Starting phenix.real_space_refine on Thu Sep 18 00:03:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asq_43823/09_2025/9asq_43823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asq_43823/09_2025/9asq_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 { model { file = "/net/cci-nas-00/data/ceres_data/9asq_43823/09_2025/9asq_43823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asq_43823/09_2025/9asq_43823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9asq_43823/09_2025/9asq_43823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asq_43823/09_2025/9asq_43823.map" } 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-2.0-5805/lib/python3.9/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, 4 Unusual residues: {' CA': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 2.75, per 1000 atoms: 0.22 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: 1.00 Conformation dependent library (CDL) restraints added in 474.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.35 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: 2.86 Time building geometry restraints manager: 1.35 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=" 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=" 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 bond pdb=" CB GLU C 737 " pdb=" CG GLU C 737 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 bond pdb=" CB MET A 427 " pdb=" CG MET A 427 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+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=" 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 angle pdb=" CA MET A 427 " pdb=" CB MET A 427 " pdb=" CG MET A 427 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA GLU C 737 " pdb=" CB GLU C 737 " pdb=" CG GLU C 737 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.87e+00 ... (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: 7.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 15.190 Find NCS groups from input model: 0.100 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:8.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 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= 0.121 Angle : 0.481 11.681 17816 Z= 0.249 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 aren 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 covalent geometry : bond 0.00283 (12837) covalent geometry : angle 0.48046 (17812) hydrogen bonds : bond 0.16108 ( 586) hydrogen bonds : angle 5.22304 ( 1630) metal coordination : bond 0.00833 ( 8) metal coordination : angle 2.13485 ( 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 : 0.517 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: 0.6609 time to fit residues: 47.5313 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 : 0.456 ------------------------------------------------------------------------------- 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: 4.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 719 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 = 0.3623 r_free = 0.3623 target = 0.070331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.042118 restraints weight = 45677.774| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.40 r_work: 0.2608 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.099 12845 Z= 0.426 Angle : 0.693 7.545 17816 Z= 0.361 Chirality : 0.045 0.210 2013 Planarity : 0.005 0.036 1937 Dihedral : 18.394 171.002 2916 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.41 % Allowed : 15.36 % Favored : 82.23 % 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 aren not related in a simple way. whole: 1.16 (0.24), residues: 1241 helix: 1.91 (0.21), residues: 616 sheet: 0.46 (0.40), residues: 163 loop : -0.67 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 57 TYR 0.024 0.002 TYR B 721 PHE 0.014 0.002 PHE H 53 TRP 0.014 0.002 TRP A1357 HIS 0.008 0.002 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.01005 (12837) covalent geometry : angle 0.68882 (17812) hydrogen bonds : bond 0.08470 ( 586) hydrogen bonds : angle 4.64848 ( 1630) metal coordination : bond 0.01346 ( 8) metal coordination : angle 4.99944 ( 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 91 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 695 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8755 (tp30) REVERT: A 809 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8563 (pmtt) REVERT: A 1260 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7834 (p0) REVERT: B 718 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7911 (pp) outliers start: 27 outliers final: 8 residues processed: 87 average time/residue: 0.6207 time to fit residues: 58.9496 Evaluate side-chains 71 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 809 LYS Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain B residue 718 LEU 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: 0.9990 chunk 13 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.0670 chunk 26 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 682 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.072822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.044805 restraints weight = 45554.519| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.35 r_work: 0.2706 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12845 Z= 0.109 Angle : 0.476 6.713 17816 Z= 0.247 Chirality : 0.036 0.138 2013 Planarity : 0.003 0.039 1937 Dihedral : 18.190 176.795 2913 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.16 % Allowed : 16.70 % Favored : 82.14 % 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 aren not related in a simple way. whole: 1.63 (0.25), residues: 1241 helix: 2.40 (0.21), residues: 608 sheet: 0.53 (0.41), residues: 162 loop : -0.49 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 57 TYR 0.019 0.001 TYR H 32 PHE 0.013 0.001 PHE A1148 TRP 0.015 0.001 TRP A1357 HIS 0.004 0.001 HIS A 869 Details of bonding type rmsd covalent geometry : bond 0.00237 (12837) covalent geometry : angle 0.47453 (17812) hydrogen bonds : bond 0.04337 ( 586) hydrogen bonds : angle 3.93951 ( 1630) metal coordination : bond 0.00982 ( 8) metal coordination : angle 2.11888 ( 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 76 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 695 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8706 (tp30) REVERT: A 740 MET cc_start: 0.9272 (ttp) cc_final: 0.9062 (ttp) outliers start: 13 outliers final: 3 residues processed: 74 average time/residue: 0.6063 time to fit residues: 49.1099 Evaluate side-chains 65 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain H residue 14 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 112 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 94 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 0.0010 chunk 105 optimal weight: 9.9990 overall best weight: 0.6130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 ASN B 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.073328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.045442 restraints weight = 45320.575| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.32 r_work: 0.2732 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12845 Z= 0.097 Angle : 0.458 7.740 17816 Z= 0.234 Chirality : 0.035 0.151 2013 Planarity : 0.003 0.037 1937 Dihedral : 17.967 178.196 2913 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.80 % Allowed : 17.23 % Favored : 81.96 % 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 aren not related in a simple way. whole: 1.88 (0.25), residues: 1241 helix: 2.65 (0.21), residues: 609 sheet: 0.62 (0.41), residues: 162 loop : -0.43 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 57 TYR 0.021 0.001 TYR H 32 PHE 0.012 0.001 PHE A1148 TRP 0.015 0.001 TRP A1357 HIS 0.003 0.001 HIS A 869 Details of bonding type rmsd covalent geometry : bond 0.00208 (12837) covalent geometry : angle 0.45671 (17812) hydrogen bonds : bond 0.03936 ( 586) hydrogen bonds : angle 3.70053 ( 1630) metal coordination : bond 0.00953 ( 8) metal coordination : angle 2.14144 ( 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 74 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 695 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8714 (tp30) REVERT: H 61 ASP cc_start: 0.8478 (m-30) cc_final: 0.8187 (p0) outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 0.6607 time to fit residues: 52.5939 Evaluate side-chains 68 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLU 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 H residue 14 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 104 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.071161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.042962 restraints weight = 45439.925| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.30 r_work: 0.2644 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12845 Z= 0.274 Angle : 0.577 8.362 17816 Z= 0.297 Chirality : 0.040 0.163 2013 Planarity : 0.004 0.039 1937 Dihedral : 17.990 176.002 2913 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.79 % Allowed : 17.41 % Favored : 80.80 % 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 aren not related in a simple way. whole: 1.60 (0.25), residues: 1241 helix: 2.39 (0.21), residues: 615 sheet: 0.58 (0.41), residues: 163 loop : -0.61 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 57 TYR 0.022 0.001 TYR H 32 PHE 0.012 0.001 PHE A1148 TRP 0.014 0.001 TRP A1357 HIS 0.005 0.001 HIS A 869 Details of bonding type rmsd covalent geometry : bond 0.00647 (12837) covalent geometry : angle 0.57449 (17812) hydrogen bonds : bond 0.06522 ( 586) hydrogen bonds : angle 4.09296 ( 1630) metal coordination : bond 0.01094 ( 8) metal coordination : angle 3.84722 ( 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 84 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 695 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8717 (tp30) REVERT: H 61 ASP cc_start: 0.8469 (m-30) cc_final: 0.8185 (p0) outliers start: 20 outliers final: 9 residues processed: 82 average time/residue: 0.5911 time to fit residues: 53.2786 Evaluate side-chains 72 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 747 THR 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 1289 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain H residue 14 VAL 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: 4.9990 chunk 102 optimal weight: 0.0060 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 682 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.072971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045128 restraints weight = 45278.840| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.32 r_work: 0.2719 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12845 Z= 0.103 Angle : 0.484 10.455 17816 Z= 0.244 Chirality : 0.035 0.165 2013 Planarity : 0.003 0.041 1937 Dihedral : 17.872 179.730 2913 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.98 % Allowed : 17.86 % Favored : 81.16 % 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 aren not related in a simple way. whole: 1.80 (0.25), residues: 1241 helix: 2.57 (0.21), residues: 616 sheet: 0.63 (0.40), residues: 163 loop : -0.51 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 57 TYR 0.023 0.001 TYR H 32 PHE 0.013 0.001 PHE A1148 TRP 0.017 0.001 TRP A1357 HIS 0.004 0.001 HIS A 869 Details of bonding type rmsd covalent geometry : bond 0.00223 (12837) covalent geometry : angle 0.48251 (17812) hydrogen bonds : bond 0.04145 ( 586) hydrogen bonds : angle 3.74227 ( 1630) metal coordination : bond 0.00937 ( 8) metal coordination : angle 2.15714 ( 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 75 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 695 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8690 (tp30) REVERT: B 700 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7306 (tpm170) REVERT: C 748 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8491 (tm-30) REVERT: H 61 ASP cc_start: 0.8535 (m-30) cc_final: 0.8231 (p0) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.6741 time to fit residues: 54.3442 Evaluate side-chains 72 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 747 THR 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 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: 20.0000 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 719 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 = 0.3637 r_free = 0.3637 target = 0.070958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042737 restraints weight = 45475.604| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.30 r_work: 0.2636 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 12845 Z= 0.298 Angle : 0.621 15.992 17816 Z= 0.315 Chirality : 0.041 0.182 2013 Planarity : 0.004 0.039 1937 Dihedral : 17.931 176.616 2913 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.79 % Allowed : 17.41 % Favored : 80.80 % 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 aren not related in a simple way. whole: 1.50 (0.25), residues: 1241 helix: 2.33 (0.21), residues: 615 sheet: 0.49 (0.40), residues: 168 loop : -0.66 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 684 TYR 0.043 0.002 TYR B 721 PHE 0.012 0.001 PHE A1148 TRP 0.014 0.002 TRP A1357 HIS 0.006 0.001 HIS B 730 Details of bonding type rmsd covalent geometry : bond 0.00701 (12837) covalent geometry : angle 0.61826 (17812) hydrogen bonds : bond 0.06894 ( 586) hydrogen bonds : angle 4.15347 ( 1630) metal coordination : bond 0.01152 ( 8) metal coordination : angle 4.09003 ( 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 82 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 602 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8890 (pt0) REVERT: A 695 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8735 (tp30) REVERT: C 744 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8566 (pp20) REVERT: H 61 ASP cc_start: 0.8576 (m-30) cc_final: 0.8271 (p0) outliers start: 20 outliers final: 13 residues processed: 79 average time/residue: 0.5888 time to fit residues: 51.2053 Evaluate side-chains 77 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 798 VAL 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 1289 THR Chi-restraints excluded: chain A residue 1326 MET Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain H residue 14 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 107 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.072248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.044156 restraints weight = 45178.455| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.28 r_work: 0.2688 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12845 Z= 0.140 Angle : 0.530 14.516 17816 Z= 0.267 Chirality : 0.037 0.199 2013 Planarity : 0.003 0.041 1937 Dihedral : 17.836 179.625 2913 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.16 % Allowed : 18.21 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.25), residues: 1241 helix: 2.46 (0.21), residues: 615 sheet: 0.53 (0.40), residues: 168 loop : -0.61 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 57 TYR 0.023 0.001 TYR B 519 PHE 0.013 0.001 PHE A1148 TRP 0.021 0.001 TRP A1357 HIS 0.005 0.001 HIS A 869 Details of bonding type rmsd covalent geometry : bond 0.00321 (12837) covalent geometry : angle 0.52887 (17812) hydrogen bonds : bond 0.04926 ( 586) hydrogen bonds : angle 3.86825 ( 1630) metal coordination : bond 0.00917 ( 8) metal coordination : angle 2.62108 ( 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 76 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 695 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8691 (tp30) REVERT: B 700 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7351 (tpm170) REVERT: C 744 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8524 (pp20) REVERT: H 61 ASP cc_start: 0.8567 (m-30) cc_final: 0.8275 (p0) outliers start: 13 outliers final: 11 residues processed: 76 average time/residue: 0.6486 time to fit residues: 53.6995 Evaluate side-chains 75 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 THR 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 798 VAL 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 1289 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain H residue 14 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.072495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044398 restraints weight = 45081.737| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.31 r_work: 0.2696 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12845 Z= 0.131 Angle : 0.531 15.087 17816 Z= 0.265 Chirality : 0.036 0.192 2013 Planarity : 0.003 0.040 1937 Dihedral : 17.713 178.796 2913 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.25 % Allowed : 17.95 % Favored : 80.80 % 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 aren not related in a simple way. whole: 1.77 (0.25), residues: 1241 helix: 2.57 (0.21), residues: 616 sheet: 0.58 (0.39), residues: 168 loop : -0.56 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 57 TYR 0.032 0.001 TYR H 32 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 covalent geometry : bond 0.00299 (12837) covalent geometry : angle 0.52994 (17812) hydrogen bonds : bond 0.04706 ( 586) hydrogen bonds : angle 3.76204 ( 1630) metal coordination : bond 0.01009 ( 8) metal coordination : angle 2.63923 ( 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 78 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 695 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8707 (tp30) REVERT: A 809 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8323 (pmtt) REVERT: B 553 TYR cc_start: 0.8971 (m-80) cc_final: 0.8568 (m-80) REVERT: B 700 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7383 (tpm170) REVERT: C 744 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8491 (pp20) outliers start: 14 outliers final: 9 residues processed: 77 average time/residue: 0.6290 time to fit residues: 52.9220 Evaluate side-chains 75 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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 1289 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain H residue 14 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 495 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 = 0.3677 r_free = 0.3677 target = 0.072706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.044696 restraints weight = 45310.450| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.31 r_work: 0.2705 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12845 Z= 0.122 Angle : 0.537 15.885 17816 Z= 0.267 Chirality : 0.036 0.190 2013 Planarity : 0.003 0.042 1937 Dihedral : 17.677 179.332 2913 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.98 % Allowed : 18.57 % 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 aren not related in a simple way. whole: 1.82 (0.25), residues: 1241 helix: 2.60 (0.21), residues: 616 sheet: 0.61 (0.39), residues: 167 loop : -0.54 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 57 TYR 0.032 0.001 TYR B 519 PHE 0.013 0.001 PHE A1148 TRP 0.024 0.001 TRP A1357 HIS 0.004 0.001 HIS A 869 Details of bonding type rmsd covalent geometry : bond 0.00278 (12837) covalent geometry : angle 0.53616 (17812) hydrogen bonds : bond 0.04568 ( 586) hydrogen bonds : angle 3.73230 ( 1630) metal coordination : bond 0.00930 ( 8) metal coordination : angle 2.38122 ( 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 76 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 695 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8696 (tp30) REVERT: A 809 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8270 (pmtt) REVERT: B 553 TYR cc_start: 0.9026 (m-80) cc_final: 0.8648 (m-80) REVERT: B 700 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7437 (tpm170) REVERT: C 744 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8469 (pp20) REVERT: H 61 ASP cc_start: 0.8343 (m-30) cc_final: 0.8024 (p0) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.6365 time to fit residues: 52.7712 Evaluate side-chains 73 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 875 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain H residue 14 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 41 optimal weight: 0.0670 chunk 6 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 495 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 = 0.3663 r_free = 0.3663 target = 0.072199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.044187 restraints weight = 44919.645| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.32 r_work: 0.2685 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12845 Z= 0.156 Angle : 0.567 15.200 17816 Z= 0.284 Chirality : 0.037 0.191 2013 Planarity : 0.004 0.039 1937 Dihedral : 17.673 178.283 2913 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.16 % Allowed : 18.48 % Favored : 80.36 % 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 aren not related in a simple way. whole: 1.73 (0.25), residues: 1241 helix: 2.53 (0.21), residues: 615 sheet: 0.59 (0.39), residues: 168 loop : -0.57 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 57 TYR 0.030 0.001 TYR H 32 PHE 0.012 0.001 PHE A1148 TRP 0.023 0.001 TRP A1357 HIS 0.005 0.001 HIS A 869 Details of bonding type rmsd covalent geometry : bond 0.00360 (12837) covalent geometry : angle 0.56589 (17812) hydrogen bonds : bond 0.05230 ( 586) hydrogen bonds : angle 3.85964 ( 1630) metal coordination : bond 0.00995 ( 8) metal coordination : angle 2.83405 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4301.25 seconds wall clock time: 74 minutes 6.91 seconds (4446.91 seconds total)