Starting phenix.real_space_refine on Wed May 14 15:29:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d8o_27253/05_2025/8d8o_27253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d8o_27253/05_2025/8d8o_27253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d8o_27253/05_2025/8d8o_27253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d8o_27253/05_2025/8d8o_27253.map" model { file = "/net/cci-nas-00/data/ceres_data/8d8o_27253/05_2025/8d8o_27253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d8o_27253/05_2025/8d8o_27253.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 89 5.16 5 C 7432 2.51 5 N 2025 2.21 5 O 2272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11819 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3203 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ASP:plan': 4, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 8615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8615 Classifications: {'peptide': 1110} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 1041} Chain breaks: 2 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.85, per 1000 atoms: 0.66 Number of scatterers: 11819 At special positions: 0 Unit cell: (93.79, 124.5, 156.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 89 16.00 O 2272 8.00 N 2025 7.00 C 7432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 880 " - pdb=" SG CYS A 891 " distance=2.03 Simple disulfide: pdb=" SG CYS A 903 " - pdb=" SG CYS A 910 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A 990 " distance=2.03 Simple disulfide: pdb=" SG CYS A 971 " - pdb=" SG CYS A1059 " distance=2.03 Simple disulfide: pdb=" SG CYS A1112 " - pdb=" SG CYS A1125 " distance=2.03 Simple disulfide: pdb=" SG CYS A1130 " - pdb=" SG CYS B1130 " distance=2.03 Simple disulfide: pdb=" SG CYS A1135 " - pdb=" SG CYS A1189 " distance=2.03 Simple disulfide: pdb=" SG CYS A1147 " - pdb=" SG CYS A1158 " distance=2.03 Simple disulfide: pdb=" SG CYS A1162 " - pdb=" SG CYS A1200 " distance=2.03 Simple disulfide: pdb=" SG CYS A1205 " - pdb=" SG CYS A1249 " distance=2.03 Simple disulfide: pdb=" SG CYS A1220 " - pdb=" SG CYS A1230 " distance=2.03 Simple disulfide: pdb=" SG CYS A1234 " - pdb=" SG CYS A1262 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 247 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 532 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 673 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 695 " - pdb=" SG CYS B 701 " distance=2.03 Simple disulfide: pdb=" SG CYS B 867 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 880 " - pdb=" SG CYS B 891 " distance=2.03 Simple disulfide: pdb=" SG CYS B 903 " - pdb=" SG CYS B 910 " distance=2.03 Simple disulfide: pdb=" SG CYS B 919 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B 956 " - pdb=" SG CYS B 990 " distance=2.03 Simple disulfide: pdb=" SG CYS B 971 " - pdb=" SG CYS B1059 " distance=2.03 Simple disulfide: pdb=" SG CYS B1112 " - pdb=" SG CYS B1125 " distance=2.03 Simple disulfide: pdb=" SG CYS B1135 " - pdb=" SG CYS B1189 " distance=2.03 Simple disulfide: pdb=" SG CYS B1147 " - pdb=" SG CYS B1158 " distance=2.03 Simple disulfide: pdb=" SG CYS B1162 " - pdb=" SG CYS B1200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1601 " pdb="ZN ZN B1601 " - pdb=" NE2 HIS B 492 " pdb="ZN ZN B1601 " - pdb=" NE2 HIS B 482 " pdb="ZN ZN B1601 " - pdb=" NE2 HIS B 486 " 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2878 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 26 sheets defined 11.0% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 922 through 927 removed outlier: 4.552A pdb=" N THR A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 932 Processing helix chain 'A' and resid 997 through 1001 removed outlier: 4.144A pdb=" N ALA A1000 " --> pdb=" O SER A 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 4.422A pdb=" N LYS B 154 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 193 removed outlier: 4.047A pdb=" N GLU B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.672A pdb=" N TYR B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 307 Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 418 through 426 Processing helix chain 'B' and resid 454 through 459 removed outlier: 4.423A pdb=" N LEU B 458 " --> pdb=" O LYS B 455 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET B 459 " --> pdb=" O GLU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 471 Processing helix chain 'B' and resid 477 through 488 removed outlier: 4.285A pdb=" N ILE B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS B 482 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 659 through 664 removed outlier: 3.532A pdb=" N GLU B 664 " --> pdb=" O ARG B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 801 removed outlier: 3.605A pdb=" N LEU B 799 " --> pdb=" O PRO B 796 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN B 800 " --> pdb=" O LEU B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 927 through 932 Processing helix chain 'B' and resid 981 through 986 removed outlier: 3.651A pdb=" N HIS B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1061 removed outlier: 3.855A pdb=" N ASN B1061 " --> pdb=" O SER B1058 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1058 through 1061' Processing helix chain 'B' and resid 1105 through 1111 removed outlier: 3.968A pdb=" N LEU B1109 " --> pdb=" O ASP B1105 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B1111 " --> pdb=" O VAL B1107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 123 removed outlier: 7.055A pdb=" N MET A 128 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR A 139 " --> pdb=" O MET A 128 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU A 130 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 902 through 904 Processing sheet with id=AA3, first strand: chain 'A' and resid 939 through 943 Processing sheet with id=AA4, first strand: chain 'A' and resid 946 through 949 removed outlier: 6.720A pdb=" N ILE A1038 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU A1054 " --> pdb=" O ILE A1038 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL A1040 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1069 through 1071 removed outlier: 3.609A pdb=" N HIS A1070 " --> pdb=" O HIS B1070 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1117 through 1118 Processing sheet with id=AA7, first strand: chain 'A' and resid 1143 through 1147 Processing sheet with id=AA8, first strand: chain 'A' and resid 1166 through 1172 Processing sheet with id=AA9, first strand: chain 'A' and resid 1216 through 1217 Processing sheet with id=AB1, first strand: chain 'A' and resid 1230 through 1231 removed outlier: 3.524A pdb=" N CYS A1230 " --> pdb=" O LEU A1247 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1239 through 1240 Processing sheet with id=AB3, first strand: chain 'B' and resid 135 through 140 removed outlier: 5.484A pdb=" N GLN B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 132 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR B 40 " --> pdb=" O TRP B 179 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TRP B 44 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N HIS B 175 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG B 46 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE B 173 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 135 through 140 removed outlier: 5.484A pdb=" N GLN B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 132 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR B 40 " --> pdb=" O TRP B 179 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TRP B 44 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N HIS B 175 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG B 46 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE B 173 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N HIS B 175 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ARG B 15 " --> pdb=" O HIS B 175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.526A pdb=" N TRP B 73 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 77 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL B 56 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 314 through 315 Processing sheet with id=AB7, first strand: chain 'B' and resid 314 through 315 removed outlier: 8.511A pdb=" N ILE B 435 " --> pdb=" O ARG B 274 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG B 276 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N PHE B 437 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N VAL B 278 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 329 through 331 Processing sheet with id=AB9, first strand: chain 'B' and resid 600 through 604 removed outlier: 6.804A pdb=" N THR B 610 " --> pdb=" O LEU B 602 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 640 through 641 removed outlier: 3.728A pdb=" N GLN B 641 " --> pdb=" O LEU B 789 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR B 790 " --> pdb=" O GLU B 714 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 645 through 647 removed outlier: 11.049A pdb=" N LEU B 705 " --> pdb=" O TYR B 776 " (cutoff:3.500A) removed outlier: 10.568A pdb=" N TYR B 776 " --> pdb=" O LEU B 705 " (cutoff:3.500A) removed outlier: 12.057A pdb=" N PHE B 707 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 11.651A pdb=" N GLN B 774 " --> pdb=" O PHE B 707 " (cutoff:3.500A) removed outlier: 10.802A pdb=" N TYR B 709 " --> pdb=" O GLY B 772 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLY B 772 " --> pdb=" O TYR B 709 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 772 " --> pdb=" O LEU B 739 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 805 through 810 Processing sheet with id=AC4, first strand: chain 'B' and resid 902 through 904 Processing sheet with id=AC5, first strand: chain 'B' and resid 939 through 943 removed outlier: 6.131A pdb=" N HIS B1022 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B1096 " --> pdb=" O ILE B1020 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B1020 " --> pdb=" O VAL B1096 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU B1098 " --> pdb=" O ALA B1018 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B1018 " --> pdb=" O LEU B1098 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 946 through 949 removed outlier: 6.817A pdb=" N GLN B1080 " --> pdb=" O PHE B1010 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B1038 " --> pdb=" O LEU B1054 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU B1054 " --> pdb=" O ILE B1038 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B1040 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1143 through 1147 removed outlier: 3.834A pdb=" N CYS B1158 " --> pdb=" O VAL B1187 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B1187 " --> pdb=" O CYS B1158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1167 through 1170 302 hydrogen bonds defined for protein. 753 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: 4.58 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3933 1.34 - 1.46: 2826 1.46 - 1.58: 5265 1.58 - 1.70: 2 1.70 - 1.81: 109 Bond restraints: 12135 Sorted by residual: bond pdb=" CB PRO B 202 " pdb=" CG PRO B 202 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.30e+00 bond pdb=" CB PRO A1237 " pdb=" CG PRO A1237 " ideal model delta sigma weight residual 1.506 1.595 -0.089 3.90e-02 6.57e+02 5.26e+00 bond pdb=" C GLU B 906 " pdb=" N PRO B 907 " ideal model delta sigma weight residual 1.333 1.354 -0.020 1.01e-02 9.80e+03 4.01e+00 bond pdb=" CB PRO B 569 " pdb=" CG PRO B 569 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.20e+00 bond pdb=" CB PRO A 113 " pdb=" CG PRO A 113 " ideal model delta sigma weight residual 1.492 1.554 -0.062 5.00e-02 4.00e+02 1.53e+00 ... (remaining 12130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 16521 3.62 - 7.24: 42 7.24 - 10.86: 2 10.86 - 14.48: 1 14.48 - 18.11: 1 Bond angle restraints: 16567 Sorted by residual: angle pdb=" CA PRO B 569 " pdb=" N PRO B 569 " pdb=" CD PRO B 569 " ideal model delta sigma weight residual 112.00 104.17 7.83 1.40e+00 5.10e-01 3.13e+01 angle pdb=" CA PRO B 202 " pdb=" N PRO B 202 " pdb=" CD PRO B 202 " ideal model delta sigma weight residual 112.00 104.83 7.17 1.40e+00 5.10e-01 2.62e+01 angle pdb=" CA PRO A1237 " pdb=" N PRO A1237 " pdb=" CD PRO A1237 " ideal model delta sigma weight residual 111.50 105.56 5.94 1.40e+00 5.10e-01 1.80e+01 angle pdb=" CA PRO A1106 " pdb=" N PRO A1106 " pdb=" CD PRO A1106 " ideal model delta sigma weight residual 112.00 107.11 4.89 1.40e+00 5.10e-01 1.22e+01 angle pdb=" N ASN B 570 " pdb=" CA ASN B 570 " pdb=" C ASN B 570 " ideal model delta sigma weight residual 114.75 110.55 4.20 1.26e+00 6.30e-01 1.11e+01 ... (remaining 16562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 6238 16.94 - 33.89: 753 33.89 - 50.83: 207 50.83 - 67.78: 37 67.78 - 84.72: 16 Dihedral angle restraints: 7251 sinusoidal: 2781 harmonic: 4470 Sorted by residual: dihedral pdb=" CB CYS A 971 " pdb=" SG CYS A 971 " pdb=" SG CYS A1059 " pdb=" CB CYS A1059 " ideal model delta sinusoidal sigma weight residual 93.00 171.12 -78.12 1 1.00e+01 1.00e-02 7.62e+01 dihedral pdb=" CB CYS A1130 " pdb=" SG CYS A1130 " pdb=" SG CYS B1130 " pdb=" CB CYS B1130 " ideal model delta sinusoidal sigma weight residual -86.00 -156.18 70.18 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CB CYS B 503 " pdb=" SG CYS B 503 " pdb=" SG CYS B 542 " pdb=" CB CYS B 542 " ideal model delta sinusoidal sigma weight residual 93.00 160.10 -67.10 1 1.00e+01 1.00e-02 5.87e+01 ... (remaining 7248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1046 0.029 - 0.059: 492 0.059 - 0.088: 144 0.088 - 0.117: 113 0.117 - 0.147: 23 Chirality restraints: 1818 Sorted by residual: chirality pdb=" CA VAL B 691 " pdb=" N VAL B 691 " pdb=" C VAL B 691 " pdb=" CB VAL B 691 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA PHE A1104 " pdb=" N PHE A1104 " pdb=" C PHE A1104 " pdb=" CB PHE A1104 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1815 not shown) Planarity restraints: 2178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 568 " -0.117 5.00e-02 4.00e+02 1.74e-01 4.83e+01 pdb=" N PRO B 569 " 0.300 5.00e-02 4.00e+02 pdb=" CA PRO B 569 " -0.097 5.00e-02 4.00e+02 pdb=" CD PRO B 569 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 112 " -0.071 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO A 113 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 671 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO B 672 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 672 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 672 " -0.041 5.00e-02 4.00e+02 ... (remaining 2175 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 270 2.69 - 3.24: 10899 3.24 - 3.79: 17772 3.79 - 4.35: 23521 4.35 - 4.90: 39722 Nonbonded interactions: 92184 Sorted by model distance: nonbonded pdb=" OG1 THR B 184 " pdb=" OE1 GLU B 187 " model vdw 2.133 3.040 nonbonded pdb=" OD2 ASP B 830 " pdb=" OH TYR B 841 " model vdw 2.204 3.040 nonbonded pdb=" NE2 HIS B 78 " pdb=" OD1 ASN B 106 " model vdw 2.245 3.120 nonbonded pdb=" O ASP B 84 " pdb=" ND2 ASN B 85 " model vdw 2.247 3.120 nonbonded pdb=" O GLU B 923 " pdb=" OG SER B 927 " model vdw 2.252 3.040 ... (remaining 92179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.770 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: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.210 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.004 0.126 12170 Z= 0.138 Angle : 0.575 18.106 16631 Z= 0.289 Chirality : 0.043 0.147 1818 Planarity : 0.006 0.174 2178 Dihedral : 15.920 84.721 4277 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.16 % Allowed : 23.89 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -0.78 (0.22), residues: 1526 helix: -1.34 (0.48), residues: 124 sheet: 0.01 (0.28), residues: 372 loop : -0.60 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 987 HIS 0.005 0.001 HIS B 78 PHE 0.024 0.001 PHE A1104 TYR 0.011 0.001 TYR B 131 ARG 0.002 0.000 ARG A1099 Details of bonding type rmsd hydrogen bonds : bond 0.15491 ( 282) hydrogen bonds : angle 7.75831 ( 753) metal coordination : bond 0.00197 ( 3) SS BOND : bond 0.00157 ( 32) SS BOND : angle 1.17272 ( 64) covalent geometry : bond 0.00360 (12135) covalent geometry : angle 0.57194 (16567) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 1.355 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.2488 time to fit residues: 36.4007 Evaluate side-chains 96 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 0.0010 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN B 175 HIS B 687 ASN B 840 GLN B1154 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.200308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.162170 restraints weight = 15573.704| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 1.88 r_work: 0.3694 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12170 Z= 0.193 Angle : 0.584 18.491 16631 Z= 0.292 Chirality : 0.045 0.152 1818 Planarity : 0.005 0.121 2178 Dihedral : 4.388 22.010 1648 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.03 % Allowed : 21.02 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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 (0.22), residues: 1526 helix: -1.37 (0.47), residues: 121 sheet: -0.18 (0.27), residues: 380 loop : -0.56 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1194 HIS 0.006 0.001 HIS B 234 PHE 0.024 0.001 PHE A1104 TYR 0.014 0.001 TYR B 169 ARG 0.003 0.000 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 282) hydrogen bonds : angle 5.89641 ( 753) metal coordination : bond 0.00360 ( 3) SS BOND : bond 0.00226 ( 32) SS BOND : angle 1.31102 ( 64) covalent geometry : bond 0.00463 (12135) covalent geometry : angle 0.57984 (16567) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 99 time to evaluate : 1.227 Fit side-chains REVERT: B 1026 ASP cc_start: 0.7930 (m-30) cc_final: 0.7649 (m-30) REVERT: B 1077 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8050 (p90) outliers start: 52 outliers final: 30 residues processed: 141 average time/residue: 0.2152 time to fit residues: 45.4559 Evaluate side-chains 124 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 756 ASP Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1077 TYR Chi-restraints excluded: chain B residue 1078 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 37 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.207555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.161003 restraints weight = 16180.880| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.27 r_work: 0.3603 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12170 Z= 0.168 Angle : 0.567 18.576 16631 Z= 0.281 Chirality : 0.044 0.147 1818 Planarity : 0.005 0.099 2178 Dihedral : 4.394 20.982 1648 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.34 % Allowed : 20.71 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -0.90 (0.22), residues: 1526 helix: -1.40 (0.47), residues: 121 sheet: -0.26 (0.28), residues: 375 loop : -0.61 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1194 HIS 0.005 0.001 HIS B 78 PHE 0.024 0.001 PHE A1104 TYR 0.012 0.001 TYR B 169 ARG 0.001 0.000 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 282) hydrogen bonds : angle 5.55689 ( 753) metal coordination : bond 0.00333 ( 3) SS BOND : bond 0.00202 ( 32) SS BOND : angle 1.28244 ( 64) covalent geometry : bond 0.00403 (12135) covalent geometry : angle 0.56234 (16567) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 100 time to evaluate : 1.220 Fit side-chains REVERT: B 765 ASP cc_start: 0.7575 (t70) cc_final: 0.7328 (t70) REVERT: B 788 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7928 (ttm) REVERT: B 920 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: B 942 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8258 (tm-30) REVERT: B 1026 ASP cc_start: 0.7856 (m-30) cc_final: 0.7515 (m-30) REVERT: B 1077 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8022 (p90) outliers start: 56 outliers final: 40 residues processed: 144 average time/residue: 0.2073 time to fit residues: 45.3815 Evaluate side-chains 141 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 756 ASP Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 823 HIS Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 942 GLN Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1077 TYR Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1135 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 109 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 152 optimal weight: 30.0000 chunk 140 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 129 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.196344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.163202 restraints weight = 15916.099| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.89 r_work: 0.3557 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 12170 Z= 0.279 Angle : 0.651 19.341 16631 Z= 0.325 Chirality : 0.047 0.167 1818 Planarity : 0.005 0.092 2178 Dihedral : 4.866 23.304 1648 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.89 % Allowed : 20.87 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -1.23 (0.21), residues: 1526 helix: -1.63 (0.45), residues: 122 sheet: -0.52 (0.27), residues: 378 loop : -0.82 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 451 HIS 0.006 0.001 HIS B 234 PHE 0.028 0.002 PHE A1104 TYR 0.021 0.002 TYR B 275 ARG 0.003 0.000 ARG B 89 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 282) hydrogen bonds : angle 5.75160 ( 753) metal coordination : bond 0.00571 ( 3) SS BOND : bond 0.00312 ( 32) SS BOND : angle 1.56967 ( 64) covalent geometry : bond 0.00672 (12135) covalent geometry : angle 0.64533 (16567) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 97 time to evaluate : 1.286 Fit side-chains REVERT: B 765 ASP cc_start: 0.7471 (t70) cc_final: 0.7206 (t70) REVERT: B 788 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8070 (ttm) outliers start: 63 outliers final: 48 residues processed: 151 average time/residue: 0.2120 time to fit residues: 48.5296 Evaluate side-chains 138 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 89 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 756 ASP Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 823 HIS Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1074 GLN Chi-restraints excluded: chain B residue 1077 TYR Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1135 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 87 optimal weight: 0.0270 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.206431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.162597 restraints weight = 16059.169| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.07 r_work: 0.3621 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12170 Z= 0.160 Angle : 0.577 18.902 16631 Z= 0.284 Chirality : 0.044 0.149 1818 Planarity : 0.004 0.080 2178 Dihedral : 4.579 22.449 1648 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.11 % Allowed : 21.96 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -1.06 (0.22), residues: 1526 helix: -1.48 (0.47), residues: 121 sheet: -0.44 (0.27), residues: 381 loop : -0.69 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 313 HIS 0.005 0.001 HIS B 78 PHE 0.024 0.001 PHE A1104 TYR 0.012 0.001 TYR B 131 ARG 0.005 0.000 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.02942 ( 282) hydrogen bonds : angle 5.45673 ( 753) metal coordination : bond 0.00326 ( 3) SS BOND : bond 0.00189 ( 32) SS BOND : angle 1.38816 ( 64) covalent geometry : bond 0.00385 (12135) covalent geometry : angle 0.57168 (16567) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 94 time to evaluate : 1.371 Fit side-chains REVERT: B 220 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6539 (mtp) REVERT: B 765 ASP cc_start: 0.7478 (t70) cc_final: 0.7191 (t70) REVERT: B 788 MET cc_start: 0.8153 (tpp) cc_final: 0.7881 (ttm) outliers start: 53 outliers final: 44 residues processed: 139 average time/residue: 0.2261 time to fit residues: 48.3689 Evaluate side-chains 133 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 756 ASP Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1135 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 26 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 143 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.207335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.161087 restraints weight = 16270.396| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.31 r_work: 0.3599 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12170 Z= 0.124 Angle : 0.541 18.121 16631 Z= 0.267 Chirality : 0.043 0.148 1818 Planarity : 0.004 0.073 2178 Dihedral : 4.345 20.667 1648 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.42 % Allowed : 22.03 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -0.93 (0.22), residues: 1526 helix: -1.32 (0.48), residues: 121 sheet: -0.34 (0.27), residues: 380 loop : -0.61 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 987 HIS 0.005 0.001 HIS B 78 PHE 0.022 0.001 PHE A1104 TYR 0.012 0.001 TYR B 131 ARG 0.004 0.000 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.02689 ( 282) hydrogen bonds : angle 5.22369 ( 753) metal coordination : bond 0.00175 ( 3) SS BOND : bond 0.00165 ( 32) SS BOND : angle 1.22569 ( 64) covalent geometry : bond 0.00295 (12135) covalent geometry : angle 0.53710 (16567) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 97 time to evaluate : 1.224 Fit side-chains REVERT: A 128 MET cc_start: 0.5378 (ppp) cc_final: 0.5015 (ptm) REVERT: A 1078 HIS cc_start: 0.8491 (OUTLIER) cc_final: 0.8273 (m-70) REVERT: B 220 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6568 (mtp) REVERT: B 650 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6964 (ptm) REVERT: B 765 ASP cc_start: 0.7472 (t70) cc_final: 0.7173 (t70) REVERT: B 788 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7887 (ttm) REVERT: B 1077 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.7869 (p90) outliers start: 57 outliers final: 41 residues processed: 141 average time/residue: 0.1972 time to fit residues: 42.8966 Evaluate side-chains 135 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 89 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain A residue 1189 CYS Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 756 ASP Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1077 TYR Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1135 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 144 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 46 optimal weight: 0.0470 chunk 125 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.208028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.162601 restraints weight = 16250.465| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.34 r_work: 0.3610 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12170 Z= 0.112 Angle : 0.543 18.015 16631 Z= 0.266 Chirality : 0.043 0.148 1818 Planarity : 0.004 0.066 2178 Dihedral : 4.253 20.445 1648 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.34 % Allowed : 22.89 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -0.81 (0.22), residues: 1526 helix: -1.17 (0.48), residues: 121 sheet: -0.25 (0.27), residues: 380 loop : -0.54 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 987 HIS 0.005 0.001 HIS B 78 PHE 0.028 0.001 PHE A 127 TYR 0.012 0.001 TYR B 131 ARG 0.002 0.000 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.02601 ( 282) hydrogen bonds : angle 5.10292 ( 753) metal coordination : bond 0.00160 ( 3) SS BOND : bond 0.00161 ( 32) SS BOND : angle 1.13164 ( 64) covalent geometry : bond 0.00268 (12135) covalent geometry : angle 0.53903 (16567) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 1.350 Fit side-chains REVERT: B 220 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6553 (mtp) REVERT: B 765 ASP cc_start: 0.7559 (t70) cc_final: 0.7258 (t70) REVERT: B 788 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7872 (ttm) REVERT: B 1077 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.7901 (p90) outliers start: 43 outliers final: 35 residues processed: 124 average time/residue: 0.2083 time to fit residues: 39.6513 Evaluate side-chains 129 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1189 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 756 ASP Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1077 TYR Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1135 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 23 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.197923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.154051 restraints weight = 16098.964| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.15 r_work: 0.3521 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12170 Z= 0.197 Angle : 0.586 18.465 16631 Z= 0.289 Chirality : 0.045 0.154 1818 Planarity : 0.004 0.070 2178 Dihedral : 4.486 20.234 1648 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.42 % Allowed : 22.11 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -1.03 (0.22), residues: 1526 helix: -1.49 (0.45), residues: 128 sheet: -0.40 (0.27), residues: 391 loop : -0.67 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 451 HIS 0.005 0.001 HIS B 234 PHE 0.025 0.002 PHE A1104 TYR 0.015 0.001 TYR B 275 ARG 0.002 0.000 ARG B1099 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 282) hydrogen bonds : angle 5.30782 ( 753) metal coordination : bond 0.00413 ( 3) SS BOND : bond 0.00254 ( 32) SS BOND : angle 1.28718 ( 64) covalent geometry : bond 0.00473 (12135) covalent geometry : angle 0.58193 (16567) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 92 time to evaluate : 1.461 Fit side-chains REVERT: B 220 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6619 (mtp) REVERT: B 444 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5675 (pm20) REVERT: B 650 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6882 (ptm) REVERT: B 765 ASP cc_start: 0.7489 (t70) cc_final: 0.7192 (t70) REVERT: B 788 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.8035 (ttm) REVERT: B 1077 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.7813 (p90) outliers start: 57 outliers final: 43 residues processed: 138 average time/residue: 0.2015 time to fit residues: 42.8144 Evaluate side-chains 138 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1189 CYS Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 756 ASP Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1077 TYR Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1135 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 142 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 0.0070 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.207292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.162317 restraints weight = 16247.049| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.31 r_work: 0.3596 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12170 Z= 0.127 Angle : 0.550 18.329 16631 Z= 0.269 Chirality : 0.043 0.147 1818 Planarity : 0.004 0.070 2178 Dihedral : 4.311 20.529 1648 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.03 % Allowed : 22.50 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -0.87 (0.22), residues: 1526 helix: -1.36 (0.46), residues: 127 sheet: -0.28 (0.27), residues: 380 loop : -0.56 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 313 HIS 0.005 0.001 HIS B 78 PHE 0.021 0.001 PHE A1104 TYR 0.013 0.001 TYR B 131 ARG 0.001 0.000 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.02629 ( 282) hydrogen bonds : angle 5.11658 ( 753) metal coordination : bond 0.00216 ( 3) SS BOND : bond 0.00172 ( 32) SS BOND : angle 1.12701 ( 64) covalent geometry : bond 0.00306 (12135) covalent geometry : angle 0.54653 (16567) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 92 time to evaluate : 1.335 Fit side-chains REVERT: B 220 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6595 (mtp) REVERT: B 444 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5610 (pm20) REVERT: B 650 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6931 (ptm) REVERT: B 765 ASP cc_start: 0.7573 (t70) cc_final: 0.7275 (t70) REVERT: B 788 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7896 (ttm) REVERT: B 1077 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.7787 (p90) outliers start: 52 outliers final: 45 residues processed: 133 average time/residue: 0.2119 time to fit residues: 44.0461 Evaluate side-chains 140 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 90 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1189 CYS Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 756 ASP Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1077 TYR Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1135 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 79 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 148 optimal weight: 0.1980 chunk 4 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.203364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.160694 restraints weight = 15862.142| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.05 r_work: 0.3667 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12170 Z= 0.114 Angle : 0.538 17.966 16631 Z= 0.263 Chirality : 0.043 0.147 1818 Planarity : 0.004 0.070 2178 Dihedral : 4.169 20.136 1648 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.96 % Allowed : 22.81 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -0.77 (0.22), residues: 1526 helix: -1.22 (0.47), residues: 127 sheet: -0.18 (0.27), residues: 380 loop : -0.52 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1194 HIS 0.008 0.001 HIS B 175 PHE 0.020 0.001 PHE A1104 TYR 0.013 0.001 TYR B 131 ARG 0.002 0.000 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.02541 ( 282) hydrogen bonds : angle 4.98922 ( 753) metal coordination : bond 0.00170 ( 3) SS BOND : bond 0.00157 ( 32) SS BOND : angle 1.03613 ( 64) covalent geometry : bond 0.00274 (12135) covalent geometry : angle 0.53522 (16567) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 92 time to evaluate : 1.323 Fit side-chains REVERT: B 220 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6732 (mtp) REVERT: B 444 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.5481 (pm20) REVERT: B 650 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7045 (ptm) REVERT: B 765 ASP cc_start: 0.7912 (t70) cc_final: 0.7590 (t70) REVERT: B 788 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8047 (ttm) REVERT: B 1077 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.7986 (p90) outliers start: 51 outliers final: 44 residues processed: 132 average time/residue: 0.2033 time to fit residues: 41.4070 Evaluate side-chains 139 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 90 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1189 CYS Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 756 ASP Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1077 TYR Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1135 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 136 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.207601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.162870 restraints weight = 16187.577| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.20 r_work: 0.3622 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12170 Z= 0.132 Angle : 0.545 17.997 16631 Z= 0.266 Chirality : 0.043 0.146 1818 Planarity : 0.004 0.072 2178 Dihedral : 4.213 20.129 1648 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.88 % Allowed : 22.81 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -0.80 (0.22), residues: 1526 helix: -1.27 (0.47), residues: 127 sheet: -0.17 (0.27), residues: 386 loop : -0.55 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1005 HIS 0.005 0.001 HIS B 78 PHE 0.021 0.001 PHE A1104 TYR 0.012 0.001 TYR B 131 ARG 0.002 0.000 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.02615 ( 282) hydrogen bonds : angle 5.02994 ( 753) metal coordination : bond 0.00218 ( 3) SS BOND : bond 0.00172 ( 32) SS BOND : angle 1.06131 ( 64) covalent geometry : bond 0.00316 (12135) covalent geometry : angle 0.54192 (16567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6123.03 seconds wall clock time: 106 minutes 40.31 seconds (6400.31 seconds total)