Starting phenix.real_space_refine on Fri Mar 15 13:56:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8o_27253/03_2024/8d8o_27253.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8o_27253/03_2024/8d8o_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_27253/03_2024/8d8o_27253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8o_27253/03_2024/8d8o_27253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8o_27253/03_2024/8d8o_27253.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8o_27253/03_2024/8d8o_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-dev-5265/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: 6.45, per 1000 atoms: 0.55 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: 3.80 Conformation dependent library (CDL) restraints added in 2.1 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: 1.33 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: 4.39 Time building geometry restraints manager: 4.29 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: 0.000 Normalize map: mean=0, sd=1: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 17.710 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 34.470 Find NCS groups from input model: 0.300 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.370 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.258 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.2479 time to fit residues: 35.9971 Evaluate side-chains 96 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 % Allowed : 21.80 % Favored : 74.17 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1194 HIS 0.005 0.001 HIS B 234 PHE 0.023 0.001 PHE A1104 TYR 0.011 0.001 TYR B 131 ARG 0.002 0.000 ARG A1099 *********************** 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 : 1.334 Fit side-chains REVERT: B 668 ASP cc_start: 0.5948 (OUTLIER) cc_final: 0.5504 (p0) REVERT: B 942 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8140 (tm-30) outliers start: 52 outliers final: 34 residues processed: 144 average time/residue: 0.2215 time to fit residues: 47.4854 Evaluate side-chains 131 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 95 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 58 THR 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 163 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 ASN 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 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 668 ASP 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 882 ASP Chi-restraints excluded: chain B residue 899 VAL 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 1078 HIS 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: 0.8980 chunk 115 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 139 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 123 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8010 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12135 Z= 0.211 Angle : 0.526 18.427 16567 Z= 0.258 Chirality : 0.043 0.146 1818 Planarity : 0.004 0.096 2178 Dihedral : 4.159 20.342 1648 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.73 % Allowed : 21.10 % Favored : 74.17 % 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: -1.22 (0.48), residues: 121 sheet: -0.08 (0.28), residues: 379 loop : -0.53 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1194 HIS 0.004 0.001 HIS B 78 PHE 0.022 0.001 PHE A1104 TYR 0.011 0.001 TYR B 131 ARG 0.001 0.000 ARG A1099 *********************** 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 162 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 101 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: B 668 ASP cc_start: 0.5884 (OUTLIER) cc_final: 0.5455 (p0) REVERT: B 765 ASP cc_start: 0.7009 (t70) cc_final: 0.6805 (t70) REVERT: B 788 MET cc_start: 0.8587 (tpp) cc_final: 0.8341 (ttm) REVERT: B 920 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7689 (mp0) outliers start: 61 outliers final: 39 residues processed: 150 average time/residue: 0.2183 time to fit residues: 49.4365 Evaluate side-chains 138 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 97 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 926 THR 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 A residue 1224 THR 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 112 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 ASN 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 264 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 673 CYS 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 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 882 ASP Chi-restraints excluded: chain B residue 920 GLU 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 1078 HIS Chi-restraints excluded: chain B residue 1096 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.0570 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 66 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 147 optimal weight: 0.0570 chunk 132 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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: 0.7982 moved from start: 0.0775 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= 0.158 Angle : 0.506 17.980 16567 Z= 0.247 Chirality : 0.042 0.147 1818 Planarity : 0.004 0.084 2178 Dihedral : 4.010 19.761 1648 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.72 % Allowed : 22.42 % Favored : 73.86 % 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: -0.61 (0.22), residues: 1526 helix: -1.04 (0.49), residues: 121 sheet: 0.00 (0.27), residues: 387 loop : -0.45 (0.21), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 987 HIS 0.004 0.001 HIS B 78 PHE 0.020 0.001 PHE A1104 TYR 0.010 0.001 TYR B 131 ARG 0.004 0.000 ARG B1114 *********************** 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 148 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 100 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: B 128 MET cc_start: 0.8813 (mtm) cc_final: 0.8535 (mtm) REVERT: B 668 ASP cc_start: 0.5779 (OUTLIER) cc_final: 0.5346 (p0) REVERT: B 765 ASP cc_start: 0.6946 (t70) cc_final: 0.6717 (t70) REVERT: B 788 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8279 (ttm) REVERT: B 920 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: B 942 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8078 (tm-30) outliers start: 48 outliers final: 34 residues processed: 137 average time/residue: 0.2206 time to fit residues: 46.0605 Evaluate side-chains 133 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 95 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 58 THR 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 163 SER Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 ASN 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 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 558 TYR Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 673 CYS 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 879 GLN Chi-restraints excluded: chain B residue 882 ASP 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 1072 LEU 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 83 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 61 optimal weight: 0.0060 chunk 126 optimal weight: 0.6980 chunk 102 optimal weight: 0.0770 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 37 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 overall best weight: 0.2354 ------------------------------------------------------------------------------- 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: 0.7947 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12135 Z= 0.128 Angle : 0.494 17.480 16567 Z= 0.240 Chirality : 0.042 0.146 1818 Planarity : 0.004 0.073 2178 Dihedral : 3.863 19.388 1648 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.41 % Allowed : 22.73 % Favored : 73.86 % 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: -0.51 (0.22), residues: 1526 helix: -0.65 (0.52), residues: 114 sheet: 0.07 (0.27), residues: 389 loop : -0.43 (0.21), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 987 HIS 0.004 0.000 HIS B 78 PHE 0.018 0.001 PHE A1104 TYR 0.011 0.001 TYR B 131 ARG 0.003 0.000 ARG B1114 *********************** 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 150 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 106 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.5435 (ppp) cc_final: 0.5129 (ptm) REVERT: B 765 ASP cc_start: 0.7002 (t70) cc_final: 0.6779 (t70) REVERT: B 788 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8276 (ttm) REVERT: B 920 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: B 942 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8059 (tm-30) outliers start: 44 outliers final: 34 residues processed: 141 average time/residue: 0.2161 time to fit residues: 46.0629 Evaluate side-chains 136 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 99 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1044 ASP Chi-restraints excluded: chain A residue 1189 CYS Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 756 ASP 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 879 GLN 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 1072 LEU Chi-restraints excluded: chain B residue 1078 HIS 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 133 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 148 optimal weight: 0.0040 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8005 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12135 Z= 0.223 Angle : 0.527 18.675 16567 Z= 0.256 Chirality : 0.043 0.146 1818 Planarity : 0.004 0.067 2178 Dihedral : 4.031 19.093 1648 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.50 % Allowed : 21.88 % Favored : 73.62 % 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: -0.61 (0.22), residues: 1526 helix: -1.02 (0.49), residues: 121 sheet: 0.00 (0.27), residues: 387 loop : -0.45 (0.21), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 842 HIS 0.004 0.001 HIS B 234 PHE 0.022 0.001 PHE A1104 TYR 0.011 0.001 TYR B 578 ARG 0.002 0.000 ARG B1114 *********************** 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 161 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 103 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.5319 (ppp) cc_final: 0.5078 (ptm) REVERT: B 128 MET cc_start: 0.8860 (mtm) cc_final: 0.8572 (mtm) REVERT: B 668 ASP cc_start: 0.5854 (OUTLIER) cc_final: 0.5418 (p0) REVERT: B 765 ASP cc_start: 0.7002 (t70) cc_final: 0.6762 (t70) REVERT: B 788 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8356 (ttm) REVERT: B 920 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: B 942 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8039 (tm-30) outliers start: 58 outliers final: 43 residues processed: 150 average time/residue: 0.2051 time to fit residues: 47.0729 Evaluate side-chains 143 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 96 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 1015 VAL Chi-restraints excluded: chain A residue 1044 ASP Chi-restraints excluded: chain A residue 1189 CYS Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain B residue 58 THR 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 163 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 ASN 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 264 LEU Chi-restraints excluded: chain B residue 284 ASP 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 608 SER Chi-restraints excluded: chain B residue 668 ASP 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 882 ASP 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 1072 LEU Chi-restraints excluded: chain B residue 1078 HIS 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 16 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 89 optimal weight: 0.0070 chunk 68 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7996 moved from start: 0.1000 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= 0.194 Angle : 0.526 19.019 16567 Z= 0.255 Chirality : 0.043 0.146 1818 Planarity : 0.004 0.067 2178 Dihedral : 4.030 19.340 1648 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.34 % Allowed : 22.11 % 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: -0.60 (0.22), residues: 1526 helix: -1.00 (0.49), residues: 121 sheet: 0.01 (0.27), residues: 387 loop : -0.45 (0.21), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 842 HIS 0.004 0.001 HIS B 78 PHE 0.026 0.001 PHE A1218 TYR 0.010 0.001 TYR B 131 ARG 0.002 0.000 ARG B1114 *********************** 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 156 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 100 time to evaluate : 1.414 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.5345 (ppp) cc_final: 0.5109 (ptm) REVERT: B 128 MET cc_start: 0.8845 (mtm) cc_final: 0.8574 (mtm) REVERT: B 668 ASP cc_start: 0.5849 (OUTLIER) cc_final: 0.5419 (p0) REVERT: B 765 ASP cc_start: 0.7017 (t70) cc_final: 0.6793 (t70) REVERT: B 788 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8317 (ttm) REVERT: B 920 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: B 942 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7975 (tm-30) outliers start: 56 outliers final: 47 residues processed: 146 average time/residue: 0.2085 time to fit residues: 46.1951 Evaluate side-chains 148 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 97 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 1044 ASP Chi-restraints excluded: chain A residue 1189 CYS Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 82 ASP 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 163 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 220 MET 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 284 ASP 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 608 SER Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 673 CYS 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 882 ASP 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 1072 LEU Chi-restraints excluded: chain B residue 1078 HIS 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 58 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1103 ASN ** A1229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8058 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12135 Z= 0.344 Angle : 0.581 19.053 16567 Z= 0.286 Chirality : 0.045 0.151 1818 Planarity : 0.004 0.066 2178 Dihedral : 4.367 19.470 1648 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.34 % Allowed : 21.96 % Favored : 73.70 % 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: -1.40 (0.46), residues: 127 sheet: -0.21 (0.27), residues: 390 loop : -0.56 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 451 HIS 0.007 0.001 HIS B 234 PHE 0.025 0.002 PHE A1104 TYR 0.017 0.001 TYR B 275 ARG 0.003 0.000 ARG B1099 *********************** 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 150 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 94 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.5431 (ppp) cc_final: 0.5202 (ptm) REVERT: B 237 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8447 (tt) REVERT: B 668 ASP cc_start: 0.5680 (OUTLIER) cc_final: 0.5286 (p0) REVERT: B 765 ASP cc_start: 0.7094 (t70) cc_final: 0.6869 (t70) REVERT: B 920 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: B 942 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8288 (tm-30) outliers start: 56 outliers final: 46 residues processed: 143 average time/residue: 0.2067 time to fit residues: 45.9558 Evaluate side-chains 141 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 91 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 1044 ASP Chi-restraints excluded: chain A residue 1189 CYS Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 58 THR 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 163 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 ASN 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 284 ASP 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 565 ASP Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain B residue 668 ASP 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 809 VAL Chi-restraints excluded: chain B residue 823 HIS Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 882 ASP 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 1072 LEU Chi-restraints excluded: chain B residue 1078 HIS 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 128 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1201 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= 0.217 Angle : 0.540 19.135 16567 Z= 0.262 Chirality : 0.043 0.146 1818 Planarity : 0.004 0.066 2178 Dihedral : 4.213 19.722 1648 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.88 % Allowed : 22.34 % 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: -0.77 (0.22), residues: 1526 helix: -1.30 (0.46), residues: 127 sheet: -0.17 (0.27), residues: 389 loop : -0.51 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 313 HIS 0.004 0.001 HIS B 78 PHE 0.020 0.001 PHE A1104 TYR 0.012 0.001 TYR B 169 ARG 0.002 0.000 ARG B1114 *********************** 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 143 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 93 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.5405 (ppp) cc_final: 0.5146 (ptm) REVERT: B 650 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6931 (ptm) REVERT: B 668 ASP cc_start: 0.5619 (OUTLIER) cc_final: 0.5219 (p0) REVERT: B 765 ASP cc_start: 0.7019 (t70) cc_final: 0.6790 (t70) REVERT: B 920 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: B 942 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: B 1077 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.7855 (p90) outliers start: 50 outliers final: 45 residues processed: 136 average time/residue: 0.2061 time to fit residues: 42.7989 Evaluate side-chains 141 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 91 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 1044 ASP Chi-restraints excluded: chain A residue 1189 CYS Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 58 THR 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 163 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 ASN 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 284 ASP 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 608 SER Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 668 ASP 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 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 882 ASP 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 1072 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 152 optimal weight: 30.0000 chunk 140 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 96 optimal weight: 2.9990 overall best weight: 1.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN B1070 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12135 Z= 0.374 Angle : 0.610 19.388 16567 Z= 0.300 Chirality : 0.045 0.161 1818 Planarity : 0.004 0.068 2178 Dihedral : 4.580 22.003 1648 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.27 % Allowed : 21.96 % 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: -1.02 (0.22), residues: 1526 helix: -1.58 (0.45), residues: 128 sheet: -0.35 (0.27), residues: 390 loop : -0.67 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 451 HIS 0.007 0.001 HIS B 234 PHE 0.026 0.002 PHE A1104 TYR 0.019 0.001 TYR B 275 ARG 0.002 0.000 ARG A1099 ********************** 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 144 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 89 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.5472 (ppp) cc_final: 0.5256 (ptm) REVERT: B 237 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8445 (tt) REVERT: B 650 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6838 (ptm) REVERT: B 765 ASP cc_start: 0.7065 (t70) cc_final: 0.6845 (t70) REVERT: B 920 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: B 942 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8275 (tm-30) outliers start: 55 outliers final: 46 residues processed: 136 average time/residue: 0.2096 time to fit residues: 43.2580 Evaluate side-chains 138 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 88 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 1044 ASP Chi-restraints excluded: chain A residue 1189 CYS Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 58 THR 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 163 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 ASN 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 284 ASP 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 565 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain B residue 650 MET 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 809 VAL Chi-restraints excluded: chain B residue 823 HIS Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 882 ASP 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 1072 LEU Chi-restraints excluded: chain B residue 1078 HIS 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 129 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 121 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 chunk 124 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.208590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.163174 restraints weight = 16134.019| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.30 r_work: 0.3632 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1331 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 : 0.531 19.094 16567 Z= 0.257 Chirality : 0.043 0.147 1818 Planarity : 0.004 0.066 2178 Dihedral : 4.196 20.438 1648 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.57 % Allowed : 22.58 % Favored : 73.86 % 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: -1.29 (0.47), residues: 127 sheet: -0.17 (0.27), residues: 388 loop : -0.49 (0.21), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 210 HIS 0.005 0.001 HIS B 78 PHE 0.017 0.001 PHE A1104 TYR 0.012 0.001 TYR B 131 ARG 0.002 0.000 ARG B1114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2645.73 seconds wall clock time: 48 minutes 30.81 seconds (2910.81 seconds total)