Starting phenix.real_space_refine on Fri Jul 3 05:46:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asq_43823/07_2026/9asq_43823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asq_43823/07_2026/9asq_43823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9asq_43823/07_2026/9asq_43823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asq_43823/07_2026/9asq_43823.map" model { file = "/net/cci-nas-00/data/ceres_data/9asq_43823/07_2026/9asq_43823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asq_43823/07_2026/9asq_43823.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.010 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 100 5.49 5 S 64 5.16 5 C 7440 2.51 5 N 2181 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12359 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 7499 Classifications: {'peptide': 916} Link IDs: {'PTRANS': 52, 'TRANS': 863} Chain breaks: 1 Chain: "B" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1893 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain breaks: 3 Chain: "C" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 203 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "E" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 2124 Classifications: {'RNA': 100} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 11, 'rna3p_pur': 43, 'rna3p_pyr': 39} Link IDs: {'rna2p': 17, 'rna3p': 82} Chain breaks: 2 Chain: "H" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 634 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 2 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 943 SG CYS A 561 43.251 80.565 45.819 1.00172.12 S ATOM 1901 SG CYS A 676 40.237 78.211 46.106 1.00178.36 S ATOM 751 SG CYS A 536 24.714 61.390 60.880 1.00181.72 S ATOM 766 SG CYS A 538 24.343 60.178 64.537 1.00190.39 S Time building chain proxies: 2.19, per 1000 atoms: 0.18 Number of scatterers: 12359 At special positions: 0 Unit cell: (87.312, 102.72, 193.456, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 64 16.00 P 100 15.00 O 2570 8.00 N 2181 7.00 C 7440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 505.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 609 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 680 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 676 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 561 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A1026 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A 549 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 536 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 538 " Number of angles added : 4 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 9 sheets defined 53.5% alpha, 12.3% beta 35 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.612A pdb=" N ARG A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 463 removed outlier: 3.580A pdb=" N ALA A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 512 Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.718A pdb=" N THR A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 removed outlier: 3.629A pdb=" N ILE A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 710 removed outlier: 3.573A pdb=" N ILE A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.697A pdb=" N CYS A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 786 Processing helix chain 'A' and resid 787 through 806 removed outlier: 3.602A pdb=" N ASN A 806 " --> pdb=" O HIS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 830 removed outlier: 3.981A pdb=" N LYS A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 817 " --> pdb=" O THR A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.790A pdb=" N CYS A 857 " --> pdb=" O ARG A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.697A pdb=" N LEU A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET A 877 " --> pdb=" O HIS A 873 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N HIS A 878 " --> pdb=" O GLN A 874 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 879 " --> pdb=" O CYS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 896 removed outlier: 3.568A pdb=" N LEU A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 920 Processing helix chain 'A' and resid 930 through 935 removed outlier: 4.473A pdb=" N HIS A 934 " --> pdb=" O ARG A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 950 Processing helix chain 'A' and resid 965 through 988 removed outlier: 3.712A pdb=" N PHE A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 971 " --> pdb=" O ARG A 967 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1004 Processing helix chain 'A' and resid 1005 through 1017 removed outlier: 3.799A pdb=" N LYS A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1021 Processing helix chain 'A' and resid 1032 through 1055 removed outlier: 3.505A pdb=" N LEU A1036 " --> pdb=" O ARG A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1069 removed outlier: 3.528A pdb=" N ALA A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1079 Processing helix chain 'A' and resid 1084 through 1090 removed outlier: 3.930A pdb=" N GLU A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1098 Processing helix chain 'A' and resid 1101 through 1115 removed outlier: 3.631A pdb=" N GLN A1105 " --> pdb=" O SER A1101 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A1109 " --> pdb=" O GLN A1105 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A1110 " --> pdb=" O LYS A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 removed outlier: 4.062A pdb=" N LEU A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1166 removed outlier: 3.519A pdb=" N GLU A1147 " --> pdb=" O ASN A1143 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1183 Processing helix chain 'A' and resid 1183 through 1195 Processing helix chain 'A' and resid 1196 through 1199 removed outlier: 3.640A pdb=" N TYR A1199 " --> pdb=" O MET A1196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1196 through 1199' Processing helix chain 'A' and resid 1203 through 1208 removed outlier: 3.994A pdb=" N LYS A1207 " --> pdb=" O ASN A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1232 Processing helix chain 'A' and resid 1233 through 1245 removed outlier: 4.137A pdb=" N VAL A1237 " --> pdb=" O ASP A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1256 removed outlier: 3.726A pdb=" N PHE A1252 " --> pdb=" O ARG A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1271 Processing helix chain 'A' and resid 1316 through 1332 Processing helix chain 'A' and resid 1334 through 1348 removed outlier: 3.597A pdb=" N ALA A1338 " --> pdb=" O PHE A1334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A1347 " --> pdb=" O PHE A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1360 Processing helix chain 'B' and resid 511 through 524 Processing helix chain 'B' and resid 560 through 577 Processing helix chain 'B' and resid 591 through 601 Processing helix chain 'B' and resid 607 through 616 Processing helix chain 'B' and resid 619 through 631 Processing helix chain 'B' and resid 669 through 685 Processing helix chain 'B' and resid 690 through 702 removed outlier: 4.187A pdb=" N LEU B 694 " --> pdb=" O ASN B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 Processing helix chain 'B' and resid 728 through 749 removed outlier: 3.679A pdb=" N LEU B 732 " --> pdb=" O ASN B 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 749 Processing helix chain 'H' and resid 22 through 32 Processing helix chain 'H' and resid 55 through 66 removed outlier: 3.571A pdb=" N ALA H 59 " --> pdb=" O ASP H 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415 removed outlier: 3.969A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N PHE A 688 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N TYR A 599 " --> pdb=" O PHE A 688 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 415 removed outlier: 3.969A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N PHE A 688 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N TYR A 599 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 11.934A pdb=" N GLU A 602 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL A 578 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A 604 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS A 618 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 711 through 712 removed outlier: 3.825A pdb=" N LYS A 711 " --> pdb=" O LYS A 849 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 756 through 758 Processing sheet with id=AA5, first strand: chain 'A' and resid 1283 through 1290 removed outlier: 6.965A pdb=" N THR A1299 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR A1289 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A1297 " --> pdb=" O THR A1289 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR A1298 " --> pdb=" O LYS A1313 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS A1313 " --> pdb=" O TYR A1298 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A1300 " --> pdb=" O CYS A1311 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N CYS A1311 " --> pdb=" O VAL A1300 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A1302 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 495 through 496 Processing sheet with id=AA7, first strand: chain 'B' and resid 529 through 534 removed outlier: 3.884A pdb=" N VAL B 529 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 542 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 548 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 640 through 641 removed outlier: 3.554A pdb=" N VAL B 654 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS B 660 " --> pdb=" O CYS B 657 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 36 through 41 removed outlier: 3.814A pdb=" N SER H 38 " --> pdb=" O GLU H 52 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.16 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: 3636 1.34 - 1.46: 2604 1.46 - 1.58: 6299 1.58 - 1.70: 198 1.70 - 1.82: 100 Bond restraints: 12837 Sorted by residual: bond pdb=" CB PRO B 528 " pdb=" CG PRO B 528 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.67e+00 bond pdb=" N9 A E 86 " pdb=" C4 A E 86 " ideal model delta sigma weight residual 1.374 1.362 0.012 6.00e-03 2.78e+04 4.13e+00 bond pdb=" CA MET A 427 " pdb=" CB MET A 427 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.37e+00 bond pdb=" N1 C E 106 " pdb=" C2 C E 106 " ideal model delta sigma weight residual 1.397 1.408 -0.011 1.00e-02 1.00e+04 1.23e+00 bond pdb=" CB ASP H 9 " pdb=" CG ASP H 9 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.21e+00 ... (remaining 12832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 17699 2.34 - 4.67: 92 4.67 - 7.01: 19 7.01 - 9.34: 1 9.34 - 11.68: 1 Bond angle restraints: 17812 Sorted by residual: angle pdb=" C1' C E 106 " pdb=" N1 C E 106 " pdb=" C2 C E 106 " ideal model delta sigma weight residual 118.80 124.43 -5.63 1.10e+00 8.26e-01 2.62e+01 angle pdb=" C1' C E 106 " pdb=" N1 C E 106 " pdb=" C6 C E 106 " ideal model delta sigma weight residual 120.80 116.03 4.77 1.20e+00 6.94e-01 1.58e+01 angle pdb=" CB MET A 427 " pdb=" CG MET A 427 " pdb=" SD MET A 427 " ideal model delta sigma weight residual 112.70 124.38 -11.68 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CA PRO B 528 " pdb=" N PRO B 528 " pdb=" CD PRO B 528 " ideal model delta sigma weight residual 112.00 106.67 5.33 1.40e+00 5.10e-01 1.45e+01 angle pdb=" C TYR B 519 " pdb=" N MET B 520 " pdb=" CA MET B 520 " ideal model delta sigma weight residual 122.38 115.89 6.49 1.81e+00 3.05e-01 1.29e+01 ... (remaining 17807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 7493 34.97 - 69.93: 385 69.93 - 104.90: 33 104.90 - 139.87: 0 139.87 - 174.83: 1 Dihedral angle restraints: 7912 sinusoidal: 4238 harmonic: 3674 Sorted by residual: dihedral pdb=" O4' U E 125 " pdb=" C1' U E 125 " pdb=" N1 U E 125 " pdb=" C2 U E 125 " ideal model delta sinusoidal sigma weight residual 232.00 57.17 174.83 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' A E 14 " pdb=" C1' A E 14 " pdb=" N9 A E 14 " pdb=" C4 A E 14 " ideal model delta sinusoidal sigma weight residual 254.00 167.78 86.22 1 1.70e+01 3.46e-03 3.10e+01 dihedral pdb=" O4' A E 13 " pdb=" C1' A E 13 " pdb=" N9 A E 13 " pdb=" C4 A E 13 " ideal model delta sinusoidal sigma weight residual -106.00 -172.80 66.80 1 1.70e+01 3.46e-03 2.01e+01 ... (remaining 7909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1404 0.028 - 0.056: 392 0.056 - 0.083: 113 0.083 - 0.111: 78 0.111 - 0.139: 26 Chirality restraints: 2013 Sorted by residual: chirality pdb=" C1' A E 128 " pdb=" O4' A E 128 " pdb=" C2' A E 128 " pdb=" N9 A E 128 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA MET A 427 " pdb=" N MET A 427 " pdb=" C MET A 427 " pdb=" CB MET A 427 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ASP H 9 " pdb=" N ASP H 9 " pdb=" C ASP H 9 " pdb=" CB ASP H 9 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 2010 not shown) Planarity restraints: 1937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 527 " -0.046 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO B 528 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 528 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 528 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 721 " -0.013 2.00e-02 2.50e+03 1.27e-02 3.23e+00 pdb=" CG TYR B 721 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 721 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 721 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 721 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 721 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 721 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 721 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 449 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C GLU A 449 " 0.030 2.00e-02 2.50e+03 pdb=" O GLU A 449 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 450 " -0.010 2.00e-02 2.50e+03 ... (remaining 1934 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2455 2.78 - 3.31: 10897 3.31 - 3.84: 20337 3.84 - 4.37: 23231 4.37 - 4.90: 38645 Nonbonded interactions: 95565 Sorted by model distance: nonbonded pdb=" OE1 GLU A 992 " pdb=" OG SER B 711 " model vdw 2.248 3.040 nonbonded pdb=" OD1 ASP B 712 " pdb=" N LYS B 713 " model vdw 2.286 3.120 nonbonded pdb=" OP1 G E 55 " pdb=" N2 G E 55 " model vdw 2.294 3.120 nonbonded pdb=" NE2 GLN B 649 " pdb=" OP1 C E 87 " model vdw 2.297 3.120 nonbonded pdb=" NZ LYS H 23 " pdb=" O VAL H 39 " model vdw 2.308 3.120 ... (remaining 95560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:7.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 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 : 0.003 0.108 12845 Z= 0.144 Angle : 0.482 11.681 17816 Z= 0.305 Chirality : 0.035 0.139 2013 Planarity : 0.003 0.068 1937 Dihedral : 18.280 174.834 5532 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.18 % Allowed : 15.27 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.25), residues: 1241 helix: 2.57 (0.21), residues: 597 sheet: 0.89 (0.43), residues: 150 loop : -0.43 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 57 TYR 0.031 0.001 TYR B 721 PHE 0.012 0.001 PHE A1148 TRP 0.020 0.001 TRP A1357 HIS 0.003 0.001 HIS A 869 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (12837) covalent geometry : angle 0.48050 / 0.31 (17812) hydrogen bonds : bond 0.16108 / 10.26 ( 586) hydrogen bonds : angle 5.22304 / 3.64 ( 1630) metal coordination : bond 0.00833 / 0.36 ( 8) metal coordination : angle 2.13485 / 1.23 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 740 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7917 (ttm) outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.6493 time to fit residues: 46.7855 Evaluate side-chains 63 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 719 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.070615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.042261 restraints weight = 45784.717| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.40 r_work: 0.2615 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.124 12845 Z= 0.444 Angle : 0.694 9.312 17816 Z= 0.371 Chirality : 0.046 0.203 2013 Planarity : 0.005 0.038 1937 Dihedral : 18.409 172.739 2916 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.59 % Allowed : 14.64 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.24), residues: 1241 helix: 1.90 (0.21), residues: 618 sheet: 0.48 (0.40), residues: 163 loop : -0.64 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1185 TYR 0.018 0.002 TYR B 698 PHE 0.014 0.002 PHE A1148 TRP 0.014 0.002 TRP A1357 HIS 0.007 0.002 HIS A 869 Details of bonding type rmsd/Z covalent geometry : bond 0.01045 / 0.44 (12837) covalent geometry : angle 0.69003 / 0.37 (17812) hydrogen bonds : bond 0.08955 / 5.82 ( 586) hydrogen bonds : angle 4.79728 / 3.39 ( 1630) metal coordination : bond 0.01299 / 0.63 ( 8) metal coordination : angle 5.02541 / 2.88 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 695 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8766 (tp30) REVERT: A 740 MET cc_start: 0.9280 (ttm) cc_final: 0.9051 (ttp) REVERT: A 809 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8454 (pmtt) REVERT: A 835 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8849 (ptp90) outliers start: 29 outliers final: 9 residues processed: 87 average time/residue: 0.5889 time to fit residues: 56.1340 Evaluate side-chains 72 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 809 LYS Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.072732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.044450 restraints weight = 45194.849| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.34 r_work: 0.2684 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12845 Z= 0.122 Angle : 0.476 7.298 17816 Z= 0.259 Chirality : 0.037 0.154 2013 Planarity : 0.004 0.035 1937 Dihedral : 18.423 176.625 2913 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.52 % Allowed : 16.88 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.25), residues: 1241 helix: 2.34 (0.21), residues: 609 sheet: 0.49 (0.40), residues: 162 loop : -0.48 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 57 TYR 0.017 0.001 TYR B 721 PHE 0.014 0.001 PHE A1148 TRP 0.016 0.001 TRP A1357 HIS 0.003 0.001 HIS A 869 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (12837) covalent geometry : angle 0.47420 / 0.26 (17812) hydrogen bonds : bond 0.05481 / 3.54 ( 586) hydrogen bonds : angle 4.20578 / 2.99 ( 1630) metal coordination : bond 0.01422 / 0.66 ( 8) metal coordination : angle 2.59486 / 1.53 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 695 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8717 (tp30) REVERT: A 740 MET cc_start: 0.9231 (ttm) cc_final: 0.8933 (ttm) outliers start: 17 outliers final: 7 residues processed: 79 average time/residue: 0.5814 time to fit residues: 50.2532 Evaluate side-chains 68 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 112 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 682 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 = 0.3655 r_free = 0.3655 target = 0.072068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.043810 restraints weight = 44934.284| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.32 r_work: 0.2672 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12845 Z= 0.186 Angle : 0.496 7.383 17816 Z= 0.266 Chirality : 0.038 0.153 2013 Planarity : 0.004 0.038 1937 Dihedral : 18.317 176.027 2913 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.70 % Allowed : 16.88 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.25), residues: 1241 helix: 2.29 (0.21), residues: 617 sheet: 0.51 (0.40), residues: 163 loop : -0.54 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 57 TYR 0.015 0.001 TYR B 721 PHE 0.013 0.001 PHE A1148 TRP 0.015 0.001 TRP A1357 HIS 0.005 0.001 HIS A 774 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (12837) covalent geometry : angle 0.49390 / 0.27 (17812) hydrogen bonds : bond 0.05926 / 3.84 ( 586) hydrogen bonds : angle 4.15140 / 2.94 ( 1630) metal coordination : bond 0.00964 / 0.38 ( 8) metal coordination : angle 3.16637 / 1.85 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 695 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8728 (tp30) REVERT: A 740 MET cc_start: 0.9262 (ttm) cc_final: 0.8977 (ttm) REVERT: B 721 TYR cc_start: 0.8153 (m-10) cc_final: 0.7905 (m-10) outliers start: 19 outliers final: 12 residues processed: 78 average time/residue: 0.5803 time to fit residues: 50.0236 Evaluate side-chains 72 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 104 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 81 optimal weight: 0.0980 chunk 96 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 744 ASN ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.072520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.044352 restraints weight = 45342.153| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.32 r_work: 0.2690 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12845 Z= 0.142 Angle : 0.471 8.259 17816 Z= 0.253 Chirality : 0.037 0.148 2013 Planarity : 0.003 0.038 1937 Dihedral : 18.281 176.901 2913 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.88 % Allowed : 16.88 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.25), residues: 1241 helix: 2.37 (0.21), residues: 616 sheet: 0.53 (0.41), residues: 163 loop : -0.53 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 57 TYR 0.014 0.001 TYR B 721 PHE 0.013 0.001 PHE A1148 TRP 0.016 0.001 TRP A1357 HIS 0.004 0.001 HIS A 869 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12837) covalent geometry : angle 0.46879 / 0.25 (17812) hydrogen bonds : bond 0.05327 / 3.46 ( 586) hydrogen bonds : angle 4.02529 / 2.86 ( 1630) metal coordination : bond 0.01128 / 0.50 ( 8) metal coordination : angle 2.80513 / 1.65 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8901 (pt0) REVERT: A 695 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8722 (tp30) REVERT: A 740 MET cc_start: 0.9248 (ttm) cc_final: 0.8952 (ttm) REVERT: A 809 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8382 (pmtt) REVERT: A 834 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8444 (mtm) REVERT: B 521 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7939 (tm-30) outliers start: 21 outliers final: 11 residues processed: 79 average time/residue: 0.6019 time to fit residues: 52.3135 Evaluate side-chains 76 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 809 LYS Chi-restraints excluded: chain A residue 834 MET Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1326 MET Chi-restraints excluded: chain B residue 521 GLN Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 682 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.072523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.044290 restraints weight = 45034.998| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.29 r_work: 0.2692 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12845 Z= 0.141 Angle : 0.472 8.421 17816 Z= 0.252 Chirality : 0.036 0.144 2013 Planarity : 0.003 0.038 1937 Dihedral : 18.225 177.340 2913 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.14 % Allowed : 17.14 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.25), residues: 1241 helix: 2.42 (0.21), residues: 616 sheet: 0.53 (0.40), residues: 163 loop : -0.54 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 57 TYR 0.010 0.001 TYR B 698 PHE 0.013 0.001 PHE A1148 TRP 0.017 0.001 TRP A1357 HIS 0.004 0.001 HIS A 774 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12837) covalent geometry : angle 0.47015 / 0.25 (17812) hydrogen bonds : bond 0.05173 / 3.36 ( 586) hydrogen bonds : angle 3.95867 / 2.81 ( 1630) metal coordination : bond 0.01011 / 0.42 ( 8) metal coordination : angle 2.73812 / 1.61 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 602 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8896 (pt0) REVERT: A 695 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8717 (tp30) REVERT: A 740 MET cc_start: 0.9248 (ttm) cc_final: 0.8957 (ttm) REVERT: A 809 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8358 (pmtt) REVERT: B 521 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7949 (tm-30) outliers start: 24 outliers final: 14 residues processed: 83 average time/residue: 0.5591 time to fit residues: 50.9558 Evaluate side-chains 77 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 809 LYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1326 MET Chi-restraints excluded: chain B residue 521 GLN Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain H residue 14 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 92 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.072792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.044680 restraints weight = 44767.922| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.37 r_work: 0.2700 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12845 Z= 0.125 Angle : 0.473 10.039 17816 Z= 0.251 Chirality : 0.036 0.145 2013 Planarity : 0.003 0.038 1937 Dihedral : 18.195 177.866 2913 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.79 % Allowed : 17.14 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.25), residues: 1241 helix: 2.47 (0.21), residues: 616 sheet: 0.53 (0.40), residues: 163 loop : -0.52 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 57 TYR 0.010 0.001 TYR B 698 PHE 0.013 0.001 PHE A1148 TRP 0.018 0.001 TRP A1357 HIS 0.004 0.001 HIS A 869 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (12837) covalent geometry : angle 0.47176 / 0.25 (17812) hydrogen bonds : bond 0.04912 / 3.18 ( 586) hydrogen bonds : angle 3.89247 / 2.76 ( 1630) metal coordination : bond 0.01051 / 0.44 ( 8) metal coordination : angle 2.62760 / 1.54 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8913 (pt0) REVERT: A 695 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8735 (tp30) REVERT: A 740 MET cc_start: 0.9254 (ttm) cc_final: 0.8982 (ttm) REVERT: A 809 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8349 (pmtt) REVERT: B 521 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: H 61 ASP cc_start: 0.8389 (m-30) cc_final: 0.8136 (m-30) REVERT: H 65 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7351 (mp0) outliers start: 20 outliers final: 14 residues processed: 79 average time/residue: 0.5792 time to fit residues: 50.3407 Evaluate side-chains 78 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 809 LYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1326 MET Chi-restraints excluded: chain B residue 521 GLN Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 65 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 107 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 521 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.071164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.042848 restraints weight = 45220.427| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.36 r_work: 0.2640 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 12845 Z= 0.292 Angle : 0.598 17.002 17816 Z= 0.312 Chirality : 0.041 0.187 2013 Planarity : 0.004 0.039 1937 Dihedral : 18.185 175.919 2913 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.14 % Allowed : 17.32 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.25), residues: 1241 helix: 2.25 (0.21), residues: 615 sheet: 0.42 (0.40), residues: 168 loop : -0.63 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 57 TYR 0.016 0.001 TYR B 698 PHE 0.012 0.002 PHE A1148 TRP 0.017 0.002 TRP A1357 HIS 0.006 0.001 HIS A 869 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.29 (12837) covalent geometry : angle 0.59507 / 0.31 (17812) hydrogen bonds : bond 0.07031 / 4.57 ( 586) hydrogen bonds : angle 4.19061 / 2.97 ( 1630) metal coordination : bond 0.01041 / 0.45 ( 8) metal coordination : angle 3.96689 / 2.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 602 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8922 (pt0) REVERT: A 695 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8741 (tp30) REVERT: A 740 MET cc_start: 0.9289 (ttm) cc_final: 0.9072 (ttm) REVERT: A 809 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8455 (pmtt) REVERT: H 61 ASP cc_start: 0.8383 (m-30) cc_final: 0.8145 (m-30) REVERT: H 65 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7398 (mp0) outliers start: 24 outliers final: 16 residues processed: 83 average time/residue: 0.5512 time to fit residues: 50.5189 Evaluate side-chains 80 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 809 LYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain B residue 514 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 65 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.072522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.044402 restraints weight = 44939.407| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.34 r_work: 0.2694 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12845 Z= 0.113 Angle : 0.506 17.512 17816 Z= 0.265 Chirality : 0.036 0.208 2013 Planarity : 0.003 0.038 1937 Dihedral : 18.202 178.601 2913 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.34 % Allowed : 18.21 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.25), residues: 1241 helix: 2.43 (0.21), residues: 615 sheet: 0.49 (0.40), residues: 168 loop : -0.55 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 57 TYR 0.010 0.001 TYR B 698 PHE 0.013 0.001 PHE A1148 TRP 0.023 0.001 TRP A1357 HIS 0.004 0.001 HIS A 869 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (12837) covalent geometry : angle 0.50486 / 0.26 (17812) hydrogen bonds : bond 0.05021 / 3.25 ( 586) hydrogen bonds : angle 3.91798 / 2.79 ( 1630) metal coordination : bond 0.01178 / 0.55 ( 8) metal coordination : angle 2.59221 / 1.52 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8894 (pt0) REVERT: A 695 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8733 (tp30) REVERT: A 740 MET cc_start: 0.9251 (ttm) cc_final: 0.9028 (ttm) REVERT: A 809 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8386 (pmtt) REVERT: C 744 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8647 (pp20) REVERT: H 61 ASP cc_start: 0.8411 (m-30) cc_final: 0.7937 (p0) REVERT: H 65 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7306 (mp0) outliers start: 15 outliers final: 10 residues processed: 74 average time/residue: 0.5882 time to fit residues: 47.6482 Evaluate side-chains 73 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 809 LYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 65 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.071961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043753 restraints weight = 44984.646| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.30 r_work: 0.2675 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12845 Z= 0.173 Angle : 0.530 17.883 17816 Z= 0.275 Chirality : 0.038 0.209 2013 Planarity : 0.004 0.039 1937 Dihedral : 18.154 177.957 2913 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.43 % Allowed : 18.12 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.25), residues: 1241 helix: 2.39 (0.21), residues: 615 sheet: 0.51 (0.40), residues: 168 loop : -0.58 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 57 TYR 0.012 0.001 TYR B 698 PHE 0.013 0.001 PHE A1148 TRP 0.023 0.001 TRP A1357 HIS 0.005 0.001 HIS A 774 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (12837) covalent geometry : angle 0.52865 / 0.27 (17812) hydrogen bonds : bond 0.05539 / 3.60 ( 586) hydrogen bonds : angle 3.95073 / 2.80 ( 1630) metal coordination : bond 0.00944 / 0.36 ( 8) metal coordination : angle 2.86927 / 1.68 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8883 (pt0) REVERT: A 695 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8717 (tp30) REVERT: A 740 MET cc_start: 0.9271 (ttm) cc_final: 0.8966 (ttm) REVERT: A 809 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8383 (pmtt) REVERT: C 744 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8582 (pp20) REVERT: H 61 ASP cc_start: 0.8416 (m-30) cc_final: 0.8108 (m-30) REVERT: H 65 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7366 (mp0) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.5764 time to fit residues: 47.4983 Evaluate side-chains 75 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 809 LYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 65 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 68 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.072884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.044851 restraints weight = 44829.109| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.28 r_work: 0.2711 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12845 Z= 0.106 Angle : 0.513 16.363 17816 Z= 0.266 Chirality : 0.036 0.195 2013 Planarity : 0.003 0.039 1937 Dihedral : 18.138 179.412 2913 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.07 % Allowed : 18.39 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.25), residues: 1241 helix: 2.48 (0.21), residues: 615 sheet: 0.55 (0.40), residues: 168 loop : -0.53 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 57 TYR 0.011 0.001 TYR B 519 PHE 0.013 0.001 PHE A1148 TRP 0.025 0.001 TRP A1357 HIS 0.006 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (12837) covalent geometry : angle 0.51219 / 0.27 (17812) hydrogen bonds : bond 0.04582 / 2.98 ( 586) hydrogen bonds : angle 3.81796 / 2.71 ( 1630) metal coordination : bond 0.01100 / 0.48 ( 8) metal coordination : angle 2.43448 / 1.43 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4067.17 seconds wall clock time: 70 minutes 9.04 seconds (4209.04 seconds total)