 " pdb=" SG CYS A 203 " pdb=" SG CYS A 226 " pdb=" CB CYS A 226 " ideal model delta sinusoidal sigma weight residual -86.00 -154.07 68.07 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CA TRP A 197 " pdb=" C TRP A 197 " pdb=" N LYS A 198 " pdb=" CA LYS A 198 " ideal model delta harmonic sigma weight residual -180.00 -144.31 -35.69 0 5.00e+00 4.00e-02 5.10e+01 dihedral pdb=" CA TRP B 197 " pdb=" C TRP B 197 " pdb=" N LYS B 198 " pdb=" CA LYS B 198 " ideal model delta harmonic sigma weight residual 180.00 -146.84 -33.16 0 5.00e+00 4.00e-02 4.40e+01 ... (remaining 10080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1743 0.059 - 0.118: 711 0.118 - 0.177: 159 0.177 - 0.236: 15 0.236 - 0.295: 4 Chirality restraints: 2632 Sorted by residual: chirality pdb=" CA PRO A 225 " pdb=" N PRO A 225 " pdb=" C PRO A 225 " pdb=" CB PRO A 225 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB ILE B 210 " pdb=" CA ILE B 210 " pdb=" CG1 ILE B 210 " pdb=" CG2 ILE B 210 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ASN B 584 " pdb=" N ASN B 584 " pdb=" C ASN B 584 " pdb=" CB ASN B 584 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2629 not shown) Planarity restraints: 2921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 894 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C ASP B 894 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP B 894 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS B 895 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 197 " -0.029 2.00e-02 2.50e+03 1.82e-02 8.30e+00 pdb=" CG TRP A 197 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 197 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 197 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 197 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 197 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 197 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 197 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 197 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 197 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 197 " -0.027 2.00e-02 2.50e+03 1.70e-02 7.20e+00 pdb=" CG TRP B 197 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 197 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP B 197 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 197 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 197 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 197 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 197 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 197 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 197 " -0.001 2.00e-02 2.50e+03 ... (remaining 2918 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 71 2.55 - 3.14: 12448 3.14 - 3.72: 26735 3.72 - 4.31: 36383 4.31 - 4.90: 59162 Nonbonded interactions: 134799 Sorted by model distance: nonbonded pdb=" O THR C 125 " pdb="CA CA C 202 " model vdw 1.962 2.510 nonbonded pdb=" O SER C 135 " pdb=" OH TYR C 141 " model vdw 2.272 2.440 nonbonded pdb="CA CA C 202 " pdb="CA CA C 203 " model vdw 2.272 1.980 nonbonded pdb=" O PRO B 309 " pdb=" N SER B 313 " model vdw 2.296 2.520 nonbonded pdb=" O TYR A 766 " pdb=" OG1 THR A 769 " model vdw 2.315 2.440 ... (remaining 134794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.580 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 46.110 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.008 0.076 17069 Z= 0.506 Angle : 1.176 11.420 23196 Z= 0.775 Chirality : 0.064 0.295 2632 Planarity : 0.005 0.041 2921 Dihedral : 12.247 84.113 6103 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.86 % Favored : 90.09 % Rotamer: Outliers : 1.76 % Allowed : 6.26 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.67 (0.15), residues: 2110 helix: -1.73 (0.13), residues: 1150 sheet: -3.11 (0.40), residues: 111 loop : -3.26 (0.18), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 197 HIS 0.007 0.001 HIS A 201 PHE 0.026 0.002 PHE B 790 TYR 0.034 0.003 TYR A 224 ARG 0.006 0.001 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 665 time to evaluate : 1.885 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: A 84 GLN cc_start: 0.8701 (pt0) cc_final: 0.7982 (pt0) REVERT: A 157 LEU cc_start: 0.8967 (mp) cc_final: 0.8559 (mt) REVERT: A 373 TYR cc_start: 0.8180 (t80) cc_final: 0.7899 (t80) REVERT: A 428 ASP cc_start: 0.8281 (t70) cc_final: 0.7736 (t0) REVERT: A 567 ILE cc_start: 0.8192 (mp) cc_final: 0.7671 (mt) REVERT: A 922 TYR cc_start: 0.7926 (m-80) cc_final: 0.7417 (m-80) REVERT: A 1028 LEU cc_start: 0.8954 (tp) cc_final: 0.8742 (tp) REVERT: A 1048 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5386 (tp) REVERT: A 1051 TRP cc_start: 0.4879 (t60) cc_final: 0.4602 (t60) REVERT: A 1063 MET cc_start: 0.8481 (mtp) cc_final: 0.8168 (mtp) REVERT: A 1162 LEU cc_start: 0.9140 (mt) cc_final: 0.8933 (mm) REVERT: A 1166 ASN cc_start: 0.7898 (m110) cc_final: 0.7460 (m110) REVERT: C 39 LEU cc_start: 0.8580 (mt) cc_final: 0.8374 (mt) REVERT: C 114 MET cc_start: 0.8132 (mtm) cc_final: 0.7793 (mtm) REVERT: B 153 PHE cc_start: 0.8108 (p90) cc_final: 0.6996 (p90) REVERT: B 158 MET cc_start: 0.7695 (ttp) cc_final: 0.7462 (ttp) REVERT: B 221 GLU cc_start: 0.7959 (tt0) cc_final: 0.7087 (tt0) REVERT: B 222 TYR cc_start: 0.7550 (m-80) cc_final: 0.7150 (m-10) REVERT: B 424 THR cc_start: 0.8698 (p) cc_final: 0.8491 (t) REVERT: B 432 LYS cc_start: 0.8878 (mttm) cc_final: 0.8448 (mmtt) REVERT: B 479 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6953 (mm) REVERT: B 835 GLU cc_start: 0.6978 (pp20) cc_final: 0.6680 (pp20) REVERT: B 882 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8394 (tm) REVERT: B 922 TYR cc_start: 0.8726 (m-10) cc_final: 0.8137 (m-80) REVERT: B 1028 LEU cc_start: 0.9088 (tp) cc_final: 0.8856 (tp) REVERT: B 1063 MET cc_start: 0.8688 (mtp) cc_final: 0.8325 (mtt) REVERT: B 1121 HIS cc_start: 0.7122 (p-80) cc_final: 0.6707 (p-80) outliers start: 31 outliers final: 7 residues processed: 683 average time/residue: 0.2957 time to fit residues: 297.1593 Evaluate side-chains 436 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 426 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1169 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 310 ASN A 324 ASN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS A 388 ASN A 527 GLN A 794 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 ASN A 929 ASN A1099 HIS C 140 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 310 ASN B 324 ASN B 358 HIS B 375 HIS ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN B 576 GLN B 584 ASN B 837 ASN B 872 ASN B 889 GLN ** B 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 940 ASN B1166 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17069 Z= 0.242 Angle : 0.748 12.814 23196 Z= 0.371 Chirality : 0.044 0.305 2632 Planarity : 0.005 0.066 2921 Dihedral : 7.119 58.197 2323 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.01 % Allowed : 15.59 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.17), residues: 2110 helix: -0.32 (0.15), residues: 1161 sheet: -2.67 (0.41), residues: 114 loop : -2.68 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 197 HIS 0.007 0.001 HIS A 201 PHE 0.055 0.002 PHE B 790 TYR 0.024 0.002 TYR C 62 ARG 0.006 0.001 ARG B 772 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 445 time to evaluate : 2.099 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: A 157 LEU cc_start: 0.8975 (mp) cc_final: 0.8673 (mt) REVERT: A 363 MET cc_start: 0.8303 (mtp) cc_final: 0.8023 (mtm) REVERT: A 428 ASP cc_start: 0.8318 (t70) cc_final: 0.7748 (t0) REVERT: A 598 MET cc_start: 0.7867 (mpp) cc_final: 0.7514 (mmt) REVERT: A 602 ARG cc_start: 0.7499 (mtt-85) cc_final: 0.7197 (mmt180) REVERT: A 764 SER cc_start: 0.8965 (p) cc_final: 0.8734 (t) REVERT: A 886 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8224 (mm) REVERT: A 922 TYR cc_start: 0.8073 (m-80) cc_final: 0.7597 (m-80) REVERT: A 1047 LEU cc_start: 0.8204 (mp) cc_final: 0.7941 (mt) REVERT: A 1048 LEU cc_start: 0.5705 (OUTLIER) cc_final: 0.5307 (tp) REVERT: A 1049 ASN cc_start: 0.8048 (m-40) cc_final: 0.7815 (m110) REVERT: A 1162 LEU cc_start: 0.9110 (mt) cc_final: 0.8816 (mm) REVERT: A 1166 ASN cc_start: 0.7659 (m110) cc_final: 0.7332 (m110) REVERT: B 221 GLU cc_start: 0.7958 (tt0) cc_final: 0.7280 (tt0) REVERT: B 222 TYR cc_start: 0.7579 (m-80) cc_final: 0.7334 (m-10) REVERT: B 332 ARG cc_start: 0.5162 (mpt-90) cc_final: 0.2021 (mpt-90) REVERT: B 377 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8574 (ttmm) REVERT: B 432 LYS cc_start: 0.8873 (mttm) cc_final: 0.8409 (mmtt) REVERT: B 534 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7397 (mp0) REVERT: B 541 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8269 (tt) REVERT: B 597 SER cc_start: 0.8587 (p) cc_final: 0.8369 (m) REVERT: B 788 TYR cc_start: 0.7357 (t80) cc_final: 0.7132 (t80) REVERT: B 882 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8582 (tm) REVERT: B 922 TYR cc_start: 0.8795 (m-10) cc_final: 0.8222 (m-80) outliers start: 88 outliers final: 42 residues processed: 497 average time/residue: 0.2575 time to fit residues: 199.0006 Evaluate side-chains 432 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 386 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 879 ASP Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 998 CYS Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1039 THR Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain B residue 1140 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS B 258 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 929 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17069 Z= 0.214 Angle : 0.703 9.845 23196 Z= 0.347 Chirality : 0.043 0.308 2632 Planarity : 0.004 0.068 2921 Dihedral : 6.469 59.394 2313 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 5.40 % Allowed : 19.00 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2110 helix: 0.24 (0.15), residues: 1156 sheet: -2.21 (0.44), residues: 115 loop : -2.44 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 197 HIS 0.006 0.001 HIS A 201 PHE 0.038 0.002 PHE B 790 TYR 0.020 0.002 TYR A 740 ARG 0.006 0.000 ARG B 770 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 410 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 MET cc_start: 0.8268 (mtp) cc_final: 0.7999 (mtm) REVERT: A 428 ASP cc_start: 0.8352 (t70) cc_final: 0.7793 (t0) REVERT: A 598 MET cc_start: 0.7850 (mpp) cc_final: 0.7538 (mmt) REVERT: A 602 ARG cc_start: 0.7508 (mtt-85) cc_final: 0.7182 (mmt180) REVERT: A 760 LEU cc_start: 0.8467 (tt) cc_final: 0.8135 (tt) REVERT: A 886 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8218 (mm) REVERT: A 922 TYR cc_start: 0.8076 (m-80) cc_final: 0.7690 (m-80) REVERT: A 1048 LEU cc_start: 0.5655 (OUTLIER) cc_final: 0.5323 (tp) REVERT: A 1049 ASN cc_start: 0.7968 (m-40) cc_final: 0.7731 (m-40) REVERT: A 1102 LEU cc_start: 0.8732 (tp) cc_final: 0.8497 (tp) REVERT: C 151 SER cc_start: 0.9267 (t) cc_final: 0.8858 (m) REVERT: B 93 TYR cc_start: 0.5185 (OUTLIER) cc_final: 0.4657 (t80) REVERT: B 221 GLU cc_start: 0.7956 (tt0) cc_final: 0.7314 (tt0) REVERT: B 332 ARG cc_start: 0.5214 (mpt-90) cc_final: 0.2037 (mpt-90) REVERT: B 377 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8566 (ttmm) REVERT: B 432 LYS cc_start: 0.8835 (mttm) cc_final: 0.8354 (mmtt) REVERT: B 536 ARG cc_start: 0.6315 (ttt90) cc_final: 0.6074 (tpt-90) REVERT: B 541 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8108 (tt) REVERT: B 922 TYR cc_start: 0.8843 (m-10) cc_final: 0.8116 (m-80) REVERT: B 1058 MET cc_start: 0.8489 (mtm) cc_final: 0.8246 (mtt) outliers start: 95 outliers final: 54 residues processed: 467 average time/residue: 0.2417 time to fit residues: 179.0139 Evaluate side-chains 436 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 378 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 879 ASP Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 998 CYS Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1039 THR Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain B residue 1169 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 0.0070 chunk 191 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A1099 HIS C 107 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 837 ASN B 929 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17069 Z= 0.195 Angle : 0.685 9.945 23196 Z= 0.335 Chirality : 0.042 0.237 2632 Planarity : 0.004 0.056 2921 Dihedral : 6.210 59.702 2313 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.29 % Allowed : 20.88 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2110 helix: 0.54 (0.15), residues: 1151 sheet: -1.99 (0.46), residues: 115 loop : -2.34 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1027 HIS 0.005 0.001 HIS B 950 PHE 0.031 0.001 PHE B 790 TYR 0.021 0.002 TYR B 788 ARG 0.005 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 411 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8425 (t) REVERT: A 216 MET cc_start: 0.7904 (mmm) cc_final: 0.7595 (mmm) REVERT: A 428 ASP cc_start: 0.8332 (t70) cc_final: 0.7792 (t0) REVERT: A 429 ASP cc_start: 0.7234 (m-30) cc_final: 0.6981 (m-30) REVERT: A 602 ARG cc_start: 0.7523 (mtt-85) cc_final: 0.7142 (mmt180) REVERT: A 886 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8254 (mm) REVERT: A 1049 ASN cc_start: 0.7834 (m-40) cc_final: 0.7602 (m-40) REVERT: C 151 SER cc_start: 0.9202 (t) cc_final: 0.8840 (m) REVERT: B 93 TYR cc_start: 0.5218 (OUTLIER) cc_final: 0.4773 (t80) REVERT: B 158 MET cc_start: 0.7831 (ttm) cc_final: 0.7597 (ttp) REVERT: B 222 TYR cc_start: 0.7486 (m-10) cc_final: 0.7212 (m-10) REVERT: B 377 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8550 (ttmm) REVERT: B 432 LYS cc_start: 0.8835 (mttm) cc_final: 0.8352 (mmmt) REVERT: B 585 PHE cc_start: 0.8214 (t80) cc_final: 0.7971 (t80) REVERT: B 845 LEU cc_start: 0.9189 (tt) cc_final: 0.8960 (tp) REVERT: B 922 TYR cc_start: 0.8838 (m-10) cc_final: 0.7943 (m-80) REVERT: B 1040 PHE cc_start: 0.7405 (t80) cc_final: 0.7131 (t80) REVERT: B 1058 MET cc_start: 0.8554 (mtm) cc_final: 0.8329 (mtt) outliers start: 93 outliers final: 63 residues processed: 465 average time/residue: 0.2447 time to fit residues: 180.3759 Evaluate side-chains 439 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 373 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 879 ASP Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 998 CYS Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1039 THR Chi-restraints excluded: chain B residue 1049 ASN Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain B residue 1169 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 151 optimal weight: 0.0770 chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 929 ASN B1121 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17069 Z= 0.329 Angle : 0.741 9.750 23196 Z= 0.370 Chirality : 0.045 0.367 2632 Planarity : 0.005 0.074 2921 Dihedral : 6.262 56.895 2313 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 5.75 % Allowed : 21.33 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 2110 helix: 0.67 (0.15), residues: 1152 sheet: -1.83 (0.48), residues: 115 loop : -2.29 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 197 HIS 0.008 0.001 HIS B 950 PHE 0.029 0.002 PHE B 790 TYR 0.026 0.002 TYR B 788 ARG 0.006 0.001 ARG B 770 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 379 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8844 (tp) REVERT: A 428 ASP cc_start: 0.8429 (t70) cc_final: 0.7924 (t70) REVERT: A 457 MET cc_start: 0.7917 (mmm) cc_final: 0.7641 (mmm) REVERT: A 501 GLN cc_start: 0.7634 (mt0) cc_final: 0.7341 (mt0) REVERT: A 598 MET cc_start: 0.8033 (mpp) cc_final: 0.7656 (mmt) REVERT: A 602 ARG cc_start: 0.7512 (mtt-85) cc_final: 0.7122 (mmt180) REVERT: A 886 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8295 (mm) REVERT: A 889 GLN cc_start: 0.8195 (tt0) cc_final: 0.7964 (tt0) REVERT: A 922 TYR cc_start: 0.8463 (m-10) cc_final: 0.8120 (m-80) REVERT: A 977 TYR cc_start: 0.8095 (m-10) cc_final: 0.7750 (m-80) REVERT: A 1049 ASN cc_start: 0.8030 (m-40) cc_final: 0.7751 (m-40) REVERT: B 93 TYR cc_start: 0.5442 (OUTLIER) cc_final: 0.4872 (t80) REVERT: B 138 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7903 (ptm-80) REVERT: B 221 GLU cc_start: 0.7916 (tt0) cc_final: 0.7659 (tt0) REVERT: B 222 TYR cc_start: 0.7525 (m-10) cc_final: 0.6997 (m-10) REVERT: B 332 ARG cc_start: 0.5062 (mpt-90) cc_final: 0.1756 (mpt-90) REVERT: B 432 LYS cc_start: 0.8929 (mttm) cc_final: 0.8439 (mmtt) REVERT: B 452 TYR cc_start: 0.8387 (t80) cc_final: 0.8064 (t80) REVERT: B 499 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8185 (t) REVERT: B 516 PHE cc_start: 0.8824 (m-80) cc_final: 0.7909 (m-10) REVERT: B 585 PHE cc_start: 0.8233 (t80) cc_final: 0.7906 (t80) REVERT: B 598 MET cc_start: 0.7399 (tpt) cc_final: 0.7196 (tpt) REVERT: B 886 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9027 (mm) REVERT: B 922 TYR cc_start: 0.8898 (m-10) cc_final: 0.8141 (m-80) REVERT: B 1040 PHE cc_start: 0.7511 (t80) cc_final: 0.7075 (t80) outliers start: 101 outliers final: 69 residues processed: 437 average time/residue: 0.2458 time to fit residues: 172.1626 Evaluate side-chains 436 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 362 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 879 ASP Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 998 CYS Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1038 CYS Chi-restraints excluded: chain B residue 1039 THR Chi-restraints excluded: chain B residue 1049 ASN Chi-restraints excluded: chain B residue 1064 THR Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain B residue 1169 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 218 GLN B 242 GLN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 ASN B 929 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17069 Z= 0.270 Angle : 0.720 10.692 23196 Z= 0.354 Chirality : 0.044 0.314 2632 Planarity : 0.005 0.071 2921 Dihedral : 6.101 59.443 2310 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 5.18 % Allowed : 22.53 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 2110 helix: 0.74 (0.15), residues: 1151 sheet: -1.71 (0.49), residues: 115 loop : -2.26 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B1027 HIS 0.005 0.001 HIS A 950 PHE 0.025 0.002 PHE B 790 TYR 0.026 0.002 TYR B 788 ARG 0.005 0.000 ARG B 770 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 382 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 MET cc_start: 0.7979 (mmm) cc_final: 0.7645 (mmm) REVERT: A 427 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8818 (tp) REVERT: A 587 MET cc_start: 0.8165 (tmm) cc_final: 0.7812 (tmm) REVERT: A 602 ARG cc_start: 0.7502 (mtt-85) cc_final: 0.7098 (mmt180) REVERT: A 886 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8339 (mm) REVERT: A 1049 ASN cc_start: 0.8064 (m-40) cc_final: 0.7728 (m-40) REVERT: B 93 TYR cc_start: 0.5484 (OUTLIER) cc_final: 0.5019 (t80) REVERT: B 138 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7922 (ptm-80) REVERT: B 221 GLU cc_start: 0.7922 (tt0) cc_final: 0.7659 (tt0) REVERT: B 222 TYR cc_start: 0.7636 (m-10) cc_final: 0.7212 (m-10) REVERT: B 332 ARG cc_start: 0.5043 (mpt-90) cc_final: 0.1777 (mpt-90) REVERT: B 432 LYS cc_start: 0.8915 (mttm) cc_final: 0.8431 (mmtt) REVERT: B 516 PHE cc_start: 0.8807 (m-80) cc_final: 0.8371 (m-80) REVERT: B 585 PHE cc_start: 0.8219 (t80) cc_final: 0.7922 (t80) REVERT: B 598 MET cc_start: 0.7559 (tpt) cc_final: 0.7321 (tpt) REVERT: B 808 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: B 922 TYR cc_start: 0.8907 (m-10) cc_final: 0.8063 (m-80) REVERT: B 1040 PHE cc_start: 0.7522 (t80) cc_final: 0.7001 (t80) outliers start: 91 outliers final: 64 residues processed: 426 average time/residue: 0.2378 time to fit residues: 161.7553 Evaluate side-chains 426 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 358 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 808 GLN Chi-restraints excluded: chain B residue 998 CYS Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1038 CYS Chi-restraints excluded: chain B residue 1039 THR Chi-restraints excluded: chain B residue 1049 ASN Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain B residue 1169 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 115 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 126 optimal weight: 0.1980 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A1020 GLN A1099 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 324 ASN B 358 HIS ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 837 ASN B 929 ASN B1099 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17069 Z= 0.196 Angle : 0.705 12.884 23196 Z= 0.341 Chirality : 0.042 0.255 2632 Planarity : 0.005 0.080 2921 Dihedral : 5.862 59.484 2310 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.72 % Allowed : 23.78 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.19), residues: 2110 helix: 0.88 (0.15), residues: 1139 sheet: -1.57 (0.49), residues: 115 loop : -2.16 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B1027 HIS 0.005 0.001 HIS A 950 PHE 0.025 0.001 PHE B 153 TYR 0.024 0.001 TYR B 788 ARG 0.011 0.001 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 402 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.8619 (p) cc_final: 0.8356 (t) REVERT: A 216 MET cc_start: 0.7825 (mmm) cc_final: 0.7483 (mmm) REVERT: A 221 GLU cc_start: 0.8461 (tp30) cc_final: 0.8066 (tp30) REVERT: A 587 MET cc_start: 0.8174 (tmm) cc_final: 0.7828 (tmm) REVERT: A 598 MET cc_start: 0.7979 (mpp) cc_final: 0.7630 (mmt) REVERT: A 602 ARG cc_start: 0.7508 (mtt-85) cc_final: 0.7091 (mmt180) REVERT: A 886 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8327 (mm) REVERT: A 1049 ASN cc_start: 0.8069 (m-40) cc_final: 0.7845 (m-40) REVERT: B 93 TYR cc_start: 0.5259 (OUTLIER) cc_final: 0.4790 (t80) REVERT: B 221 GLU cc_start: 0.7918 (tt0) cc_final: 0.7589 (tt0) REVERT: B 222 TYR cc_start: 0.7424 (m-10) cc_final: 0.7005 (m-10) REVERT: B 332 ARG cc_start: 0.4960 (mpt-90) cc_final: 0.1668 (mpt-90) REVERT: B 432 LYS cc_start: 0.8880 (mttm) cc_final: 0.8442 (mmmt) REVERT: B 585 PHE cc_start: 0.8223 (t80) cc_final: 0.7979 (t80) REVERT: B 882 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8354 (tm) REVERT: B 922 TYR cc_start: 0.8914 (m-10) cc_final: 0.8045 (m-80) REVERT: B 961 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7947 (pp) REVERT: B 1040 PHE cc_start: 0.7407 (t80) cc_final: 0.6829 (t80) outliers start: 83 outliers final: 61 residues processed: 445 average time/residue: 0.2439 time to fit residues: 173.0848 Evaluate side-chains 439 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 374 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 773 ASP Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 998 CYS Chi-restraints excluded: chain B residue 1038 CYS Chi-restraints excluded: chain B residue 1039 THR Chi-restraints excluded: chain B residue 1049 ASN Chi-restraints excluded: chain B residue 1064 THR Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1122 MET Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain B residue 1169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 358 HIS ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1099 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17069 Z= 0.314 Angle : 0.753 11.567 23196 Z= 0.368 Chirality : 0.045 0.295 2632 Planarity : 0.005 0.076 2921 Dihedral : 5.974 56.825 2310 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 5.40 % Allowed : 23.66 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 2110 helix: 0.87 (0.15), residues: 1144 sheet: -1.60 (0.49), residues: 117 loop : -2.19 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B1027 HIS 0.006 0.001 HIS B 950 PHE 0.064 0.002 PHE B 790 TYR 0.030 0.002 TYR B 788 ARG 0.007 0.001 ARG B1113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 373 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 MET cc_start: 0.7802 (mmm) cc_final: 0.7441 (mmm) REVERT: A 587 MET cc_start: 0.8194 (tmm) cc_final: 0.7961 (tmm) REVERT: A 598 MET cc_start: 0.8115 (mpp) cc_final: 0.7781 (mmt) REVERT: A 602 ARG cc_start: 0.7562 (mtt-85) cc_final: 0.7137 (mmt180) REVERT: A 886 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8376 (mm) REVERT: A 977 TYR cc_start: 0.8007 (m-10) cc_final: 0.7715 (m-80) REVERT: A 1049 ASN cc_start: 0.8308 (m-40) cc_final: 0.8068 (m-40) REVERT: B 93 TYR cc_start: 0.5636 (OUTLIER) cc_final: 0.5071 (t80) REVERT: B 127 GLU cc_start: 0.7472 (tp30) cc_final: 0.7262 (tp30) REVERT: B 222 TYR cc_start: 0.7626 (m-10) cc_final: 0.7378 (m-10) REVERT: B 332 ARG cc_start: 0.5002 (mpt-90) cc_final: 0.1713 (mpt-90) REVERT: B 432 LYS cc_start: 0.8912 (mttm) cc_final: 0.8461 (mmtt) REVERT: B 477 VAL cc_start: 0.8970 (t) cc_final: 0.8663 (p) REVERT: B 585 PHE cc_start: 0.8289 (t80) cc_final: 0.7988 (t80) REVERT: B 598 MET cc_start: 0.7581 (tpt) cc_final: 0.7341 (tpt) REVERT: B 808 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: B 922 TYR cc_start: 0.8951 (m-10) cc_final: 0.8215 (m-80) REVERT: B 961 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8085 (pp) REVERT: B 1032 ILE cc_start: 0.8934 (mm) cc_final: 0.8729 (mt) REVERT: B 1040 PHE cc_start: 0.7485 (t80) cc_final: 0.6857 (t80) REVERT: B 1165 LEU cc_start: 0.8867 (mt) cc_final: 0.8608 (mt) outliers start: 95 outliers final: 69 residues processed: 424 average time/residue: 0.2326 time to fit residues: 158.4432 Evaluate side-chains 435 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 362 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 808 GLN Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 998 CYS Chi-restraints excluded: chain B residue 1038 CYS Chi-restraints excluded: chain B residue 1039 THR Chi-restraints excluded: chain B residue 1049 ASN Chi-restraints excluded: chain B residue 1064 THR Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain B residue 1140 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 ASN B1099 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17069 Z= 0.306 Angle : 0.767 12.576 23196 Z= 0.373 Chirality : 0.045 0.281 2632 Planarity : 0.005 0.074 2921 Dihedral : 6.001 55.322 2310 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 4.61 % Allowed : 24.63 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 2110 helix: 0.83 (0.15), residues: 1136 sheet: -1.55 (0.49), residues: 117 loop : -2.22 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B1027 HIS 0.006 0.001 HIS A 950 PHE 0.057 0.002 PHE B 790 TYR 0.025 0.002 TYR B 788 ARG 0.005 0.000 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 370 time to evaluate : 2.024 Fit side-chains revert: symmetry clash REVERT: A 587 MET cc_start: 0.8234 (tmm) cc_final: 0.7958 (tmm) REVERT: A 598 MET cc_start: 0.8031 (mpp) cc_final: 0.7677 (mmt) REVERT: A 602 ARG cc_start: 0.7573 (mtt-85) cc_final: 0.7144 (mmt180) REVERT: A 833 MET cc_start: 0.8436 (mmm) cc_final: 0.8084 (mtp) REVERT: A 886 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8372 (mm) REVERT: A 1049 ASN cc_start: 0.8379 (m-40) cc_final: 0.8094 (m-40) REVERT: A 1071 MET cc_start: 0.8297 (tpp) cc_final: 0.8059 (mmt) REVERT: A 1094 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8571 (t) REVERT: C 54 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7760 (mmmt) REVERT: B 93 TYR cc_start: 0.5686 (OUTLIER) cc_final: 0.5075 (t80) REVERT: B 127 GLU cc_start: 0.7409 (tp30) cc_final: 0.7199 (tp30) REVERT: B 222 TYR cc_start: 0.7656 (m-10) cc_final: 0.7456 (m-10) REVERT: B 332 ARG cc_start: 0.5124 (mpt-90) cc_final: 0.1803 (mpt-90) REVERT: B 432 LYS cc_start: 0.8938 (mttm) cc_final: 0.8534 (mmtt) REVERT: B 457 MET cc_start: 0.6019 (tpt) cc_final: 0.5761 (tpt) REVERT: B 477 VAL cc_start: 0.8992 (t) cc_final: 0.8682 (p) REVERT: B 585 PHE cc_start: 0.8297 (t80) cc_final: 0.8078 (t80) REVERT: B 598 MET cc_start: 0.7594 (tpt) cc_final: 0.7355 (tpt) REVERT: B 808 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: B 922 TYR cc_start: 0.8931 (m-10) cc_final: 0.8202 (m-80) REVERT: B 961 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8247 (pp) REVERT: B 1040 PHE cc_start: 0.7566 (t80) cc_final: 0.6907 (t80) REVERT: B 1066 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7627 (mt-10) REVERT: B 1139 MET cc_start: 0.7971 (tmm) cc_final: 0.7730 (tmm) REVERT: B 1165 LEU cc_start: 0.8876 (mt) cc_final: 0.8599 (mt) outliers start: 81 outliers final: 70 residues processed: 416 average time/residue: 0.2321 time to fit residues: 155.8478 Evaluate side-chains 437 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 362 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 808 GLN Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 879 ASP Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 998 CYS Chi-restraints excluded: chain B residue 1038 CYS Chi-restraints excluded: chain B residue 1039 THR Chi-restraints excluded: chain B residue 1049 ASN Chi-restraints excluded: chain B residue 1064 THR Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1122 MET Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain B residue 1140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 209 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 166 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN A1099 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 358 HIS ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17069 Z= 0.200 Angle : 0.751 16.169 23196 Z= 0.357 Chirality : 0.044 0.297 2632 Planarity : 0.005 0.070 2921 Dihedral : 5.831 56.830 2310 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.04 % Allowed : 25.65 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 2110 helix: 0.90 (0.15), residues: 1131 sheet: -1.48 (0.49), residues: 116 loop : -2.15 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B1027 HIS 0.005 0.001 HIS A 950 PHE 0.054 0.002 PHE B 790 TYR 0.025 0.001 TYR B 452 ARG 0.005 0.000 ARG B 770 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 388 time to evaluate : 2.112 Fit side-chains revert: symmetry clash REVERT: A 216 MET cc_start: 0.7777 (mmm) cc_final: 0.7453 (mmm) REVERT: A 221 GLU cc_start: 0.8444 (tp30) cc_final: 0.8063 (tp30) REVERT: A 587 MET cc_start: 0.8129 (tmm) cc_final: 0.7850 (tmm) REVERT: A 598 MET cc_start: 0.8029 (mpp) cc_final: 0.7732 (mmt) REVERT: A 602 ARG cc_start: 0.7495 (mtt-85) cc_final: 0.7100 (mmt180) REVERT: A 772 ARG cc_start: 0.7245 (mmm160) cc_final: 0.7028 (mmm160) REVERT: A 886 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8326 (mm) REVERT: A 1049 ASN cc_start: 0.8247 (m-40) cc_final: 0.8011 (m-40) REVERT: A 1094 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8541 (t) REVERT: B 93 TYR cc_start: 0.5501 (OUTLIER) cc_final: 0.4924 (t80) REVERT: B 127 GLU cc_start: 0.7381 (tp30) cc_final: 0.7170 (tp30) REVERT: B 221 GLU cc_start: 0.7991 (tt0) cc_final: 0.7593 (tt0) REVERT: B 332 ARG cc_start: 0.4961 (mpt-90) cc_final: 0.1684 (mpt-90) REVERT: B 432 LYS cc_start: 0.8937 (mttm) cc_final: 0.8497 (mmmt) REVERT: B 477 VAL cc_start: 0.9040 (t) cc_final: 0.8737 (p) REVERT: B 585 PHE cc_start: 0.8228 (t80) cc_final: 0.7999 (t80) REVERT: B 808 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: B 922 TYR cc_start: 0.8920 (m-10) cc_final: 0.8261 (m-80) REVERT: B 961 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8071 (pp) REVERT: B 1040 PHE cc_start: 0.7474 (t80) cc_final: 0.6822 (t80) REVERT: B 1139 MET cc_start: 0.8039 (tmm) cc_final: 0.7728 (tmm) outliers start: 71 outliers final: 56 residues processed: 428 average time/residue: 0.2438 time to fit residues: 166.3192 Evaluate side-chains 424 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 363 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain C residue 47 PHE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 808 GLN Chi-restraints excluded: chain B residue 879 ASP Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 998 CYS Chi-restraints excluded: chain B residue 1038 CYS Chi-restraints excluded: chain B residue 1039 THR Chi-restraints excluded: chain B residue 1064 THR Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain B residue 1140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 171 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 358 HIS ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 ASN B1099 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.120094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.101698 restraints weight = 40881.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.104486 restraints weight = 20161.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.106172 restraints weight = 12532.268| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17069 Z= 0.313 Angle : 0.785 18.214 23196 Z= 0.380 Chirality : 0.045 0.270 2632 Planarity : 0.005 0.090 2921 Dihedral : 5.904 55.079 2310 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.21 % Allowed : 26.34 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 2110 helix: 0.88 (0.15), residues: 1141 sheet: -1.49 (0.49), residues: 117 loop : -2.15 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B1027 HIS 0.005 0.001 HIS A 950 PHE 0.054 0.002 PHE B 790 TYR 0.027 0.002 TYR B 788 ARG 0.007 0.001 ARG C 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3972.96 seconds wall clock time: 72 minutes 33.89 seconds (4353.89 seconds total)