Starting phenix.real_space_refine on Wed Aug 5 20:42:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asm_43819/08_2026/9asm_43819.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asm_43819/08_2026/9asm_43819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9asm_43819/08_2026/9asm_43819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asm_43819/08_2026/9asm_43819.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9asm_43819/08_2026/9asm_43819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asm_43819/08_2026/9asm_43819.map" } resolution = 2.8 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= 0.011 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 95 5.49 5 S 61 5.16 5 C 7017 2.51 5 N 2052 2.21 5 O 2419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11648 Number of models: 1 Model: "" Number of chains: 6 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: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1921 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 10, 'TRANS': 229} Chain breaks: 2 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: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2019 Classifications: {'RNA': 95} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 42, 'rna3p_pyr': 40} Link IDs: {'rna2p': 12, 'rna3p': 82} Chain breaks: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 2, ' ZN': 2} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 943 SG CYS A 561 44.408 20.542 145.715 1.00172.12 S ATOM 1901 SG CYS A 676 41.093 22.263 145.277 1.00178.36 S ATOM 751 SG CYS A 536 24.267 38.767 130.972 1.00181.72 S ATOM 766 SG CYS A 538 24.235 40.054 127.365 1.00190.39 S Time building chain proxies: 2.45, per 1000 atoms: 0.21 Number of scatterers: 11648 At special positions: 0 Unit cell: (87.312, 101.008, 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 61 16.00 P 95 15.00 O 2419 8.00 N 2052 7.00 C 7017 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: 0.96 Conformation dependent library (CDL) restraints added in 465.7 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 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 8 sheets defined 55.5% alpha, 12.4% beta 34 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.549A pdb=" N ARG A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 463 removed outlier: 3.763A 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: 3.564A pdb=" N THR A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 removed outlier: 3.615A pdb=" N ILE A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 709 removed outlier: 3.513A pdb=" N ILE A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.634A pdb=" N CYS A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 786 removed outlier: 6.538A pdb=" N TYR A 784 " --> pdb=" O GLN A 781 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A 785 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 807 removed outlier: 3.572A pdb=" N ASN A 806 " --> pdb=" O HIS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 830 removed outlier: 3.896A pdb=" N LYS A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 817 " --> pdb=" O THR A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.824A pdb=" N CYS A 857 " --> pdb=" O ARG A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.719A pdb=" N LEU A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET A 877 " --> pdb=" O HIS A 873 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N HIS A 878 " --> pdb=" O GLN A 874 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU A 879 " --> pdb=" O CYS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 897 removed outlier: 3.585A pdb=" N LEU A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 920 Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.547A pdb=" N VAL A 932 " --> pdb=" O ASP A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 950 Processing helix chain 'A' and resid 965 through 988 removed outlier: 3.670A pdb=" N PHE A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 971 " --> pdb=" O ARG A 967 " (cutoff:3.500A) removed outlier: 3.905A 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: 3.836A pdb=" N LYS A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) removed outlier: 3.916A 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 1027 through 1031 removed outlier: 4.257A pdb=" N LEU A1030 " --> pdb=" O GLY A1027 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS A1031 " --> pdb=" O PRO A1028 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1027 through 1031' Processing helix chain 'A' and resid 1032 through 1055 Processing helix chain 'A' and resid 1056 through 1069 removed outlier: 3.566A pdb=" N ALA A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 Processing helix chain 'A' and resid 1084 through 1090 removed outlier: 3.828A pdb=" N GLU A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1098 removed outlier: 3.627A pdb=" N ILE A1098 " --> pdb=" O ARG A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1115 removed outlier: 3.727A pdb=" N GLN A1105 " --> pdb=" O SER A1101 " (cutoff:3.500A) removed outlier: 3.941A 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: 4.133A pdb=" N LEU A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1166 removed outlier: 3.986A pdb=" N SER A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1182 Processing helix chain 'A' and resid 1183 through 1194 Processing helix chain 'A' and resid 1195 through 1199 removed outlier: 3.915A pdb=" N GLU A1198 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A1199 " --> pdb=" O MET A1196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1195 through 1199' Processing helix chain 'A' and resid 1203 through 1208 removed outlier: 4.170A 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: 4.114A pdb=" N VAL A1237 " --> pdb=" O ASP A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1256 removed outlier: 3.671A 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: 3.585A pdb=" N ALA A1338 " --> pdb=" O PHE A1334 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A1347 " --> pdb=" O PHE A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1360 removed outlier: 3.834A pdb=" N LEU A1352 " --> pdb=" O TYR A1348 " (cutoff:3.500A) 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 removed outlier: 3.608A pdb=" N ASN B 631 " --> pdb=" O CYS B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.710A pdb=" N GLN B 674 " --> pdb=" O ARG B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 702 removed outlier: 4.286A pdb=" N LEU B 694 " --> pdb=" O ASN B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 removed outlier: 3.694A pdb=" N LEU B 718 " --> pdb=" O SER B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 749 removed outlier: 3.657A pdb=" N LEU B 732 " --> pdb=" O ASN B 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 749 removed outlier: 3.833A pdb=" N LEU C 732 " --> pdb=" O ASN C 728 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415 removed outlier: 6.652A pdb=" N ARG A 414 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N PHE A 688 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 9.604A 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: 6.652A pdb=" N ARG A 414 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N PHE A 688 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N TYR A 599 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 11.877A pdb=" N GLU A 602 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL A 578 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A 604 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 4.067A 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: 3.837A 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: 6.967A pdb=" N THR A1299 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR A1289 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A1297 " --> pdb=" O THR A1289 " (cutoff:3.500A) removed outlier: 6.802A 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: 6.778A pdb=" N VAL A1300 " --> pdb=" O CYS A1311 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N CYS A1311 " --> pdb=" O VAL A1300 " (cutoff:3.500A) removed outlier: 3.557A 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: 4.124A pdb=" N VAL B 529 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE B 542 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 548 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 5.202A 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 644 489 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.27 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: 3318 1.34 - 1.46: 2515 1.46 - 1.58: 5986 1.58 - 1.70: 187 1.70 - 1.81: 97 Bond restraints: 12103 Sorted by residual: bond pdb=" CB GLU C 737 " pdb=" CG GLU C 737 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CA MET A 949 " pdb=" C MET A 949 " ideal model delta sigma weight residual 1.522 1.504 0.018 1.37e-02 5.33e+03 1.79e+00 bond pdb=" N1 U E 84 " pdb=" C2 U E 84 " ideal model delta sigma weight residual 1.381 1.392 -0.011 9.00e-03 1.23e+04 1.57e+00 bond pdb=" N MET A 427 " pdb=" CA MET A 427 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.48e+00 bond pdb=" CB GLU C 747 " pdb=" CG GLU C 747 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 ... (remaining 12098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 16583 2.49 - 4.99: 202 4.99 - 7.48: 11 7.48 - 9.98: 2 9.98 - 12.47: 1 Bond angle restraints: 16799 Sorted by residual: angle pdb=" C1' U E 84 " pdb=" N1 U E 84 " pdb=" C2 U E 84 " ideal model delta sigma weight residual 117.70 123.50 -5.80 1.20e+00 6.94e-01 2.33e+01 angle pdb=" C PRO A 426 " pdb=" N MET A 427 " pdb=" CA MET A 427 " ideal model delta sigma weight residual 121.54 130.51 -8.97 1.91e+00 2.74e-01 2.21e+01 angle pdb=" CA MET A 427 " pdb=" CB MET A 427 " pdb=" CG MET A 427 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CB MET A 427 " pdb=" CG MET A 427 " pdb=" SD MET A 427 " ideal model delta sigma weight residual 112.70 125.17 -12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" N1 U E 84 " pdb=" C2 U E 84 " pdb=" O2 U E 84 " ideal model delta sigma weight residual 122.80 125.54 -2.74 7.00e-01 2.04e+00 1.54e+01 ... (remaining 16794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 7121 35.78 - 71.56: 310 71.56 - 107.33: 32 107.33 - 143.11: 1 143.11 - 178.89: 2 Dihedral angle restraints: 7466 sinusoidal: 4008 harmonic: 3458 Sorted by residual: dihedral pdb=" O4' U E 84 " pdb=" C1' U E 84 " pdb=" N1 U E 84 " pdb=" C2 U E 84 " ideal model delta sinusoidal sigma weight residual 200.00 65.46 134.54 1 1.50e+01 4.44e-03 7.26e+01 dihedral pdb=" O4' C E 15 " pdb=" C1' C E 15 " pdb=" N1 C E 15 " pdb=" C2 C E 15 " ideal model delta sinusoidal sigma weight residual 232.00 53.11 178.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C E 124 " pdb=" C1' C E 124 " pdb=" N1 C E 124 " pdb=" C2 C E 124 " ideal model delta sinusoidal sigma weight residual -128.00 45.17 -173.17 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 7463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1249 0.029 - 0.059: 363 0.059 - 0.088: 116 0.088 - 0.118: 77 0.118 - 0.147: 97 Chirality restraints: 1902 Sorted by residual: chirality pdb=" CB ILE A 508 " pdb=" CA ILE A 508 " pdb=" CG1 ILE A 508 " pdb=" CG2 ILE A 508 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.43e-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 5.24e-01 chirality pdb=" C1' U E 84 " pdb=" O4' U E 84 " pdb=" C2' U E 84 " pdb=" N1 U E 84 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 1899 not shown) Planarity restraints: 1820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 748 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" CD GLU C 748 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU C 748 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU C 748 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 597 " -0.016 2.00e-02 2.50e+03 1.26e-02 3.16e+00 pdb=" CG TYR B 597 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 597 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 597 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 597 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 597 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 597 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 597 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A E 13 " -0.019 2.00e-02 2.50e+03 9.86e-03 2.67e+00 pdb=" N9 A E 13 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A E 13 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A E 13 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A E 13 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A E 13 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A E 13 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A E 13 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A E 13 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A E 13 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A E 13 " -0.002 2.00e-02 2.50e+03 ... (remaining 1817 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2973 2.81 - 3.33: 10056 3.33 - 3.85: 19154 3.85 - 4.38: 22262 4.38 - 4.90: 36273 Nonbonded interactions: 90718 Sorted by model distance: nonbonded pdb=" O2' G E 55 " pdb=" O4' G E 56 " model vdw 2.283 3.040 nonbonded pdb=" O2' U E 23 " pdb=" OP1 U E 25 " model vdw 2.330 3.040 nonbonded pdb=" O LYS C 726 " pdb=" NZ LYS C 726 " model vdw 2.337 3.120 nonbonded pdb=" N ASP A1260 " pdb=" OD1 ASP A1260 " model vdw 2.342 3.120 nonbonded pdb=" NH2 ARG B 522 " pdb=" O5' A E 47 " model vdw 2.346 3.120 ... (remaining 90713 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: 8.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 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 0.043 12111 Z= 0.166 Angle : 0.597 12.470 16803 Z= 0.405 Chirality : 0.046 0.147 1902 Planarity : 0.004 0.043 1820 Dihedral : 17.971 178.888 5224 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.04 % Allowed : 15.04 % Favored : 83.92 % 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: 1.39 (0.25), residues: 1168 helix: 2.25 (0.22), residues: 567 sheet: 0.46 (0.42), residues: 143 loop : -0.63 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 961 TYR 0.031 0.001 TYR B 597 PHE 0.016 0.001 PHE A1148 TRP 0.027 0.001 TRP A1357 HIS 0.011 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.17 (12103) covalent geometry : angle 0.59437 / 0.40 (16799) hydrogen bonds : bond 0.17558 / 12.13 ( 562) hydrogen bonds : angle 5.28621 / 3.88 ( 1546) metal coordination : bond 0.01595 / 0.75 ( 8) metal coordination : angle 3.97195 / 2.34 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.405 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 71 average time/residue: 0.6075 time to fit residues: 46.8538 Evaluate side-chains 69 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain B residue 552 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1008 HIS B 600 HIS B 648 ASN ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.078838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.046364 restraints weight = 34241.367| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.79 r_work: 0.2682 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.0619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12111 Z= 0.219 Angle : 0.533 7.198 16803 Z= 0.292 Chirality : 0.039 0.151 1902 Planarity : 0.004 0.039 1820 Dihedral : 18.504 179.249 2761 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.99 % Allowed : 12.87 % Favored : 85.15 % 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: 1168 helix: 2.25 (0.22), residues: 584 sheet: 0.44 (0.41), residues: 150 loop : -0.68 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 961 TYR 0.028 0.001 TYR B 597 PHE 0.017 0.001 PHE A1148 TRP 0.012 0.001 TRP A1357 HIS 0.011 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (12103) covalent geometry : angle 0.52837 / 0.29 (16799) hydrogen bonds : bond 0.07092 / 4.77 ( 562) hydrogen bonds : angle 4.46193 / 3.28 ( 1546) metal coordination : bond 0.01826 / 0.85 ( 8) metal coordination : angle 4.71045 / 2.75 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.334 Fit side-chains REVERT: A 511 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8805 (mttm) REVERT: A 877 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7978 (mtt) outliers start: 21 outliers final: 7 residues processed: 72 average time/residue: 0.5387 time to fit residues: 42.5086 Evaluate side-chains 66 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1344 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 74 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 122 optimal weight: 50.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 600 HIS ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** 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 = 0.3700 r_free = 0.3700 target = 0.079493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.047311 restraints weight = 34919.339| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.84 r_work: 0.2706 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12111 Z= 0.131 Angle : 0.462 6.703 16803 Z= 0.256 Chirality : 0.036 0.139 1902 Planarity : 0.004 0.040 1820 Dihedral : 18.465 179.554 2753 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.23 % Allowed : 14.10 % Favored : 84.67 % 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: 1.59 (0.25), residues: 1168 helix: 2.36 (0.21), residues: 586 sheet: 0.59 (0.40), residues: 153 loop : -0.63 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 961 TYR 0.032 0.001 TYR B 597 PHE 0.014 0.001 PHE A1148 TRP 0.014 0.001 TRP A1357 HIS 0.012 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (12103) covalent geometry : angle 0.45940 / 0.26 (16799) hydrogen bonds : bond 0.05667 / 3.79 ( 562) hydrogen bonds : angle 4.11515 / 3.04 ( 1546) metal coordination : bond 0.01433 / 0.69 ( 8) metal coordination : angle 3.26056 / 1.90 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.437 Fit side-chains REVERT: A 511 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8803 (mttm) REVERT: B 720 GLN cc_start: 0.7784 (pp30) cc_final: 0.7439 (pp30) REVERT: B 721 TYR cc_start: 0.9096 (m-10) cc_final: 0.8610 (m-10) REVERT: C 737 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8113 (tm-30) outliers start: 13 outliers final: 5 residues processed: 69 average time/residue: 0.6241 time to fit residues: 46.9423 Evaluate side-chains 65 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1344 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 58 optimal weight: 0.0870 chunk 23 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 600 HIS ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** 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 = 0.3724 r_free = 0.3724 target = 0.080559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.048517 restraints weight = 34675.260| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.88 r_work: 0.2744 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12111 Z= 0.098 Angle : 0.429 7.070 16803 Z= 0.239 Chirality : 0.035 0.135 1902 Planarity : 0.004 0.043 1820 Dihedral : 18.385 179.749 2752 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.14 % Allowed : 14.10 % Favored : 84.77 % 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: 1.78 (0.25), residues: 1168 helix: 2.53 (0.21), residues: 587 sheet: 0.63 (0.40), residues: 154 loop : -0.55 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 961 TYR 0.034 0.001 TYR B 597 PHE 0.017 0.001 PHE B 542 TRP 0.016 0.001 TRP A1357 HIS 0.012 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (12103) covalent geometry : angle 0.42737 / 0.24 (16799) hydrogen bonds : bond 0.04570 / 3.01 ( 562) hydrogen bonds : angle 3.79143 / 2.80 ( 1546) metal coordination : bond 0.01359 / 0.60 ( 8) metal coordination : angle 2.73921 / 1.61 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.346 Fit side-chains REVERT: A 511 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8836 (mtmm) REVERT: B 520 MET cc_start: 0.8259 (tmm) cc_final: 0.8056 (tmm) REVERT: B 634 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7277 (mpt) REVERT: B 657 CYS cc_start: 0.8758 (t) cc_final: 0.7861 (m) REVERT: B 720 GLN cc_start: 0.7567 (pp30) cc_final: 0.7097 (pp30) REVERT: B 721 TYR cc_start: 0.8939 (m-10) cc_final: 0.8505 (m-10) REVERT: C 745 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8396 (tm-30) outliers start: 12 outliers final: 2 residues processed: 66 average time/residue: 0.6247 time to fit residues: 44.6572 Evaluate side-chains 62 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain C residue 745 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.079271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.046961 restraints weight = 34208.487| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.75 r_work: 0.2697 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12111 Z= 0.177 Angle : 0.486 7.847 16803 Z= 0.264 Chirality : 0.038 0.145 1902 Planarity : 0.004 0.040 1820 Dihedral : 18.311 179.661 2748 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.42 % Allowed : 13.62 % Favored : 84.96 % 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 are not related in a simple way. whole: 1.72 (0.25), residues: 1168 helix: 2.50 (0.21), residues: 587 sheet: 0.51 (0.40), residues: 156 loop : -0.57 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 961 TYR 0.031 0.001 TYR B 597 PHE 0.016 0.001 PHE A1148 TRP 0.015 0.001 TRP A1357 HIS 0.011 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (12103) covalent geometry : angle 0.48187 / 0.26 (16799) hydrogen bonds : bond 0.05887 / 3.89 ( 562) hydrogen bonds : angle 3.91448 / 2.89 ( 1546) metal coordination : bond 0.01753 / 0.82 ( 8) metal coordination : angle 4.21216 / 2.44 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.439 Fit side-chains REVERT: A 511 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8796 (mtmm) REVERT: B 657 CYS cc_start: 0.8809 (t) cc_final: 0.7941 (m) REVERT: C 745 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8443 (tm-30) REVERT: C 747 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8237 (pp20) outliers start: 15 outliers final: 8 residues processed: 73 average time/residue: 0.5293 time to fit residues: 42.1723 Evaluate side-chains 66 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1344 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 0.0370 chunk 13 optimal weight: 0.7980 chunk 125 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 GLN ** B 660 HIS ** 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 = 0.3724 r_free = 0.3724 target = 0.080536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.048230 restraints weight = 34256.376| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.81 r_work: 0.2736 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12111 Z= 0.100 Angle : 0.440 8.681 16803 Z= 0.242 Chirality : 0.035 0.132 1902 Planarity : 0.004 0.041 1820 Dihedral : 18.320 179.826 2748 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.04 % Allowed : 14.00 % Favored : 84.96 % 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 are not related in a simple way. whole: 1.84 (0.25), residues: 1168 helix: 2.60 (0.21), residues: 587 sheet: 0.61 (0.40), residues: 155 loop : -0.54 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 961 TYR 0.032 0.001 TYR B 597 PHE 0.013 0.001 PHE B 542 TRP 0.013 0.001 TRP A1357 HIS 0.011 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (12103) covalent geometry : angle 0.43799 / 0.24 (16799) hydrogen bonds : bond 0.04553 / 3.00 ( 562) hydrogen bonds : angle 3.72379 / 2.75 ( 1546) metal coordination : bond 0.01439 / 0.68 ( 8) metal coordination : angle 2.92180 / 1.72 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.261 Fit side-chains REVERT: A 511 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8806 (mtmm) REVERT: B 634 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7264 (mpt) REVERT: B 657 CYS cc_start: 0.8790 (t) cc_final: 0.7965 (m) REVERT: C 745 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8417 (tm-30) REVERT: C 747 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8212 (pp20) outliers start: 11 outliers final: 3 residues processed: 66 average time/residue: 0.5962 time to fit residues: 42.6245 Evaluate side-chains 61 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain B residue 634 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 96 optimal weight: 40.0000 chunk 95 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.078555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.046277 restraints weight = 34361.714| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.76 r_work: 0.2668 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12111 Z= 0.216 Angle : 0.526 9.503 16803 Z= 0.281 Chirality : 0.039 0.154 1902 Planarity : 0.004 0.046 1820 Dihedral : 18.264 179.584 2748 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.85 % Allowed : 14.19 % Favored : 84.96 % 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 are not related in a simple way. whole: 1.71 (0.25), residues: 1168 helix: 2.51 (0.22), residues: 586 sheet: 0.47 (0.40), residues: 156 loop : -0.59 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 961 TYR 0.032 0.002 TYR B 597 PHE 0.018 0.001 PHE A1148 TRP 0.014 0.001 TRP A1357 HIS 0.011 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (12103) covalent geometry : angle 0.52141 / 0.28 (16799) hydrogen bonds : bond 0.06290 / 4.15 ( 562) hydrogen bonds : angle 3.93411 / 2.89 ( 1546) metal coordination : bond 0.01794 / 0.83 ( 8) metal coordination : angle 4.60077 / 2.65 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.262 Fit side-chains REVERT: A 511 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8794 (mtmm) REVERT: B 657 CYS cc_start: 0.8840 (t) cc_final: 0.7999 (m) REVERT: C 745 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8429 (tm-30) REVERT: C 747 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8228 (pp20) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.6495 time to fit residues: 46.6637 Evaluate side-chains 64 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain B residue 547 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 96 optimal weight: 40.0000 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 111 optimal weight: 0.2980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.080350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048121 restraints weight = 34132.661| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.80 r_work: 0.2738 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12111 Z= 0.101 Angle : 0.457 11.503 16803 Z= 0.250 Chirality : 0.035 0.133 1902 Planarity : 0.004 0.043 1820 Dihedral : 18.280 179.824 2748 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.57 % Allowed : 14.76 % Favored : 84.67 % 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: 1.88 (0.25), residues: 1168 helix: 2.64 (0.21), residues: 587 sheet: 0.59 (0.40), residues: 155 loop : -0.51 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 961 TYR 0.031 0.001 TYR B 597 PHE 0.013 0.001 PHE B 542 TRP 0.017 0.001 TRP A1357 HIS 0.012 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (12103) covalent geometry : angle 0.45499 / 0.25 (16799) hydrogen bonds : bond 0.04500 / 2.96 ( 562) hydrogen bonds : angle 3.71561 / 2.74 ( 1546) metal coordination : bond 0.01486 / 0.71 ( 8) metal coordination : angle 3.10835 / 1.83 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.353 Fit side-chains REVERT: A 511 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8792 (mtmm) REVERT: B 634 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7300 (mpt) REVERT: C 745 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8417 (tm-30) REVERT: C 747 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8226 (pp20) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 0.5914 time to fit residues: 39.7721 Evaluate side-chains 62 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 634 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.079586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.047339 restraints weight = 34286.291| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.79 r_work: 0.2704 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12111 Z= 0.132 Angle : 0.480 11.921 16803 Z= 0.258 Chirality : 0.036 0.137 1902 Planarity : 0.004 0.044 1820 Dihedral : 18.231 179.897 2748 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.57 % Allowed : 14.95 % Favored : 84.48 % 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: 1.88 (0.25), residues: 1168 helix: 2.65 (0.21), residues: 587 sheet: 0.53 (0.40), residues: 155 loop : -0.50 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 961 TYR 0.032 0.001 TYR B 597 PHE 0.015 0.001 PHE A1148 TRP 0.016 0.001 TRP A1357 HIS 0.012 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (12103) covalent geometry : angle 0.47707 / 0.26 (16799) hydrogen bonds : bond 0.05009 / 3.30 ( 562) hydrogen bonds : angle 3.73210 / 2.75 ( 1546) metal coordination : bond 0.01577 / 0.73 ( 8) metal coordination : angle 3.48037 / 2.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.328 Fit side-chains REVERT: A 511 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8774 (mtmm) REVERT: C 745 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8384 (tm-30) REVERT: C 747 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8230 (pp20) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.5482 time to fit residues: 37.5692 Evaluate side-chains 63 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain B residue 547 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 125 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.079831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047487 restraints weight = 34740.731| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.82 r_work: 0.2710 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12111 Z= 0.117 Angle : 0.479 13.885 16803 Z= 0.257 Chirality : 0.036 0.139 1902 Planarity : 0.004 0.047 1820 Dihedral : 18.239 179.959 2748 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.57 % Allowed : 14.85 % Favored : 84.58 % 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: 1.89 (0.25), residues: 1168 helix: 2.66 (0.21), residues: 587 sheet: 0.56 (0.40), residues: 155 loop : -0.50 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 961 TYR 0.034 0.001 TYR B 597 PHE 0.014 0.001 PHE B 542 TRP 0.018 0.001 TRP A1357 HIS 0.012 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (12103) covalent geometry : angle 0.47648 / 0.26 (16799) hydrogen bonds : bond 0.04759 / 3.14 ( 562) hydrogen bonds : angle 3.70293 / 2.73 ( 1546) metal coordination : bond 0.01582 / 0.74 ( 8) metal coordination : angle 3.36388 / 1.97 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.295 Fit side-chains REVERT: A 511 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8765 (mtmm) REVERT: C 745 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 747 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8226 (pp20) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.5862 time to fit residues: 40.2314 Evaluate side-chains 63 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1289 THR Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain B residue 547 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 0.0030 chunk 117 optimal weight: 10.0000 chunk 6 optimal weight: 0.0270 chunk 46 optimal weight: 0.0060 chunk 92 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 50.0000 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 0.2980 chunk 118 optimal weight: 9.9990 overall best weight: 0.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.081756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.049666 restraints weight = 34643.006| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.90 r_work: 0.2772 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12111 Z= 0.093 Angle : 0.461 12.824 16803 Z= 0.250 Chirality : 0.034 0.147 1902 Planarity : 0.004 0.041 1820 Dihedral : 18.238 179.505 2748 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.57 % Allowed : 14.95 % Favored : 84.48 % 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: 2.04 (0.25), residues: 1168 helix: 2.73 (0.21), residues: 587 sheet: 0.77 (0.41), residues: 153 loop : -0.43 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 961 TYR 0.033 0.001 TYR B 597 PHE 0.015 0.001 PHE B 542 TRP 0.021 0.001 TRP A1357 HIS 0.011 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (12103) covalent geometry : angle 0.45976 / 0.25 (16799) hydrogen bonds : bond 0.03430 / 2.25 ( 562) hydrogen bonds : angle 3.50195 / 2.59 ( 1546) metal coordination : bond 0.01126 / 0.48 ( 8) metal coordination : angle 2.55918 / 1.49 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3635.55 seconds wall clock time: 62 minutes 33.56 seconds (3753.56 seconds total)