Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 12:12:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8o_27253/08_2023/8d8o_27253.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8o_27253/08_2023/8d8o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8o_27253/08_2023/8d8o_27253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8o_27253/08_2023/8d8o_27253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8o_27253/08_2023/8d8o_27253.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8o_27253/08_2023/8d8o_27253.pdb" } 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 Residue "A PHE 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1026": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 11819 Number of models: 1 Model: "" Number of chains: 2 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: 8616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8616 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1110, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 1041, None: 1} Not linked: pdbres="GLU B1201 " pdbres=" ZN B1601 " 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 Time building chain proxies: 6.28, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 2.0 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: 1.45 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: 4.96 Time building geometry restraints manager: 5.08 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: 99.62 - 106.52: 450 106.52 - 113.41: 6479 113.41 - 120.30: 4175 120.30 - 127.20: 5276 127.20 - 134.09: 187 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 2.440 nonbonded pdb=" OD2 ASP B 830 " pdb=" OH TYR B 841 " model vdw 2.204 2.440 nonbonded pdb=" NE2 HIS B 78 " pdb=" OD1 ASN B 106 " model vdw 2.245 2.520 nonbonded pdb=" O ASP B 84 " pdb=" ND2 ASN B 85 " model vdw 2.247 2.520 nonbonded pdb=" O GLU B 923 " pdb=" OG SER B 927 " model vdw 2.252 2.440 ... (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 ========== 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: 0.010 Normalize map: mean=0, sd=1: 6.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 18.480 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 37.020 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.250 ------------------------------------------------------------------------------- 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 12135 Z= 0.244 Angle : 0.572 18.106 16567 Z= 0.288 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 % 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 *********************** 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 fitting. 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: 0.2528 time to fit residues: 36.8812 Evaluate side-chains 96 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0169 ------------------------------------------------------------------------------- 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: 7.9990 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 overall best weight: 0.8304 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN B 840 GLN B1154 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.0486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 12135 Z= 0.237 Angle : 0.539 18.701 16567 Z= 0.267 Chirality : 0.043 0.146 1818 Planarity : 0.005 0.118 2178 Dihedral : 4.208 21.692 1648 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer Outliers : 4.03 % 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: -0.74 (0.22), residues: 1526 helix: -1.26 (0.48), residues: 121 sheet: -0.04 (0.28), residues: 370 loop : -0.54 (0.20), residues: 1035 *********************** 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 156 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 104 time to evaluate : 1.236 Fit side-chains outliers start: 52 outliers final: 34 residues processed: 144 average time/residue: 0.2101 time to fit residues: 45.8056 Evaluate side-chains 130 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 96 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1084 time to fit residues: 8.5005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 115 optimal weight: 0.0970 chunk 94 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 123 optimal weight: 0.2980 chunk 138 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 12135 Z= 0.185 Angle : 0.518 18.348 16567 Z= 0.254 Chirality : 0.043 0.146 1818 Planarity : 0.004 0.094 2178 Dihedral : 4.110 20.095 1648 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer Outliers : 2.40 % 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: -0.67 (0.22), residues: 1526 helix: -1.17 (0.49), residues: 121 sheet: 0.04 (0.28), residues: 369 loop : -0.51 (0.20), residues: 1036 *********************** 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 135 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 1.403 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 11 residues processed: 133 average time/residue: 0.2222 time to fit residues: 44.4218 Evaluate side-chains 106 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.365 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1101 time to fit residues: 4.1151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 139 optimal weight: 0.0980 chunk 147 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 39 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12135 Z= 0.179 Angle : 0.515 17.988 16567 Z= 0.252 Chirality : 0.043 0.147 1818 Planarity : 0.004 0.082 2178 Dihedral : 4.062 19.636 1648 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 1.24 % 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: -0.63 (0.22), residues: 1526 helix: -1.08 (0.49), residues: 121 sheet: -0.02 (0.27), residues: 387 loop : -0.46 (0.21), residues: 1018 *********************** 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 119 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 1.489 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 115 average time/residue: 0.2405 time to fit residues: 41.8223 Evaluate side-chains 104 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1145 time to fit residues: 3.7944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 110 optimal weight: 0.3980 chunk 61 optimal weight: 0.0980 chunk 126 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.0370 chunk 132 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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** B 823 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12135 Z= 0.208 Angle : 0.526 18.223 16567 Z= 0.256 Chirality : 0.043 0.145 1818 Planarity : 0.004 0.072 2178 Dihedral : 4.112 19.568 1648 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.85 % 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: -0.65 (0.22), residues: 1526 helix: -1.09 (0.49), residues: 121 sheet: -0.05 (0.27), residues: 387 loop : -0.47 (0.21), residues: 1018 *********************** 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 108 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.434 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 105 average time/residue: 0.2355 time to fit residues: 37.0351 Evaluate side-chains 99 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1083 time to fit residues: 3.1724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 12135 Z= 0.345 Angle : 0.586 18.804 16567 Z= 0.289 Chirality : 0.045 0.155 1818 Planarity : 0.004 0.070 2178 Dihedral : 4.482 21.950 1648 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 2.09 % 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: -1.38 (0.47), residues: 121 sheet: -0.21 (0.27), residues: 380 loop : -0.60 (0.20), residues: 1025 *********************** 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 125 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.406 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 119 average time/residue: 0.2547 time to fit residues: 45.1986 Evaluate side-chains 108 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.448 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1060 time to fit residues: 4.8352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 0.0670 chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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** B 262 ASN B 285 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12135 Z= 0.190 Angle : 0.532 18.374 16567 Z= 0.259 Chirality : 0.043 0.145 1818 Planarity : 0.004 0.069 2178 Dihedral : 4.217 19.962 1648 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.08 % 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: -0.76 (0.22), residues: 1526 helix: -1.22 (0.48), residues: 121 sheet: -0.18 (0.27), residues: 388 loop : -0.51 (0.21), residues: 1017 *********************** 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 98 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.368 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 97 average time/residue: 0.2577 time to fit residues: 37.5651 Evaluate side-chains 91 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1169 time to fit residues: 2.1835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 12135 Z= 0.243 Angle : 0.553 18.216 16567 Z= 0.269 Chirality : 0.043 0.146 1818 Planarity : 0.004 0.065 2178 Dihedral : 4.261 19.871 1648 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 0.62 % 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: -0.82 (0.22), residues: 1526 helix: -1.37 (0.46), residues: 127 sheet: -0.16 (0.27), residues: 378 loop : -0.55 (0.20), residues: 1021 *********************** 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 100 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 1.242 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 96 average time/residue: 0.2498 time to fit residues: 35.9825 Evaluate side-chains 94 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.398 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1210 time to fit residues: 3.3653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 136 optimal weight: 0.0170 chunk 90 optimal weight: 0.9980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1103 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 12135 Z= 0.248 Angle : 0.555 18.331 16567 Z= 0.270 Chirality : 0.043 0.146 1818 Planarity : 0.004 0.065 2178 Dihedral : 4.295 19.917 1648 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer Outliers : 0.54 % 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: -0.84 (0.22), residues: 1526 helix: -1.36 (0.46), residues: 127 sheet: -0.22 (0.27), residues: 388 loop : -0.55 (0.21), residues: 1011 *********************** 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 95 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 1.395 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 0.2425 time to fit residues: 34.5344 Evaluate side-chains 89 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1091 time to fit residues: 2.7128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 152 optimal weight: 20.0000 chunk 140 optimal weight: 0.0570 chunk 121 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 74 optimal weight: 0.0060 chunk 96 optimal weight: 1.9990 overall best weight: 0.3714 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 12135 Z= 0.153 Angle : 0.523 17.771 16567 Z= 0.254 Chirality : 0.043 0.146 1818 Planarity : 0.004 0.065 2178 Dihedral : 4.062 19.815 1648 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer Outliers : 0.23 % 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: -0.66 (0.22), residues: 1526 helix: -1.04 (0.49), residues: 121 sheet: -0.13 (0.27), residues: 390 loop : -0.44 (0.21), residues: 1015 ********************** 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 95 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 1.628 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 95 average time/residue: 0.2432 time to fit residues: 34.8831 Evaluate side-chains 87 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 1.492 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1115 time to fit residues: 2.3476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 17 optimal weight: 0.0020 chunk 33 optimal weight: 9.9990 chunk 121 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 = 0.4519 r_free = 0.4519 target = 0.209368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.164437 restraints weight = 16072.963| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.22 r_work: 0.3672 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 12135 Z= 0.164 Angle : 0.518 17.707 16567 Z= 0.251 Chirality : 0.043 0.146 1818 Planarity : 0.004 0.067 2178 Dihedral : 3.996 19.500 1648 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.16 % 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: -0.60 (0.22), residues: 1526 helix: -0.97 (0.49), residues: 121 sheet: -0.06 (0.27), residues: 388 loop : -0.42 (0.21), residues: 1017 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2573.71 seconds wall clock time: 47 minutes 53.32 seconds (2873.32 seconds total)