Starting phenix.real_space_refine on Mon Jul 6 06:04:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjm_60150/07_2026/8zjm_60150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjm_60150/07_2026/8zjm_60150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjm_60150/07_2026/8zjm_60150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjm_60150/07_2026/8zjm_60150.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjm_60150/07_2026/8zjm_60150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjm_60150/07_2026/8zjm_60150.cif" } resolution = 4.52 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= 0.002 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: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 21052 2.51 5 N 5538 2.21 5 O 6092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32858 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1608 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "B" Number of atoms: 13436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1642, 13436 Classifications: {'peptide': 1642} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1583} Chain: "C" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1385 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "D" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1608 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "E" Number of atoms: 13436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1642, 13436 Classifications: {'peptide': 1642} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1583} Chain: "F" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1385 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Time building chain proxies: 6.45, per 1000 atoms: 0.20 Number of scatterers: 32858 At special positions: 0 Unit cell: (272.65, 166.25, 154.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 6092 8.00 N 5538 7.00 C 21052 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: 3.02 Conformation dependent library (CDL) restraints added in 1.7 seconds 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7696 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 22 sheets defined 54.7% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.588A pdb=" N ILE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 559 removed outlier: 3.524A pdb=" N GLU A 546 " --> pdb=" O PRO A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 626 Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.861A pdb=" N VAL A 637 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 638' Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 679 through 698 Processing helix chain 'B' and resid 85 through 108 removed outlier: 3.879A pdb=" N VAL B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 131 Processing helix chain 'B' and resid 137 through 160 Processing helix chain 'B' and resid 168 through 172 removed outlier: 4.133A pdb=" N ILE B 172 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 180 through 205 removed outlier: 5.524A pdb=" N LYS B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.994A pdb=" N GLY B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.516A pdb=" N ILE B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.839A pdb=" N ARG B 360 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 removed outlier: 3.660A pdb=" N VAL B 382 " --> pdb=" O PRO B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.756A pdb=" N LYS B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 642 removed outlier: 3.854A pdb=" N LEU B 638 " --> pdb=" O ASN B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 648 No H-bonds generated for 'chain 'B' and resid 646 through 648' Processing helix chain 'B' and resid 649 through 657 removed outlier: 3.631A pdb=" N LYS B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 666 Processing helix chain 'B' and resid 668 through 683 Processing helix chain 'B' and resid 686 through 705 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 728 through 743 Processing helix chain 'B' and resid 749 through 759 removed outlier: 3.915A pdb=" N ALA B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 778 Processing helix chain 'B' and resid 783 through 804 removed outlier: 4.002A pdb=" N ASN B 788 " --> pdb=" O GLY B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 820 Processing helix chain 'B' and resid 820 through 828 removed outlier: 4.193A pdb=" N ASN B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 846 Processing helix chain 'B' and resid 852 through 866 Processing helix chain 'B' and resid 874 through 891 Proline residue: B 880 - end of helix removed outlier: 4.401A pdb=" N ASP B 891 " --> pdb=" O SER B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 915 removed outlier: 4.378A pdb=" N ASP B 898 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 943 removed outlier: 5.818A pdb=" N ARG B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 963 Processing helix chain 'B' and resid 965 through 973 removed outlier: 3.749A pdb=" N HIS B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 972 " --> pdb=" O HIS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 998 Processing helix chain 'B' and resid 1006 through 1032 Processing helix chain 'B' and resid 1041 through 1055 removed outlier: 4.328A pdb=" N ASN B1045 " --> pdb=" O GLN B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1063 Processing helix chain 'B' and resid 1065 through 1077 removed outlier: 4.001A pdb=" N ARG B1069 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1095 removed outlier: 3.620A pdb=" N GLU B1082 " --> pdb=" O ASP B1078 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B1095 " --> pdb=" O TRP B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1099 Processing helix chain 'B' and resid 1101 through 1115 removed outlier: 4.866A pdb=" N GLY B1107 " --> pdb=" O PRO B1103 " (cutoff:3.500A) Proline residue: B1108 - end of helix Processing helix chain 'B' and resid 1117 through 1139 removed outlier: 3.733A pdb=" N ARG B1121 " --> pdb=" O GLU B1117 " (cutoff:3.500A) Proline residue: B1126 - end of helix Processing helix chain 'B' and resid 1140 through 1142 No H-bonds generated for 'chain 'B' and resid 1140 through 1142' Processing helix chain 'B' and resid 1144 through 1162 Processing helix chain 'B' and resid 1165 through 1182 Processing helix chain 'B' and resid 1184 through 1212 Processing helix chain 'B' and resid 1217 through 1235 Processing helix chain 'B' and resid 1236 through 1254 Processing helix chain 'B' and resid 1256 through 1271 Processing helix chain 'B' and resid 1292 through 1311 Processing helix chain 'B' and resid 1313 through 1332 removed outlier: 4.648A pdb=" N GLU B1323 " --> pdb=" O LYS B1319 " (cutoff:3.500A) Processing helix chain 'B' and resid 1334 through 1355 Processing helix chain 'B' and resid 1390 through 1402 Processing helix chain 'B' and resid 1416 through 1421 removed outlier: 3.807A pdb=" N SER B1420 " --> pdb=" O GLU B1416 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1455 removed outlier: 4.461A pdb=" N LEU B1451 " --> pdb=" O PRO B1447 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1539 Processing helix chain 'B' and resid 1544 through 1556 removed outlier: 3.739A pdb=" N ASP B1556 " --> pdb=" O SER B1552 " (cutoff:3.500A) Processing helix chain 'B' and resid 1561 through 1570 Processing helix chain 'B' and resid 1572 through 1579 removed outlier: 3.863A pdb=" N LEU B1576 " --> pdb=" O THR B1572 " (cutoff:3.500A) Processing helix chain 'B' and resid 1580 through 1584 removed outlier: 3.573A pdb=" N GLN B1583 " --> pdb=" O PRO B1580 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU B1584 " --> pdb=" O GLU B1581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1580 through 1584' Processing helix chain 'B' and resid 1585 through 1610 Proline residue: B1598 - end of helix Processing helix chain 'B' and resid 1614 through 1636 removed outlier: 3.768A pdb=" N LEU B1618 " --> pdb=" O GLN B1614 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 removed outlier: 4.110A pdb=" N LEU C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 86 through 96 Processing helix chain 'C' and resid 96 through 105 removed outlier: 3.643A pdb=" N VAL C 101 " --> pdb=" O TRP C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 removed outlier: 3.853A pdb=" N ASP C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 164 through 175 Processing helix chain 'D' and resid 531 through 540 removed outlier: 3.589A pdb=" N ILE D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 559 removed outlier: 3.524A pdb=" N GLU D 546 " --> pdb=" O PRO D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 626 Proline residue: D 623 - end of helix Processing helix chain 'D' and resid 634 through 638 removed outlier: 3.861A pdb=" N VAL D 637 " --> pdb=" O ASN D 634 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU D 638 " --> pdb=" O LYS D 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 634 through 638' Processing helix chain 'D' and resid 658 through 673 Processing helix chain 'D' and resid 679 through 698 Processing helix chain 'E' and resid 85 through 108 removed outlier: 3.878A pdb=" N VAL E 100 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 131 Processing helix chain 'E' and resid 137 through 160 Processing helix chain 'E' and resid 168 through 172 removed outlier: 4.133A pdb=" N ILE E 172 " --> pdb=" O ASN E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 177 Processing helix chain 'E' and resid 180 through 205 removed outlier: 5.524A pdb=" N LYS E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER E 203 " --> pdb=" O GLN E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.993A pdb=" N GLY E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 291 Processing helix chain 'E' and resid 329 through 334 removed outlier: 3.516A pdb=" N ILE E 333 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.839A pdb=" N ARG E 360 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.659A pdb=" N VAL E 382 " --> pdb=" O PRO E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 417 Processing helix chain 'E' and resid 521 through 523 No H-bonds generated for 'chain 'E' and resid 521 through 523' Processing helix chain 'E' and resid 537 through 544 Processing helix chain 'E' and resid 575 through 580 Processing helix chain 'E' and resid 581 through 586 Processing helix chain 'E' and resid 591 through 605 removed outlier: 3.756A pdb=" N LYS E 604 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN E 605 " --> pdb=" O GLN E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 642 removed outlier: 3.854A pdb=" N LEU E 638 " --> pdb=" O ASN E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 648 No H-bonds generated for 'chain 'E' and resid 646 through 648' Processing helix chain 'E' and resid 649 through 657 removed outlier: 3.631A pdb=" N LYS E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 666 Processing helix chain 'E' and resid 668 through 683 Processing helix chain 'E' and resid 686 through 705 Processing helix chain 'E' and resid 712 through 722 Processing helix chain 'E' and resid 728 through 743 Processing helix chain 'E' and resid 749 through 759 removed outlier: 3.915A pdb=" N ALA E 759 " --> pdb=" O ALA E 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 778 Processing helix chain 'E' and resid 783 through 804 removed outlier: 4.001A pdb=" N ASN E 788 " --> pdb=" O GLY E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 820 Processing helix chain 'E' and resid 820 through 828 removed outlier: 4.192A pdb=" N ASN E 825 " --> pdb=" O PRO E 821 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP E 826 " --> pdb=" O SER E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 832 through 846 Processing helix chain 'E' and resid 852 through 866 Processing helix chain 'E' and resid 874 through 891 Proline residue: E 880 - end of helix removed outlier: 4.401A pdb=" N ASP E 891 " --> pdb=" O SER E 887 " (cutoff:3.500A) Processing helix chain 'E' and resid 894 through 915 removed outlier: 4.379A pdb=" N ASP E 898 " --> pdb=" O SER E 894 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU E 900 " --> pdb=" O LYS E 896 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA E 901 " --> pdb=" O PRO E 897 " (cutoff:3.500A) Processing helix chain 'E' and resid 921 through 943 removed outlier: 5.818A pdb=" N ARG E 934 " --> pdb=" O GLU E 930 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG E 935 " --> pdb=" O ARG E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 949 through 963 Processing helix chain 'E' and resid 965 through 973 removed outlier: 3.749A pdb=" N HIS E 971 " --> pdb=" O SER E 967 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR E 972 " --> pdb=" O HIS E 968 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 998 Processing helix chain 'E' and resid 1006 through 1032 Processing helix chain 'E' and resid 1041 through 1055 removed outlier: 4.328A pdb=" N ASN E1045 " --> pdb=" O GLN E1041 " (cutoff:3.500A) Processing helix chain 'E' and resid 1058 through 1063 Processing helix chain 'E' and resid 1065 through 1077 removed outlier: 4.000A pdb=" N ARG E1069 " --> pdb=" O SER E1065 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN E1070 " --> pdb=" O GLN E1066 " (cutoff:3.500A) Processing helix chain 'E' and resid 1078 through 1095 removed outlier: 3.619A pdb=" N GLU E1082 " --> pdb=" O ASP E1078 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY E1095 " --> pdb=" O TRP E1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 1096 through 1099 Processing helix chain 'E' and resid 1101 through 1115 removed outlier: 4.867A pdb=" N GLY E1107 " --> pdb=" O PRO E1103 " (cutoff:3.500A) Proline residue: E1108 - end of helix Processing helix chain 'E' and resid 1117 through 1139 removed outlier: 3.733A pdb=" N ARG E1121 " --> pdb=" O GLU E1117 " (cutoff:3.500A) Proline residue: E1126 - end of helix Processing helix chain 'E' and resid 1140 through 1142 No H-bonds generated for 'chain 'E' and resid 1140 through 1142' Processing helix chain 'E' and resid 1144 through 1162 Processing helix chain 'E' and resid 1165 through 1182 Processing helix chain 'E' and resid 1184 through 1212 Processing helix chain 'E' and resid 1217 through 1235 Processing helix chain 'E' and resid 1236 through 1254 Processing helix chain 'E' and resid 1256 through 1271 Processing helix chain 'E' and resid 1292 through 1311 Processing helix chain 'E' and resid 1313 through 1332 removed outlier: 4.648A pdb=" N GLU E1323 " --> pdb=" O LYS E1319 " (cutoff:3.500A) Processing helix chain 'E' and resid 1334 through 1355 Processing helix chain 'E' and resid 1390 through 1402 Processing helix chain 'E' and resid 1416 through 1421 removed outlier: 3.807A pdb=" N SER E1420 " --> pdb=" O GLU E1416 " (cutoff:3.500A) Processing helix chain 'E' and resid 1447 through 1455 removed outlier: 4.461A pdb=" N LEU E1451 " --> pdb=" O PRO E1447 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1539 Processing helix chain 'E' and resid 1544 through 1556 removed outlier: 3.738A pdb=" N ASP E1556 " --> pdb=" O SER E1552 " (cutoff:3.500A) Processing helix chain 'E' and resid 1561 through 1570 Processing helix chain 'E' and resid 1572 through 1579 removed outlier: 3.863A pdb=" N LEU E1576 " --> pdb=" O THR E1572 " (cutoff:3.500A) Processing helix chain 'E' and resid 1580 through 1584 removed outlier: 3.574A pdb=" N GLN E1583 " --> pdb=" O PRO E1580 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU E1584 " --> pdb=" O GLU E1581 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1580 through 1584' Processing helix chain 'E' and resid 1585 through 1610 Proline residue: E1598 - end of helix Processing helix chain 'E' and resid 1614 through 1636 removed outlier: 3.769A pdb=" N LEU E1618 " --> pdb=" O GLN E1614 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 removed outlier: 4.109A pdb=" N LEU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 66 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 86 through 96 Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.643A pdb=" N VAL F 101 " --> pdb=" O TRP F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 3.854A pdb=" N ASP F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 164 through 175 Processing sheet with id=AA1, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA2, first strand: chain 'A' and resid 615 through 618 removed outlier: 3.587A pdb=" N ALA A 615 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 642 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 644 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR A 646 " --> pdb=" O CYS A 650 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS A 650 " --> pdb=" O TYR A 646 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 40 removed outlier: 7.260A pdb=" N ARG B 46 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N MET B 40 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TRP B 44 " --> pdb=" O MET B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 252 through 253 removed outlier: 3.988A pdb=" N THR B 252 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 247 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 252 through 253 removed outlier: 3.988A pdb=" N THR B 252 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 247 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 296 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL B 326 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N CYS B 298 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 324 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE B 300 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 326 " --> pdb=" O PRO B 347 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASP B 328 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N PHE B 345 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY B 398 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE B 231 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TRP B 400 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TYR B 222 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 283 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN B 278 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA B 428 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 280 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 484 through 485 removed outlier: 6.708A pdb=" N CYS B 508 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS B 452 " --> pdb=" O CYS B 508 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU B 450 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR B 512 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 448 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS B 514 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE B 446 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER B 516 " --> pdb=" O ASN B 444 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASN B 444 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU B 450 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA B 623 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 484 through 485 removed outlier: 6.708A pdb=" N CYS B 508 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS B 452 " --> pdb=" O CYS B 508 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU B 450 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR B 512 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 448 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS B 514 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE B 446 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER B 516 " --> pdb=" O ASN B 444 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASN B 444 " --> pdb=" O SER B 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 495 through 496 removed outlier: 3.725A pdb=" N GLY B 548 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1362 through 1367 removed outlier: 3.822A pdb=" N TYR B1367 " --> pdb=" O LYS B1379 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B1379 " --> pdb=" O TYR B1367 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE B1380 " --> pdb=" O VAL B1504 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU B1503 " --> pdb=" O ALA B1492 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B1492 " --> pdb=" O GLU B1503 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR B1490 " --> pdb=" O LYS B1505 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B1507 " --> pdb=" O THR B1488 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR B1488 " --> pdb=" O ILE B1507 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN B1460 " --> pdb=" O THR B1491 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1467 through 1469 Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 44 removed outlier: 3.507A pdb=" N VAL C 44 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 51 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN C 2 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLY C 54 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE C 4 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP C 56 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS C 6 " --> pdb=" O TRP C 56 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C 58 " --> pdb=" O CYS C 6 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL C 8 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 7 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE C 78 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL C 113 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE C 80 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR C 115 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE C 82 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 110 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU C 155 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU C 112 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 561 through 562 Processing sheet with id=AB4, first strand: chain 'D' and resid 615 through 618 removed outlier: 3.587A pdb=" N ALA D 615 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE D 642 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 644 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR D 646 " --> pdb=" O CYS D 650 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS D 650 " --> pdb=" O TYR D 646 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 36 through 40 removed outlier: 7.261A pdb=" N ARG E 46 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N MET E 40 " --> pdb=" O TRP E 44 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TRP E 44 " --> pdb=" O MET E 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 252 through 253 removed outlier: 3.988A pdb=" N THR E 252 " --> pdb=" O ASP E 247 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP E 247 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 252 through 253 removed outlier: 3.988A pdb=" N THR E 252 " --> pdb=" O ASP E 247 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP E 247 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU E 296 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL E 326 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS E 298 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL E 324 " --> pdb=" O CYS E 298 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE E 300 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL E 326 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASP E 328 " --> pdb=" O PHE E 345 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N PHE E 345 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY E 398 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE E 231 " --> pdb=" O GLY E 398 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TRP E 400 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR E 222 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP E 283 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN E 278 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA E 428 " --> pdb=" O GLN E 278 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL E 280 " --> pdb=" O ALA E 428 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 484 through 485 removed outlier: 6.709A pdb=" N CYS E 508 " --> pdb=" O HIS E 452 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS E 452 " --> pdb=" O CYS E 508 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU E 450 " --> pdb=" O TYR E 510 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR E 512 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E 448 " --> pdb=" O THR E 512 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS E 514 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE E 446 " --> pdb=" O LYS E 514 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER E 516 " --> pdb=" O ASN E 444 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASN E 444 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU E 450 " --> pdb=" O ALA E 623 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA E 623 " --> pdb=" O LEU E 450 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 484 through 485 removed outlier: 6.709A pdb=" N CYS E 508 " --> pdb=" O HIS E 452 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS E 452 " --> pdb=" O CYS E 508 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU E 450 " --> pdb=" O TYR E 510 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR E 512 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E 448 " --> pdb=" O THR E 512 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS E 514 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE E 446 " --> pdb=" O LYS E 514 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER E 516 " --> pdb=" O ASN E 444 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASN E 444 " --> pdb=" O SER E 516 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.725A pdb=" N GLY E 548 " --> pdb=" O PHE E 531 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 1362 through 1367 removed outlier: 3.823A pdb=" N TYR E1367 " --> pdb=" O LYS E1379 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS E1379 " --> pdb=" O TYR E1367 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE E1380 " --> pdb=" O VAL E1504 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU E1503 " --> pdb=" O ALA E1492 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA E1492 " --> pdb=" O GLU E1503 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR E1490 " --> pdb=" O LYS E1505 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE E1507 " --> pdb=" O THR E1488 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR E1488 " --> pdb=" O ILE E1507 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN E1460 " --> pdb=" O THR E1491 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 1467 through 1469 Processing sheet with id=AC4, first strand: chain 'F' and resid 41 through 44 removed outlier: 3.508A pdb=" N VAL F 44 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL F 51 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN F 2 " --> pdb=" O ASN F 52 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY F 54 " --> pdb=" O GLN F 2 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE F 4 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP F 56 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS F 6 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR F 58 " --> pdb=" O CYS F 6 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL F 8 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 7 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE F 78 " --> pdb=" O ILE F 111 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL F 113 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE F 80 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR F 115 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE F 82 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 110 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU F 155 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU F 112 " --> pdb=" O LEU F 155 " (cutoff:3.500A) 1669 hydrogen bonds defined for protein. 4881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.15 Time building geometry restraints manager: 3.96 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: 10552 1.34 - 1.46: 6166 1.46 - 1.58: 16544 1.58 - 1.70: 0 1.70 - 1.82: 294 Bond restraints: 33556 Sorted by residual: bond pdb=" C THR E1494 " pdb=" N PHE E1495 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.58e-02 4.01e+03 7.34e+00 bond pdb=" C THR B1494 " pdb=" N PHE B1495 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.58e-02 4.01e+03 7.00e+00 bond pdb=" CG1 ILE B 983 " pdb=" CD1 ILE B 983 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.24e+00 bond pdb=" CG1 ILE E 983 " pdb=" CD1 ILE E 983 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.19e+00 bond pdb=" C ASP B1443 " pdb=" N LYS B1444 " ideal model delta sigma weight residual 1.333 1.302 0.031 1.61e-02 3.86e+03 3.69e+00 ... (remaining 33551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 44057 2.39 - 4.77: 1083 4.77 - 7.16: 143 7.16 - 9.55: 33 9.55 - 11.94: 8 Bond angle restraints: 45324 Sorted by residual: angle pdb=" N VAL C 46 " pdb=" CA VAL C 46 " pdb=" C VAL C 46 " ideal model delta sigma weight residual 112.12 106.57 5.55 8.40e-01 1.42e+00 4.36e+01 angle pdb=" N VAL F 46 " pdb=" CA VAL F 46 " pdb=" C VAL F 46 " ideal model delta sigma weight residual 112.12 106.62 5.50 8.40e-01 1.42e+00 4.28e+01 angle pdb=" N PHE E1563 " pdb=" CA PHE E1563 " pdb=" C PHE E1563 " ideal model delta sigma weight residual 110.97 106.17 4.80 1.09e+00 8.42e-01 1.94e+01 angle pdb=" N PHE B1563 " pdb=" CA PHE B1563 " pdb=" C PHE B1563 " ideal model delta sigma weight residual 110.97 106.21 4.76 1.09e+00 8.42e-01 1.91e+01 angle pdb=" N VAL F 36 " pdb=" CA VAL F 36 " pdb=" C VAL F 36 " ideal model delta sigma weight residual 113.22 107.86 5.36 1.23e+00 6.61e-01 1.90e+01 ... (remaining 45319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 18393 18.00 - 36.00: 1788 36.00 - 54.00: 225 54.00 - 71.99: 44 71.99 - 89.99: 26 Dihedral angle restraints: 20476 sinusoidal: 8586 harmonic: 11890 Sorted by residual: dihedral pdb=" CA GLN D 541 " pdb=" C GLN D 541 " pdb=" N PRO D 542 " pdb=" CA PRO D 542 " ideal model delta harmonic sigma weight residual -180.00 -141.03 -38.97 0 5.00e+00 4.00e-02 6.07e+01 dihedral pdb=" CA GLN A 541 " pdb=" C GLN A 541 " pdb=" N PRO A 542 " pdb=" CA PRO A 542 " ideal model delta harmonic sigma weight residual -180.00 -141.09 -38.91 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA GLN B1041 " pdb=" C GLN B1041 " pdb=" N LEU B1042 " pdb=" CA LEU B1042 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4536 0.086 - 0.171: 466 0.171 - 0.257: 16 0.257 - 0.342: 4 0.342 - 0.428: 2 Chirality restraints: 5024 Sorted by residual: chirality pdb=" CG LEU B1338 " pdb=" CB LEU B1338 " pdb=" CD1 LEU B1338 " pdb=" CD2 LEU B1338 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CG LEU E1338 " pdb=" CB LEU E1338 " pdb=" CD1 LEU E1338 " pdb=" CD2 LEU E1338 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CG LEU B 879 " pdb=" CB LEU B 879 " pdb=" CD1 LEU B 879 " pdb=" CD2 LEU B 879 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 5021 not shown) Planarity restraints: 5796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1425 " 0.016 2.00e-02 2.50e+03 2.57e-02 1.32e+01 pdb=" CG TYR B1425 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR B1425 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B1425 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B1425 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B1425 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B1425 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B1425 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E1425 " 0.016 2.00e-02 2.50e+03 2.56e-02 1.31e+01 pdb=" CG TYR E1425 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR E1425 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR E1425 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR E1425 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E1425 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E1425 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E1425 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 896 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.31e+00 pdb=" N PRO B 897 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 897 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 897 " 0.038 5.00e-02 4.00e+02 ... (remaining 5793 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 842 2.62 - 3.19: 36213 3.19 - 3.76: 60514 3.76 - 4.33: 84018 4.33 - 4.90: 122391 Nonbonded interactions: 303978 Sorted by model distance: nonbonded pdb=" OG1 THR E1521 " pdb=" OH TYR E1566 " model vdw 2.055 3.040 nonbonded pdb=" OG1 THR B1521 " pdb=" OH TYR B1566 " model vdw 2.055 3.040 nonbonded pdb=" OE1 GLU E 256 " pdb=" OH TYR E 447 " model vdw 2.064 3.040 nonbonded pdb=" O PRO D 711 " pdb=" OH TYR E 63 " model vdw 2.064 3.040 nonbonded pdb=" OE1 GLU B 256 " pdb=" OH TYR B 447 " model vdw 2.064 3.040 ... (remaining 303973 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 2.600 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.260 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 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 : 0.006 0.080 33556 Z= 0.286 Angle : 0.921 11.937 45324 Z= 0.505 Chirality : 0.051 0.428 5024 Planarity : 0.005 0.068 5796 Dihedral : 14.084 89.994 12780 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 50.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.05 % 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: -2.54 (0.12), residues: 4022 helix: -1.34 (0.11), residues: 1980 sheet: -1.69 (0.24), residues: 422 loop : -1.97 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 66 TYR 0.061 0.003 TYR B1425 PHE 0.030 0.003 PHE E1372 TRP 0.025 0.003 TRP B1006 HIS 0.016 0.002 HIS B1179 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.29 (33556) covalent geometry : angle 0.92090 / 0.51 (45324) hydrogen bonds : bond 0.20359 / 13.98 ( 1663) hydrogen bonds : angle 8.10160 / 5.74 ( 4881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.070 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.1042 time to fit residues: 0.8617 Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.068 Evaluate side-chains 80 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.8975 (p-90) cc_final: 0.8361 (p-90) REVERT: B 1132 MET cc_start: 0.8056 (ppp) cc_final: 0.7853 (ppp) REVERT: B 1221 MET cc_start: 0.9483 (mpp) cc_final: 0.9270 (mpp) REVERT: B 1482 MET cc_start: 0.3487 (ptt) cc_final: 0.1295 (mmt) REVERT: B 1538 TRP cc_start: 0.7782 (m-90) cc_final: 0.7496 (m-90) REVERT: B 1585 LYS cc_start: 0.8595 (mppt) cc_final: 0.8254 (mttt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0933 time to fit residues: 12.1286 Evaluate side-chains 67 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.504 Evaluate side-chains 7 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.055 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0960 time to fit residues: 0.7976 Evaluate side-chains 5 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0270 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.0370 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 596 GLN B 30 GLN ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN ** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN B1097 HIS B1203 ASN ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1517 ASN B1535 GLN ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.048479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.046764 restraints weight = 56846.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.046764 restraints weight = 56354.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.046764 restraints weight = 56369.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.046763 restraints weight = 56369.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.046763 restraints weight = 56461.072| |-----------------------------------------------------------------------------| r_work (final): 0.3545 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.058211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.038502 restraints weight = 195928.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.038526 restraints weight = 152835.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.038780 restraints weight = 122519.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.039021 restraints weight = 104148.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.039387 restraints weight = 93774.119| |-----------------------------------------------------------------------------| r_work (final): 0.3410 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.054003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.043450 restraints weight = 23434.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.044050 restraints weight = 20179.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.044451 restraints weight = 17894.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.044791 restraints weight = 16339.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.045142 restraints weight = 15150.962| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33556 Z= 0.169 Angle : 0.727 9.260 45324 Z= 0.380 Chirality : 0.046 0.206 5024 Planarity : 0.005 0.061 5796 Dihedral : 6.115 32.898 4394 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 24.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.27 % Allowed : 6.39 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.74 (0.13), residues: 4022 helix: -0.59 (0.11), residues: 2048 sheet: -1.59 (0.25), residues: 422 loop : -1.62 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E1345 TYR 0.027 0.002 TYR E1362 PHE 0.024 0.002 PHE B1372 TRP 0.014 0.002 TRP F 56 HIS 0.011 0.001 HIS B1179 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (33556) covalent geometry : angle 0.72664 / 0.38 (45324) hydrogen bonds : bond 0.05298 / 3.55 ( 1663) hydrogen bonds : angle 6.56646 / 4.60 ( 4881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.068 Fit side-chains revert: symmetry clash REVERT: A 596 GLN cc_start: 0.5178 (OUTLIER) cc_final: 0.4948 (pm20) outliers start: 1 outliers final: 0 residues processed: 5 average time/residue: 0.0467 time to fit residues: 0.3666 Evaluate side-chains 5 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.070 Evaluate side-chains 92 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.9177 (p-90) cc_final: 0.8657 (p-90) REVERT: B 802 MET cc_start: 0.8428 (ppp) cc_final: 0.8167 (ppp) REVERT: B 929 MET cc_start: 0.4525 (tmm) cc_final: 0.3612 (ttt) REVERT: B 957 MET cc_start: 0.9488 (pmm) cc_final: 0.8998 (pmm) REVERT: B 1212 MET cc_start: 0.9190 (mpp) cc_final: 0.8918 (mmm) REVERT: B 1231 TYR cc_start: 0.9092 (m-80) cc_final: 0.8873 (m-80) REVERT: B 1426 MET cc_start: 0.4518 (mtt) cc_final: 0.4059 (mtt) REVERT: B 1482 MET cc_start: 0.3468 (ptt) cc_final: 0.1726 (tpt) REVERT: B 1549 MET cc_start: 0.4183 (mmp) cc_final: 0.3721 (tpp) outliers start: 4 outliers final: 0 residues processed: 91 average time/residue: 0.0825 time to fit residues: 12.3584 Evaluate side-chains 69 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.507 Evaluate side-chains 6 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.054 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.1139 time to fit residues: 0.7997 Evaluate side-chains 6 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 191 optimal weight: 0.0070 chunk 323 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 387 optimal weight: 0.2980 chunk 76 optimal weight: 0.0050 chunk 263 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 overall best weight: 0.4412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 937 ASN B1145 HIS ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1607 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.060110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.043349 restraints weight = 21803.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.042798 restraints weight = 24626.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.042798 restraints weight = 25277.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.042798 restraints weight = 25277.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.042798 restraints weight = 25277.783| |-----------------------------------------------------------------------------| r_work (final): 0.3339 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.058830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.039576 restraints weight = 196565.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.039451 restraints weight = 163209.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.039980 restraints weight = 122228.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.039980 restraints weight = 101927.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.039980 restraints weight = 101927.741| |-----------------------------------------------------------------------------| r_work (final): 0.3434 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.055078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.047532 restraints weight = 20905.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.048057 restraints weight = 17916.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.048363 restraints weight = 16000.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.048639 restraints weight = 14782.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.048776 restraints weight = 13858.686| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33556 Z= 0.143 Angle : 0.677 7.955 45324 Z= 0.352 Chirality : 0.045 0.179 5024 Planarity : 0.005 0.063 5796 Dihedral : 5.789 31.584 4394 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.11 % Allowed : 4.70 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.47 (0.13), residues: 4022 helix: -0.28 (0.11), residues: 2034 sheet: -1.60 (0.26), residues: 410 loop : -1.59 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 931 TYR 0.019 0.002 TYR B1289 PHE 0.022 0.002 PHE C 169 TRP 0.015 0.002 TRP E1538 HIS 0.008 0.001 HIS B1179 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (33556) covalent geometry : angle 0.67720 / 0.35 (45324) hydrogen bonds : bond 0.04692 / 3.15 ( 1663) hydrogen bonds : angle 6.20810 / 4.34 ( 4881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.068 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0398 time to fit residues: 0.3346 Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.066 Evaluate side-chains 88 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.9153 (p-90) cc_final: 0.8565 (p-90) REVERT: B 680 MET cc_start: -0.2567 (ptt) cc_final: -0.2842 (ptm) REVERT: B 929 MET cc_start: 0.4257 (tmm) cc_final: 0.3690 (ttp) REVERT: B 957 MET cc_start: 0.9392 (pmm) cc_final: 0.9116 (pmm) REVERT: B 1212 MET cc_start: 0.9099 (mpp) cc_final: 0.8802 (mmm) REVERT: B 1426 MET cc_start: 0.4580 (mtt) cc_final: 0.3984 (mtt) REVERT: B 1482 MET cc_start: 0.2755 (ptt) cc_final: 0.1095 (tpt) REVERT: B 1549 MET cc_start: 0.4199 (mmp) cc_final: 0.3608 (tpp) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.0886 time to fit residues: 12.8555 Evaluate side-chains 69 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.454 Evaluate side-chains 7 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.055 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 6 average time/residue: 0.1152 time to fit residues: 0.8066 Evaluate side-chains 5 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 91 optimal weight: 0.0070 chunk 208 optimal weight: 7.9990 chunk 264 optimal weight: 0.0770 chunk 60 optimal weight: 0.6980 chunk 323 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 354 optimal weight: 0.0970 chunk 393 optimal weight: 0.0060 chunk 243 optimal weight: 0.0060 chunk 122 optimal weight: 0.0050 chunk 281 optimal weight: 20.0000 overall best weight: 0.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 HIS ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1359 GLN B1517 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.061084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.044205 restraints weight = 21055.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.044205 restraints weight = 22997.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.044205 restraints weight = 22997.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.044205 restraints weight = 22997.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.044205 restraints weight = 22997.800| |-----------------------------------------------------------------------------| r_work (final): 0.3371 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.059545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.039942 restraints weight = 191807.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.040001 restraints weight = 148558.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.040355 restraints weight = 116058.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.040372 restraints weight = 98928.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.040372 restraints weight = 97649.734| |-----------------------------------------------------------------------------| r_work (final): 0.3431 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.055468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.047752 restraints weight = 20637.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.048147 restraints weight = 17655.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.048563 restraints weight = 15937.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.048814 restraints weight = 14586.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.049050 restraints weight = 13667.555| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33556 Z= 0.136 Angle : 0.651 8.516 45324 Z= 0.337 Chirality : 0.044 0.201 5024 Planarity : 0.005 0.055 5796 Dihedral : 5.474 29.167 4394 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.29 (0.13), residues: 4022 helix: -0.10 (0.11), residues: 2050 sheet: -1.42 (0.26), residues: 388 loop : -1.61 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1345 TYR 0.031 0.002 TYR B1637 PHE 0.021 0.002 PHE B 348 TRP 0.022 0.001 TRP B1538 HIS 0.006 0.001 HIS E 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (33556) covalent geometry : angle 0.65140 / 0.34 (45324) hydrogen bonds : bond 0.04256 / 2.87 ( 1663) hydrogen bonds : angle 5.82885 / 4.07 ( 4881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.066 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0301 time to fit residues: 0.2349 Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.071 Evaluate side-chains 87 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.9168 (p-90) cc_final: 0.8566 (p-90) REVERT: B 1231 TYR cc_start: 0.9338 (m-80) cc_final: 0.8845 (m-80) REVERT: B 1426 MET cc_start: 0.4561 (mtt) cc_final: 0.4004 (mtt) REVERT: B 1482 MET cc_start: 0.2659 (ptt) cc_final: 0.1019 (tpt) REVERT: B 1549 MET cc_start: 0.4087 (mmp) cc_final: 0.3523 (tpp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0893 time to fit residues: 12.7075 Evaluate side-chains 71 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.535 Evaluate side-chains 6 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.056 Fit side-chains revert: symmetry clash REVERT: F 45 MET cc_start: 0.1970 (mpp) cc_final: 0.1651 (ptp) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.1120 time to fit residues: 0.7896 Evaluate side-chains 5 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 351 optimal weight: 0.7980 chunk 112 optimal weight: 0.0970 chunk 322 optimal weight: 0.1980 chunk 131 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 360 optimal weight: 6.9990 chunk 329 optimal weight: 0.0050 chunk 170 optimal weight: 30.0000 chunk 198 optimal weight: 6.9990 chunk 328 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 HIS ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.061267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.044139 restraints weight = 21951.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.043740 restraints weight = 24154.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.043740 restraints weight = 25458.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.043740 restraints weight = 25458.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.043740 restraints weight = 25458.180| |-----------------------------------------------------------------------------| r_work (final): 0.3362 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.059932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.040504 restraints weight = 192022.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.040843 restraints weight = 157820.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.041199 restraints weight = 122345.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.041379 restraints weight = 101117.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.041379 restraints weight = 90277.850| |-----------------------------------------------------------------------------| r_work (final): 0.3471 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.055953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.047528 restraints weight = 19911.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.048072 restraints weight = 16986.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.048466 restraints weight = 15140.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.048699 restraints weight = 13879.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.048978 restraints weight = 12967.828| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33556 Z= 0.126 Angle : 0.635 7.452 45324 Z= 0.327 Chirality : 0.044 0.275 5024 Planarity : 0.004 0.056 5796 Dihedral : 5.289 28.091 4394 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.06 (0.13), residues: 4022 helix: 0.10 (0.11), residues: 2050 sheet: -1.37 (0.26), residues: 392 loop : -1.51 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1345 TYR 0.022 0.001 TYR E1637 PHE 0.020 0.001 PHE C 169 TRP 0.023 0.001 TRP E1538 HIS 0.006 0.001 HIS E1281 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (33556) covalent geometry : angle 0.63465 / 0.33 (45324) hydrogen bonds : bond 0.04048 / 2.73 ( 1663) hydrogen bonds : angle 5.65180 / 3.96 ( 4881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.067 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0465 time to fit residues: 0.3683 Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.067 Evaluate side-chains 86 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.9163 (p-90) cc_final: 0.8542 (p-90) REVERT: B 802 MET cc_start: 0.8068 (ppp) cc_final: 0.7756 (ppp) REVERT: B 929 MET cc_start: 0.3665 (tmm) cc_final: 0.3149 (ttp) REVERT: B 1231 TYR cc_start: 0.9337 (m-80) cc_final: 0.8903 (m-80) REVERT: B 1426 MET cc_start: 0.4604 (mtt) cc_final: 0.3698 (mtm) REVERT: B 1482 MET cc_start: 0.2592 (ptt) cc_final: 0.1180 (tpt) REVERT: B 1522 MET cc_start: 0.7482 (mtm) cc_final: 0.7272 (mtp) REVERT: B 1549 MET cc_start: 0.4062 (mmp) cc_final: 0.3521 (tpp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1020 time to fit residues: 13.9822 Evaluate side-chains 72 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.503 Evaluate side-chains 7 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.054 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.1428 time to fit residues: 1.1303 Evaluate side-chains 5 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 81 optimal weight: 7.9990 chunk 305 optimal weight: 0.8980 chunk 54 optimal weight: 0.0980 chunk 70 optimal weight: 7.9990 chunk 353 optimal weight: 0.0980 chunk 363 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 131 optimal weight: 0.0980 chunk 153 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1424 GLN B1427 GLN B1517 ASN B1536 HIS ** B1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.052462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.043759 restraints weight = 26883.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.043838 restraints weight = 25472.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.044009 restraints weight = 24700.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.044037 restraints weight = 23974.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.044037 restraints weight = 23671.440| |-----------------------------------------------------------------------------| r_work (final): 0.3470 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.060190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.040814 restraints weight = 192335.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.040720 restraints weight = 154188.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.041021 restraints weight = 118185.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 13)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.041021 restraints weight = 103124.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.041021 restraints weight = 103124.222| |-----------------------------------------------------------------------------| r_work (final): 0.3479 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.054776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.046897 restraints weight = 20365.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.047534 restraints weight = 16804.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.047934 restraints weight = 14603.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.048364 restraints weight = 13048.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.048594 restraints weight = 12071.100| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33556 Z= 0.122 Angle : 0.626 7.747 45324 Z= 0.320 Chirality : 0.043 0.186 5024 Planarity : 0.004 0.056 5796 Dihedral : 5.160 27.475 4394 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.93 (0.13), residues: 4022 helix: 0.22 (0.11), residues: 2058 sheet: -1.61 (0.25), residues: 408 loop : -1.37 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 935 TYR 0.019 0.001 TYR B1637 PHE 0.032 0.001 PHE B 798 TRP 0.025 0.001 TRP E1538 HIS 0.008 0.001 HIS D 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (33556) covalent geometry : angle 0.62579 / 0.32 (45324) hydrogen bonds : bond 0.03905 / 2.63 ( 1663) hydrogen bonds : angle 5.52032 / 3.85 ( 4881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.054 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0422 time to fit residues: 0.3010 Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.051 Evaluate side-chains 91 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.9127 (p-90) cc_final: 0.8467 (p-90) REVERT: B 1231 TYR cc_start: 0.9336 (m-80) cc_final: 0.8747 (m-80) REVERT: B 1243 TYR cc_start: 0.9379 (m-80) cc_final: 0.9081 (m-10) REVERT: B 1426 MET cc_start: 0.4664 (mtt) cc_final: 0.3731 (mtm) REVERT: B 1482 MET cc_start: 0.2498 (ptt) cc_final: 0.1044 (tpt) REVERT: B 1522 MET cc_start: 0.7428 (mtm) cc_final: 0.7217 (mtp) REVERT: B 1549 MET cc_start: 0.4441 (mmp) cc_final: 0.4144 (tpp) REVERT: B 1585 LYS cc_start: 0.8247 (mppt) cc_final: 0.7840 (mttt) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.0976 time to fit residues: 14.2883 Evaluate side-chains 72 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.520 Evaluate side-chains 7 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.055 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.1374 time to fit residues: 1.0923 Evaluate side-chains 5 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 109 optimal weight: 1.9990 chunk 50 optimal weight: 0.0270 chunk 16 optimal weight: 3.9990 chunk 338 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 325 optimal weight: 0.0270 chunk 253 optimal weight: 0.0980 chunk 385 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 176 optimal weight: 0.0670 chunk 302 optimal weight: 0.9990 overall best weight: 0.2436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1517 ASN ** B1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.052905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.044235 restraints weight = 26817.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.044392 restraints weight = 25266.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.044454 restraints weight = 24293.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.044454 restraints weight = 23702.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.044454 restraints weight = 23702.171| |-----------------------------------------------------------------------------| r_work (final): 0.3543 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.060463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.040974 restraints weight = 191576.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.041028 restraints weight = 150326.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.041396 restraints weight = 117548.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.041396 restraints weight = 98917.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.041396 restraints weight = 98917.117| |-----------------------------------------------------------------------------| r_work (final): 0.3473 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.054855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.046115 restraints weight = 20518.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.046644 restraints weight = 17465.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.047093 restraints weight = 15576.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.047353 restraints weight = 14082.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.047641 restraints weight = 13162.955| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33556 Z= 0.122 Angle : 0.637 8.283 45324 Z= 0.324 Chirality : 0.043 0.203 5024 Planarity : 0.004 0.059 5796 Dihedral : 5.042 26.959 4394 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.85 (0.13), residues: 4022 helix: 0.30 (0.11), residues: 2068 sheet: -1.60 (0.25), residues: 408 loop : -1.35 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1345 TYR 0.016 0.001 TYR E 730 PHE 0.020 0.001 PHE E 976 TRP 0.026 0.001 TRP E1538 HIS 0.006 0.001 HIS C 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (33556) covalent geometry : angle 0.63714 / 0.32 (45324) hydrogen bonds : bond 0.03880 / 2.62 ( 1663) hydrogen bonds : angle 5.39884 / 3.77 ( 4881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.074 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0474 time to fit residues: 0.3219 Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.066 Evaluate side-chains 92 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.9074 (p-90) cc_final: 0.8320 (p-90) REVERT: B 243 MET cc_start: 0.2787 (ppp) cc_final: 0.1977 (tmm) REVERT: B 802 MET cc_start: 0.7651 (ppp) cc_final: 0.7337 (ppp) REVERT: B 1231 TYR cc_start: 0.9265 (m-80) cc_final: 0.8920 (m-80) REVERT: B 1426 MET cc_start: 0.4519 (mtt) cc_final: 0.3534 (mtm) REVERT: B 1435 MET cc_start: 0.7909 (tpt) cc_final: 0.7624 (tpt) REVERT: B 1482 MET cc_start: 0.2622 (ptt) cc_final: 0.1200 (tpt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1010 time to fit residues: 14.9257 Evaluate side-chains 71 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.554 Evaluate side-chains 8 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1278 time to fit residues: 1.1584 Evaluate side-chains 4 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 332 optimal weight: 0.8980 chunk 69 optimal weight: 0.0770 chunk 345 optimal weight: 2.9990 chunk 359 optimal weight: 1.9990 chunk 382 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 190 optimal weight: 0.7980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 HIS ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.052616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.044093 restraints weight = 27056.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.044401 restraints weight = 24608.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.044552 restraints weight = 23014.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.044630 restraints weight = 22118.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.044807 restraints weight = 21492.704| |-----------------------------------------------------------------------------| r_work (final): 0.3627 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.060227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.040477 restraints weight = 193178.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.041077 restraints weight = 151965.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.041088 restraints weight = 131294.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.040969 restraints weight = 119717.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.041027 restraints weight = 116516.992| |-----------------------------------------------------------------------------| r_work (final): 0.3448 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.055072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.046938 restraints weight = 20223.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.047535 restraints weight = 16855.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.047978 restraints weight = 14799.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.048202 restraints weight = 13441.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.048472 restraints weight = 12626.662| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33556 Z= 0.123 Angle : 0.631 7.143 45324 Z= 0.323 Chirality : 0.044 0.215 5024 Planarity : 0.005 0.091 5796 Dihedral : 5.030 27.256 4394 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.77 (0.13), residues: 4022 helix: 0.38 (0.11), residues: 2054 sheet: -1.60 (0.25), residues: 408 loop : -1.30 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 935 TYR 0.019 0.001 TYR E1289 PHE 0.014 0.001 PHE A 642 TRP 0.024 0.001 TRP E1538 HIS 0.013 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (33556) covalent geometry : angle 0.63133 / 0.32 (45324) hydrogen bonds : bond 0.03865 / 2.59 ( 1663) hydrogen bonds : angle 5.39481 / 3.75 ( 4881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0386 time to fit residues: 0.2606 Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.074 Evaluate side-chains 93 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.9150 (p-90) cc_final: 0.8502 (p-90) REVERT: B 243 MET cc_start: 0.3537 (ppp) cc_final: 0.2702 (tmm) REVERT: B 802 MET cc_start: 0.7611 (ppp) cc_final: 0.7207 (ppp) REVERT: B 964 MET cc_start: 0.4571 (tpt) cc_final: 0.4211 (tpt) REVERT: B 1231 TYR cc_start: 0.9401 (m-80) cc_final: 0.9120 (m-10) REVERT: B 1426 MET cc_start: 0.4777 (mtt) cc_final: 0.3800 (mtm) REVERT: B 1482 MET cc_start: 0.3288 (ptt) cc_final: 0.1923 (tpt) REVERT: B 1522 MET cc_start: 0.6819 (mtm) cc_final: 0.6571 (mtp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0946 time to fit residues: 14.3230 Evaluate side-chains 74 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.509 Evaluate side-chains 5 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.1330 time to fit residues: 0.7842 Evaluate side-chains 4 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 318 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 327 optimal weight: 0.9990 chunk 70 optimal weight: 0.0030 chunk 179 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 218 optimal weight: 0.0020 chunk 185 optimal weight: 8.9990 chunk 247 optimal weight: 0.0040 chunk 149 optimal weight: 0.9980 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1517 ASN ** B1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.052540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.043975 restraints weight = 26898.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.044126 restraints weight = 24889.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.044396 restraints weight = 23477.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.044460 restraints weight = 22610.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.044460 restraints weight = 22075.143| |-----------------------------------------------------------------------------| r_work (final): 0.3613 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.060640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.041318 restraints weight = 192241.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.041135 restraints weight = 156636.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.041794 restraints weight = 120741.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.041794 restraints weight = 96636.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.041794 restraints weight = 96636.646| |-----------------------------------------------------------------------------| r_work (final): 0.3476 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.055228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.046968 restraints weight = 20546.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.047651 restraints weight = 16812.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.048097 restraints weight = 14498.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.048362 restraints weight = 13077.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.048646 restraints weight = 12221.589| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33556 Z= 0.121 Angle : 0.634 8.005 45324 Z= 0.324 Chirality : 0.044 0.179 5024 Planarity : 0.004 0.072 5796 Dihedral : 4.975 25.576 4394 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.72 (0.13), residues: 4022 helix: 0.43 (0.11), residues: 2052 sheet: -1.57 (0.24), residues: 438 loop : -1.27 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 66 TYR 0.018 0.001 TYR E1289 PHE 0.032 0.001 PHE B 766 TRP 0.018 0.001 TRP B1538 HIS 0.013 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (33556) covalent geometry : angle 0.63384 / 0.32 (45324) hydrogen bonds : bond 0.03796 / 2.56 ( 1663) hydrogen bonds : angle 5.32725 / 3.70 ( 4881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.067 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0833 time to fit residues: 0.5534 Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.047 Evaluate side-chains 89 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.9165 (p-90) cc_final: 0.8598 (p-90) REVERT: B 243 MET cc_start: 0.3371 (ppp) cc_final: 0.2569 (tmm) REVERT: B 1231 TYR cc_start: 0.9404 (m-80) cc_final: 0.9094 (m-10) REVERT: B 1426 MET cc_start: 0.4535 (mtt) cc_final: 0.3387 (mtm) REVERT: B 1482 MET cc_start: 0.2951 (ptt) cc_final: 0.1532 (tpt) REVERT: B 1522 MET cc_start: 0.7179 (mtm) cc_final: 0.6911 (mtp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0977 time to fit residues: 14.1240 Evaluate side-chains 74 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.519 Evaluate side-chains 6 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.055 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.1246 time to fit residues: 0.8721 Evaluate side-chains 5 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 372 optimal weight: 5.9990 chunk 103 optimal weight: 0.2980 chunk 158 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 120 optimal weight: 0.0670 chunk 113 optimal weight: 3.9990 chunk 285 optimal weight: 0.0060 chunk 11 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 148 optimal weight: 0.0070 overall best weight: 0.8754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1517 ASN ** B1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.055853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.042040 restraints weight = 25416.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.042040 restraints weight = 25175.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.042040 restraints weight = 25175.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.042040 restraints weight = 25175.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.042040 restraints weight = 25175.646| |-----------------------------------------------------------------------------| r_work (final): 0.3395 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.060357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.040665 restraints weight = 191689.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.040590 restraints weight = 148850.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.040712 restraints weight = 118543.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.041289 restraints weight = 106493.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.041291 restraints weight = 92049.046| |-----------------------------------------------------------------------------| r_work (final): 0.3467 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.055422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.047148 restraints weight = 20288.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.047798 restraints weight = 16797.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.048239 restraints weight = 14577.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.048499 restraints weight = 13213.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.048746 restraints weight = 12415.183| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33556 Z= 0.122 Angle : 0.636 7.352 45324 Z= 0.326 Chirality : 0.044 0.172 5024 Planarity : 0.004 0.067 5796 Dihedral : 4.945 25.156 4394 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.60 (0.13), residues: 4022 helix: 0.55 (0.12), residues: 2024 sheet: -1.48 (0.24), residues: 430 loop : -1.25 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 66 TYR 0.017 0.001 TYR B1289 PHE 0.019 0.001 PHE E 766 TRP 0.015 0.001 TRP E1538 HIS 0.013 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (33556) covalent geometry : angle 0.63558 / 0.33 (45324) hydrogen bonds : bond 0.03783 / 2.54 ( 1663) hydrogen bonds : angle 5.33392 / 3.70 ( 4881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.075 Fit side-chains REVERT: A 625 MET cc_start: 0.4635 (pmm) cc_final: 0.4398 (pmm) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0446 time to fit residues: 0.2970 Evaluate side-chains 4 residues out of total 183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.046 Evaluate side-chains 92 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.9157 (p-90) cc_final: 0.8572 (p-90) REVERT: B 243 MET cc_start: 0.3488 (ppp) cc_final: 0.2692 (tmm) REVERT: B 964 MET cc_start: 0.4614 (tpt) cc_final: 0.4401 (tpt) REVERT: B 1231 TYR cc_start: 0.9404 (m-80) cc_final: 0.9082 (m-10) REVERT: B 1426 MET cc_start: 0.4521 (mtt) cc_final: 0.3397 (mtm) REVERT: B 1482 MET cc_start: 0.2962 (ptt) cc_final: 0.1536 (tpt) REVERT: B 1522 MET cc_start: 0.7208 (mtm) cc_final: 0.6938 (mtp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0880 time to fit residues: 13.2068 Evaluate side-chains 76 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.539 Evaluate side-chains 5 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.055 Fit side-chains REVERT: C 1 MET cc_start: 0.6489 (tpt) cc_final: 0.6254 (tpt) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.1383 time to fit residues: 0.8046 Evaluate side-chains 5 residues out of total 153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 119 optimal weight: 5.9990 chunk 265 optimal weight: 8.9990 chunk 268 optimal weight: 0.3980 chunk 363 optimal weight: 0.2980 chunk 388 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 356 optimal weight: 0.0770 chunk 258 optimal weight: 0.0050 chunk 235 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 395 optimal weight: 7.9990 overall best weight: 0.2752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 HIS ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1517 ASN B1545 HIS ** B1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.056164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.041886 restraints weight = 25802.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.041988 restraints weight = 25164.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.041993 restraints weight = 24598.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.041993 restraints weight = 24483.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.041993 restraints weight = 24482.082| |-----------------------------------------------------------------------------| r_work (final): 0.3474 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.060968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.041250 restraints weight = 191052.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.041531 restraints weight = 148289.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.041535 restraints weight = 120121.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.041757 restraints weight = 101116.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.041757 restraints weight = 91741.161| |-----------------------------------------------------------------------------| r_work (final): 0.3510 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.055602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.047241 restraints weight = 20457.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.047927 restraints weight = 16647.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.048379 restraints weight = 14486.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.048691 restraints weight = 13105.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.048906 restraints weight = 12215.749| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33556 Z= 0.123 Angle : 0.637 7.143 45324 Z= 0.326 Chirality : 0.044 0.165 5024 Planarity : 0.004 0.060 5796 Dihedral : 4.936 24.437 4394 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.59 (0.13), residues: 4022 helix: 0.54 (0.12), residues: 2020 sheet: -1.49 (0.24), residues: 442 loop : -1.19 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 66 TYR 0.018 0.001 TYR B1289 PHE 0.026 0.001 PHE B 798 TRP 0.014 0.001 TRP E 102 HIS 0.011 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (33556) covalent geometry : angle 0.63690 / 0.33 (45324) hydrogen bonds : bond 0.03752 / 2.53 ( 1663) hydrogen bonds : angle 5.25713 / 3.64 ( 4881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4778.06 seconds wall clock time: 84 minutes 13.30 seconds (5053.30 seconds total)