Starting phenix.real_space_refine on Wed Apr 30 23:40:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ox4_17256/04_2025/8ox4_17256.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ox4_17256/04_2025/8ox4_17256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ox4_17256/04_2025/8ox4_17256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ox4_17256/04_2025/8ox4_17256.map" model { file = "/net/cci-nas-00/data/ceres_data/8ox4_17256/04_2025/8ox4_17256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ox4_17256/04_2025/8ox4_17256.cif" } resolution = 3.4 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 6310 2.51 5 N 1610 2.21 5 O 1786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9757 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 7015 Classifications: {'peptide': 870} Link IDs: {'PTRANS': 20, 'TRANS': 849} Chain breaks: 4 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.37, per 1000 atoms: 0.65 Number of scatterers: 9757 At special positions: 0 Unit cell: (87.992, 95.756, 170.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 3 15.00 Mg 1 11.99 O 1786 8.00 N 1610 7.00 C 6310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 56.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.678A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 removed outlier: 3.601A pdb=" N ILE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 174 removed outlier: 3.503A pdb=" N VAL A 146 " --> pdb=" O TYR A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.726A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 366 removed outlier: 3.510A pdb=" N VAL A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 392 removed outlier: 3.840A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 400 removed outlier: 4.351A pdb=" N THR A 398 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 402 No H-bonds generated for 'chain 'A' and resid 401 through 402' Processing helix chain 'A' and resid 403 through 422 removed outlier: 4.008A pdb=" N GLU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 448 removed outlier: 4.033A pdb=" N ILE A 448 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 552 through 564 removed outlier: 3.750A pdb=" N ASN A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 removed outlier: 3.980A pdb=" N GLU A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 648 Processing helix chain 'A' and resid 662 through 677 removed outlier: 4.452A pdb=" N GLU A 668 " --> pdb=" O LYS A 664 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 669 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 682 through 695 removed outlier: 3.855A pdb=" N LEU A 687 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP A 688 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 removed outlier: 3.580A pdb=" N ALA A 724 " --> pdb=" O LYS A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 746 Processing helix chain 'A' and resid 757 through 773 Processing helix chain 'A' and resid 803 through 811 removed outlier: 3.576A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 858 Processing helix chain 'A' and resid 869 through 885 removed outlier: 3.674A pdb=" N VAL A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 897 through 904 removed outlier: 3.603A pdb=" N THR A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 930 No H-bonds generated for 'chain 'A' and resid 928 through 930' Processing helix chain 'A' and resid 931 through 938 removed outlier: 3.502A pdb=" N LEU A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 960 removed outlier: 4.033A pdb=" N TYR A 956 " --> pdb=" O ARG A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 969 removed outlier: 3.731A pdb=" N PHE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 973 removed outlier: 4.102A pdb=" N GLY A 973 " --> pdb=" O PHE A 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 970 through 973' Processing helix chain 'A' and resid 981 through 991 removed outlier: 3.982A pdb=" N THR A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 987 " --> pdb=" O TRP A 983 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 Processing helix chain 'A' and resid 1008 through 1014 Processing helix chain 'A' and resid 1015 through 1018 Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.592A pdb=" N GLN A1023 " --> pdb=" O TYR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1057 Proline residue: A1051 - end of helix removed outlier: 4.056A pdb=" N GLN A1057 " --> pdb=" O GLY A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1092 removed outlier: 3.795A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1118 removed outlier: 3.732A pdb=" N PHE A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1126 removed outlier: 3.696A pdb=" N HIS A1123 " --> pdb=" O SER A1119 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A1124 " --> pdb=" O ALA A1120 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU A1125 " --> pdb=" O GLY A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1140 removed outlier: 3.553A pdb=" N LEU A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1171 removed outlier: 3.527A pdb=" N TRP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS A1156 " --> pdb=" O THR A1152 " (cutoff:3.500A) Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1173 through 1181 removed outlier: 3.661A pdb=" N HIS A1181 " --> pdb=" O LYS A1177 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 75 removed outlier: 3.772A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.557A pdb=" N ILE B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Proline residue: B 63 - end of helix removed outlier: 3.654A pdb=" N ILE B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.793A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 171 through 177 removed outlier: 4.307A pdb=" N ALA B 175 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.639A pdb=" N ARG B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.841A pdb=" N MET B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B 243 " --> pdb=" O VAL B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 243' Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.514A pdb=" N ASP B 305 " --> pdb=" O HIS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 351 removed outlier: 3.659A pdb=" N GLY B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 426 through 427 removed outlier: 3.833A pdb=" N TYR A 427 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 801 through 802 removed outlier: 6.581A pdb=" N ILE A 801 " --> pdb=" O CYS A 866 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE A 728 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N CYS A 865 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 730 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE A 451 " --> pdb=" O TRP A 729 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU A 731 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N SER A 453 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 888 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A 908 " --> pdb=" O THR A 888 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA A 890 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.539A pdb=" N THR A 465 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE A 471 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU A 701 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 701 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 592 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.539A pdb=" N THR A 465 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE A 471 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU A 701 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 540 removed outlier: 3.546A pdb=" N MET A 538 " --> pdb=" O GLN A 549 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 567 through 572 removed outlier: 6.669A pdb=" N THR A 578 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1095 through 1096 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.842A pdb=" N VAL B 118 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU B 275 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET B 120 " --> pdb=" O TYR B 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 109 removed outlier: 4.108A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1347 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: 3.53 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3070 1.35 - 1.48: 2608 1.48 - 1.60: 4232 1.60 - 1.73: 4 1.73 - 1.86: 76 Bond restraints: 9990 Sorted by residual: bond pdb=" C1' ACP A1201 " pdb=" O4' ACP A1201 " ideal model delta sigma weight residual 1.390 1.618 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ACP A1201 " pdb=" C2' ACP A1201 " ideal model delta sigma weight residual 1.527 1.315 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C4' ACP A1201 " pdb=" O4' ACP A1201 " ideal model delta sigma weight residual 1.428 1.305 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C6 ACP A1201 " pdb=" N6 ACP A1201 " ideal model delta sigma weight residual 1.335 1.452 -0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C2' ACP A1201 " pdb=" O2' ACP A1201 " ideal model delta sigma weight residual 1.401 1.493 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 9985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 13469 3.05 - 6.09: 75 6.09 - 9.14: 7 9.14 - 12.19: 3 12.19 - 15.23: 3 Bond angle restraints: 13557 Sorted by residual: angle pdb=" O3A ACP A1201 " pdb=" PA ACP A1201 " pdb=" O5' ACP A1201 " ideal model delta sigma weight residual 93.75 108.98 -15.23 3.00e+00 1.11e-01 2.58e+01 angle pdb=" N1 ACP A1201 " pdb=" C6 ACP A1201 " pdb=" N6 ACP A1201 " ideal model delta sigma weight residual 119.32 104.55 14.77 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C5 ACP A1201 " pdb=" C6 ACP A1201 " pdb=" N6 ACP A1201 " ideal model delta sigma weight residual 122.65 135.47 -12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" C3B ACP A1201 " pdb=" PB ACP A1201 " pdb=" O3A ACP A1201 " ideal model delta sigma weight residual 98.05 109.44 -11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" O1B ACP A1201 " pdb=" PB ACP A1201 " pdb=" O2B ACP A1201 " ideal model delta sigma weight residual 119.60 109.44 10.16 3.00e+00 1.11e-01 1.15e+01 ... (remaining 13552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.56: 5817 33.56 - 67.12: 150 67.12 - 100.68: 16 100.68 - 134.24: 4 134.24 - 167.80: 1 Dihedral angle restraints: 5988 sinusoidal: 2480 harmonic: 3508 Sorted by residual: dihedral pdb=" O1A ACP A1201 " pdb=" O3A ACP A1201 " pdb=" PA ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sinusoidal sigma weight residual 311.25 143.45 167.80 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA PRO B 90 " pdb=" C PRO B 90 " pdb=" N CYS B 91 " pdb=" CA CYS B 91 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ILE A 463 " pdb=" C ILE A 463 " pdb=" N MET A 464 " pdb=" CA MET A 464 " ideal model delta harmonic sigma weight residual -180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1392 0.066 - 0.132: 125 0.132 - 0.198: 8 0.198 - 0.264: 1 0.264 - 0.330: 1 Chirality restraints: 1527 Sorted by residual: chirality pdb=" C2' ACP A1201 " pdb=" C1' ACP A1201 " pdb=" C3' ACP A1201 " pdb=" O2' ACP A1201 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ILE A 864 " pdb=" N ILE A 864 " pdb=" C ILE A 864 " pdb=" CB ILE A 864 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 1524 not shown) Planarity restraints: 1701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A1131 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C GLN A1131 " 0.038 2.00e-02 2.50e+03 pdb=" O GLN A1131 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A1132 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 169 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO B 170 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 195 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO B 196 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.024 5.00e-02 4.00e+02 ... (remaining 1698 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 65 2.50 - 3.10: 7405 3.10 - 3.70: 14750 3.70 - 4.30: 22555 4.30 - 4.90: 37160 Nonbonded interactions: 81935 Sorted by model distance: nonbonded pdb=" O LEU A 441 " pdb=" OH TYR A 924 " model vdw 1.898 3.040 nonbonded pdb=" OD2 ASP A 454 " pdb="MG MG A1202 " model vdw 1.947 2.170 nonbonded pdb=" O THR A 978 " pdb=" OH TYR A1069 " model vdw 1.988 3.040 nonbonded pdb=" O VAL A 990 " pdb=" OG SER A 994 " model vdw 2.046 3.040 nonbonded pdb=" O THR A 635 " pdb=" OG1 THR A 639 " model vdw 2.057 3.040 ... (remaining 81930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.570 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.040 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 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 : 0.005 0.228 9998 Z= 0.235 Angle : 0.615 15.233 13578 Z= 0.288 Chirality : 0.040 0.330 1527 Planarity : 0.004 0.047 1698 Dihedral : 15.727 167.799 3721 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1186 helix: -0.18 (0.22), residues: 565 sheet: 0.35 (0.47), residues: 131 loop : -0.80 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1171 HIS 0.003 0.001 HIS A 535 PHE 0.011 0.001 PHE A1132 TYR 0.012 0.001 TYR A 427 ARG 0.003 0.000 ARG A 602 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 3) link_NAG-ASN : angle 1.27202 ( 9) link_BETA1-4 : bond 0.01166 ( 2) link_BETA1-4 : angle 2.73507 ( 6) hydrogen bonds : bond 0.24929 ( 466) hydrogen bonds : angle 8.83843 ( 1347) SS BOND : bond 0.00558 ( 3) SS BOND : angle 1.25635 ( 6) covalent geometry : bond 0.00492 ( 9990) covalent geometry : angle 0.61102 (13557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 CYS cc_start: 0.7910 (t) cc_final: 0.6926 (t) REVERT: A 535 HIS cc_start: 0.8220 (p-80) cc_final: 0.7454 (p-80) REVERT: A 654 LEU cc_start: 0.6891 (mp) cc_final: 0.6538 (mp) REVERT: A 799 LEU cc_start: 0.8033 (mp) cc_final: 0.7535 (tt) REVERT: A 864 ILE cc_start: 0.7763 (mm) cc_final: 0.7477 (mm) REVERT: B 29 ASP cc_start: 0.6342 (t0) cc_final: 0.6072 (t70) REVERT: B 45 LEU cc_start: 0.7526 (mt) cc_final: 0.7264 (mt) REVERT: B 79 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7143 (mt-10) REVERT: B 277 GLU cc_start: 0.5944 (mt-10) cc_final: 0.5718 (mt-10) REVERT: B 310 MET cc_start: 0.8072 (tmm) cc_final: 0.7774 (tmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2379 time to fit residues: 44.7189 Evaluate side-chains 114 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.2980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.0050 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS A 526 GLN A 741 ASN A1138 ASN B 254 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.239678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.231744 restraints weight = 9925.946| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 0.29 r_work: 0.4321 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.4243 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9998 Z= 0.159 Angle : 0.604 9.531 13578 Z= 0.311 Chirality : 0.043 0.238 1527 Planarity : 0.005 0.044 1698 Dihedral : 10.407 179.465 1442 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.57 % Allowed : 7.44 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1186 helix: 0.33 (0.21), residues: 597 sheet: 0.37 (0.46), residues: 146 loop : -0.83 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1171 HIS 0.005 0.001 HIS A 939 PHE 0.029 0.002 PHE A 113 TYR 0.013 0.001 TYR A 924 ARG 0.003 0.000 ARG A 412 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 3) link_NAG-ASN : angle 1.35060 ( 9) link_BETA1-4 : bond 0.01897 ( 2) link_BETA1-4 : angle 3.03409 ( 6) hydrogen bonds : bond 0.04942 ( 466) hydrogen bonds : angle 5.67088 ( 1347) SS BOND : bond 0.00309 ( 3) SS BOND : angle 1.09711 ( 6) covalent geometry : bond 0.00366 ( 9990) covalent geometry : angle 0.59973 (13557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 875 MET cc_start: 0.7659 (ttp) cc_final: 0.7237 (ttt) REVERT: B 79 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7419 (mt-10) outliers start: 6 outliers final: 2 residues processed: 125 average time/residue: 0.2540 time to fit residues: 46.7531 Evaluate side-chains 109 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 439 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 73 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS ** A 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.236580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.227373 restraints weight = 9945.481| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 0.34 r_work: 0.4297 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.4213 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9998 Z= 0.157 Angle : 0.565 9.451 13578 Z= 0.287 Chirality : 0.042 0.251 1527 Planarity : 0.004 0.037 1698 Dihedral : 9.097 172.050 1442 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.24 % Allowed : 10.01 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1186 helix: 0.52 (0.22), residues: 593 sheet: 0.31 (0.45), residues: 151 loop : -0.86 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1171 HIS 0.011 0.001 HIS A 535 PHE 0.023 0.002 PHE A 113 TYR 0.012 0.001 TYR A 924 ARG 0.004 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00060 ( 3) link_NAG-ASN : angle 1.50797 ( 9) link_BETA1-4 : bond 0.01801 ( 2) link_BETA1-4 : angle 3.15107 ( 6) hydrogen bonds : bond 0.04370 ( 466) hydrogen bonds : angle 5.26233 ( 1347) SS BOND : bond 0.00338 ( 3) SS BOND : angle 1.05710 ( 6) covalent geometry : bond 0.00374 ( 9990) covalent geometry : angle 0.55958 (13557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 448 ILE cc_start: 0.9135 (mt) cc_final: 0.8933 (mt) REVERT: A 1131 GLN cc_start: 0.7499 (pp30) cc_final: 0.7013 (pt0) REVERT: B 45 LEU cc_start: 0.7680 (mt) cc_final: 0.7477 (mt) outliers start: 13 outliers final: 7 residues processed: 125 average time/residue: 0.2647 time to fit residues: 49.2960 Evaluate side-chains 118 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 59 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN A1087 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.239304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.229624 restraints weight = 9976.905| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 0.41 r_work: 0.4293 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.4193 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9998 Z= 0.151 Angle : 0.546 9.541 13578 Z= 0.277 Chirality : 0.041 0.252 1527 Planarity : 0.004 0.037 1698 Dihedral : 8.405 163.892 1442 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.72 % Allowed : 11.63 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1186 helix: 0.59 (0.22), residues: 600 sheet: 0.40 (0.45), residues: 147 loop : -0.92 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1171 HIS 0.009 0.001 HIS A 535 PHE 0.026 0.002 PHE A 646 TYR 0.012 0.001 TYR A 924 ARG 0.005 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 3) link_NAG-ASN : angle 1.50562 ( 9) link_BETA1-4 : bond 0.01810 ( 2) link_BETA1-4 : angle 3.25252 ( 6) hydrogen bonds : bond 0.03996 ( 466) hydrogen bonds : angle 5.03340 ( 1347) SS BOND : bond 0.00278 ( 3) SS BOND : angle 1.05897 ( 6) covalent geometry : bond 0.00365 ( 9990) covalent geometry : angle 0.54035 (13557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.5078 (tpt) cc_final: 0.4736 (tpp) REVERT: A 397 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.7881 (p0) REVERT: A 1131 GLN cc_start: 0.7481 (pp30) cc_final: 0.7170 (pt0) outliers start: 18 outliers final: 10 residues processed: 135 average time/residue: 0.2371 time to fit residues: 47.0890 Evaluate side-chains 123 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 51 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1087 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.236267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.226681 restraints weight = 9861.431| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 0.33 r_work: 0.4298 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.4184 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9998 Z= 0.160 Angle : 0.555 9.553 13578 Z= 0.280 Chirality : 0.041 0.252 1527 Planarity : 0.004 0.039 1698 Dihedral : 8.108 154.696 1442 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.81 % Allowed : 13.06 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1186 helix: 0.60 (0.22), residues: 599 sheet: 0.39 (0.45), residues: 147 loop : -0.95 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1171 HIS 0.005 0.001 HIS A 535 PHE 0.029 0.002 PHE A 646 TYR 0.012 0.001 TYR A 924 ARG 0.005 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 3) link_NAG-ASN : angle 1.51113 ( 9) link_BETA1-4 : bond 0.01848 ( 2) link_BETA1-4 : angle 3.42503 ( 6) hydrogen bonds : bond 0.03925 ( 466) hydrogen bonds : angle 4.96583 ( 1347) SS BOND : bond 0.00285 ( 3) SS BOND : angle 1.07890 ( 6) covalent geometry : bond 0.00390 ( 9990) covalent geometry : angle 0.54904 (13557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.7887 (p0) REVERT: A 1087 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7846 (tm130) REVERT: A 1104 PHE cc_start: 0.7939 (m-10) cc_final: 0.7665 (m-10) REVERT: A 1131 GLN cc_start: 0.7456 (pp30) cc_final: 0.7138 (pt0) REVERT: B 45 LEU cc_start: 0.7707 (mt) cc_final: 0.7063 (mt) outliers start: 19 outliers final: 13 residues processed: 125 average time/residue: 0.2134 time to fit residues: 39.0381 Evaluate side-chains 121 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 104 optimal weight: 0.0030 chunk 41 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 81 optimal weight: 0.0020 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1087 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.241571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.203714 restraints weight = 9908.842| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.13 r_work: 0.3638 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9998 Z= 0.114 Angle : 0.519 9.546 13578 Z= 0.262 Chirality : 0.040 0.253 1527 Planarity : 0.004 0.035 1698 Dihedral : 7.862 147.180 1442 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.72 % Allowed : 14.01 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1186 helix: 0.76 (0.22), residues: 601 sheet: 0.56 (0.46), residues: 145 loop : -0.93 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1171 HIS 0.004 0.001 HIS A1118 PHE 0.023 0.001 PHE A 646 TYR 0.012 0.001 TYR A 924 ARG 0.006 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 3) link_NAG-ASN : angle 1.50520 ( 9) link_BETA1-4 : bond 0.01818 ( 2) link_BETA1-4 : angle 3.26490 ( 6) hydrogen bonds : bond 0.03576 ( 466) hydrogen bonds : angle 4.82072 ( 1347) SS BOND : bond 0.00244 ( 3) SS BOND : angle 0.89993 ( 6) covalent geometry : bond 0.00263 ( 9990) covalent geometry : angle 0.51275 (13557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.7948 (p0) REVERT: A 1104 PHE cc_start: 0.8048 (m-10) cc_final: 0.7815 (m-10) REVERT: A 1131 GLN cc_start: 0.7465 (pp30) cc_final: 0.6984 (pt0) REVERT: B 45 LEU cc_start: 0.7757 (mt) cc_final: 0.7171 (mt) REVERT: B 348 HIS cc_start: 0.6677 (t-90) cc_final: 0.6474 (t70) outliers start: 18 outliers final: 11 residues processed: 121 average time/residue: 0.2027 time to fit residues: 36.0355 Evaluate side-chains 123 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 100 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.240218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.239050 restraints weight = 9982.710| |-----------------------------------------------------------------------------| r_work (start): 0.4484 rms_B_bonded: 0.05 r_work: 0.4464 rms_B_bonded: 0.21 restraints_weight: 0.5000 r_work: 0.4428 rms_B_bonded: 0.68 restraints_weight: 0.2500 r_work: 0.4267 rms_B_bonded: 3.72 restraints_weight: 0.1250 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9998 Z= 0.136 Angle : 0.528 9.564 13578 Z= 0.267 Chirality : 0.040 0.254 1527 Planarity : 0.004 0.037 1698 Dihedral : 7.681 136.301 1442 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.53 % Allowed : 14.68 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1186 helix: 0.78 (0.22), residues: 601 sheet: 0.59 (0.46), residues: 145 loop : -0.94 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1171 HIS 0.007 0.001 HIS A1118 PHE 0.034 0.001 PHE A 646 TYR 0.011 0.001 TYR A 924 ARG 0.006 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 3) link_NAG-ASN : angle 1.51890 ( 9) link_BETA1-4 : bond 0.01783 ( 2) link_BETA1-4 : angle 3.37475 ( 6) hydrogen bonds : bond 0.03627 ( 466) hydrogen bonds : angle 4.75510 ( 1347) SS BOND : bond 0.00258 ( 3) SS BOND : angle 0.98147 ( 6) covalent geometry : bond 0.00327 ( 9990) covalent geometry : angle 0.52153 (13557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.7913 (p0) REVERT: A 554 ASP cc_start: 0.7387 (t0) cc_final: 0.7179 (t0) REVERT: A 1055 TYR cc_start: 0.8337 (m-80) cc_final: 0.8056 (m-80) REVERT: A 1104 PHE cc_start: 0.7988 (m-10) cc_final: 0.7712 (m-10) REVERT: B 144 ASN cc_start: 0.7627 (t0) cc_final: 0.7307 (t0) REVERT: B 318 MET cc_start: 0.4072 (tpp) cc_final: 0.3849 (tpp) outliers start: 16 outliers final: 13 residues processed: 123 average time/residue: 0.2273 time to fit residues: 41.3685 Evaluate side-chains 122 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1087 GLN ** 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 = 0.4486 r_free = 0.4486 target = 0.240661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.179742 restraints weight = 99327.762| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 11.38 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9998 Z= 0.133 Angle : 0.524 9.592 13578 Z= 0.265 Chirality : 0.040 0.255 1527 Planarity : 0.004 0.037 1698 Dihedral : 7.582 130.739 1442 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.33 % Allowed : 15.06 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1186 helix: 0.81 (0.22), residues: 601 sheet: 0.66 (0.46), residues: 145 loop : -0.94 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1171 HIS 0.004 0.001 HIS A 535 PHE 0.028 0.001 PHE A 646 TYR 0.011 0.001 TYR A 924 ARG 0.003 0.000 ARG B 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00032 ( 3) link_NAG-ASN : angle 1.50705 ( 9) link_BETA1-4 : bond 0.01815 ( 2) link_BETA1-4 : angle 3.32980 ( 6) hydrogen bonds : bond 0.03554 ( 466) hydrogen bonds : angle 4.69857 ( 1347) SS BOND : bond 0.00232 ( 3) SS BOND : angle 0.98300 ( 6) covalent geometry : bond 0.00319 ( 9990) covalent geometry : angle 0.51821 (13557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7804 (p0) REVERT: A 1104 PHE cc_start: 0.7820 (m-10) cc_final: 0.7532 (m-10) REVERT: B 144 ASN cc_start: 0.7915 (t0) cc_final: 0.7672 (t0) REVERT: B 318 MET cc_start: 0.4841 (tpp) cc_final: 0.4426 (tpp) outliers start: 14 outliers final: 11 residues processed: 121 average time/residue: 0.3176 time to fit residues: 59.2951 Evaluate side-chains 118 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 39 optimal weight: 0.0370 chunk 35 optimal weight: 10.0000 chunk 108 optimal weight: 0.0670 chunk 77 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 18 optimal weight: 0.0570 overall best weight: 0.2312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.241030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.188288 restraints weight = 9948.014| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.32 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9998 Z= 0.099 Angle : 0.509 9.539 13578 Z= 0.256 Chirality : 0.039 0.255 1527 Planarity : 0.004 0.041 1698 Dihedral : 7.414 127.065 1442 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.14 % Allowed : 15.35 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1186 helix: 1.01 (0.22), residues: 601 sheet: 0.70 (0.46), residues: 146 loop : -0.93 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1171 HIS 0.004 0.001 HIS A1118 PHE 0.026 0.001 PHE A 646 TYR 0.011 0.001 TYR A 924 ARG 0.007 0.000 ARG B 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 3) link_NAG-ASN : angle 1.54880 ( 9) link_BETA1-4 : bond 0.01771 ( 2) link_BETA1-4 : angle 3.01868 ( 6) hydrogen bonds : bond 0.03172 ( 466) hydrogen bonds : angle 4.53714 ( 1347) SS BOND : bond 0.00261 ( 3) SS BOND : angle 0.80958 ( 6) covalent geometry : bond 0.00221 ( 9990) covalent geometry : angle 0.50340 (13557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7609 (p0) REVERT: A 535 HIS cc_start: 0.8546 (p-80) cc_final: 0.8079 (p-80) REVERT: A 1104 PHE cc_start: 0.7755 (m-10) cc_final: 0.7462 (m-10) REVERT: B 144 ASN cc_start: 0.7624 (t0) cc_final: 0.7296 (t0) REVERT: B 318 MET cc_start: 0.4062 (tpp) cc_final: 0.3821 (tpp) outliers start: 12 outliers final: 10 residues processed: 124 average time/residue: 0.1992 time to fit residues: 36.5330 Evaluate side-chains 116 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 13 optimal weight: 0.0470 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 630 HIS ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.240434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.232675 restraints weight = 9895.856| |-----------------------------------------------------------------------------| r_work (start): 0.4447 rms_B_bonded: 0.33 r_work: 0.4344 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.4263 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9998 Z= 0.118 Angle : 0.528 9.560 13578 Z= 0.265 Chirality : 0.040 0.256 1527 Planarity : 0.004 0.039 1698 Dihedral : 7.410 123.189 1442 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.53 % Allowed : 16.21 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1186 helix: 0.97 (0.22), residues: 601 sheet: 0.76 (0.46), residues: 146 loop : -0.91 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1171 HIS 0.011 0.001 HIS A1118 PHE 0.038 0.001 PHE A 646 TYR 0.011 0.001 TYR B 122 ARG 0.010 0.000 ARG B 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 3) link_NAG-ASN : angle 1.51639 ( 9) link_BETA1-4 : bond 0.01695 ( 2) link_BETA1-4 : angle 3.04479 ( 6) hydrogen bonds : bond 0.03322 ( 466) hydrogen bonds : angle 4.56098 ( 1347) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.88247 ( 6) covalent geometry : bond 0.00283 ( 9990) covalent geometry : angle 0.52240 (13557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7611 (p0) REVERT: A 1055 TYR cc_start: 0.8231 (m-80) cc_final: 0.7669 (m-80) REVERT: A 1131 GLN cc_start: 0.7711 (pp30) cc_final: 0.7126 (pt0) REVERT: B 144 ASN cc_start: 0.7568 (t0) cc_final: 0.7175 (t0) REVERT: B 318 MET cc_start: 0.4296 (tpp) cc_final: 0.4058 (tpp) outliers start: 16 outliers final: 12 residues processed: 119 average time/residue: 0.2107 time to fit residues: 36.8007 Evaluate side-chains 118 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 850 GLN Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1114 MET Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 chunk 51 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 101 optimal weight: 0.2980 chunk 105 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.240895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.234735 restraints weight = 9857.654| |-----------------------------------------------------------------------------| r_work (start): 0.4456 rms_B_bonded: 0.25 r_work: 0.4384 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.4299 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9998 Z= 0.111 Angle : 0.526 9.545 13578 Z= 0.265 Chirality : 0.040 0.256 1527 Planarity : 0.004 0.040 1698 Dihedral : 7.348 120.139 1442 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.33 % Allowed : 16.78 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1186 helix: 0.96 (0.22), residues: 601 sheet: 0.51 (0.46), residues: 152 loop : -0.86 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A1171 HIS 0.011 0.001 HIS A1118 PHE 0.044 0.001 PHE A 646 TYR 0.011 0.001 TYR A 924 ARG 0.011 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 3) link_NAG-ASN : angle 1.54279 ( 9) link_BETA1-4 : bond 0.01637 ( 2) link_BETA1-4 : angle 2.91841 ( 6) hydrogen bonds : bond 0.03276 ( 466) hydrogen bonds : angle 4.53564 ( 1347) SS BOND : bond 0.00233 ( 3) SS BOND : angle 0.83593 ( 6) covalent geometry : bond 0.00260 ( 9990) covalent geometry : angle 0.52148 (13557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4730.03 seconds wall clock time: 84 minutes 34.13 seconds (5074.13 seconds total)