Starting phenix.real_space_refine on Sun Jul 5 10:10:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uy5_26863/07_2026/7uy5_26863.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uy5_26863/07_2026/7uy5_26863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uy5_26863/07_2026/7uy5_26863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uy5_26863/07_2026/7uy5_26863.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uy5_26863/07_2026/7uy5_26863.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uy5_26863/07_2026/7uy5_26863.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uy5_26863/07_2026/7uy5_26863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uy5_26863/07_2026/7uy5_26863.cif" } resolution = 3.5 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1932 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 170 5.49 5 S 89 5.16 5 C 15927 2.51 5 N 4315 2.21 5 O 5269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s 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: 25772 Number of models: 1 Model: "" Number of chains: 13 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1367 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 7, 'GLN:plan1': 3, 'TYR:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 8542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8542 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 22, 'TRANS': 989} Chain breaks: 3 Chain: "D" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "E" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1195 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 952 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "G" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1747 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 2, 'TRANS': 205} Chain: "B" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3293 Classifications: {'RNA': 156} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 24, 'rna3p_pur': 62, 'rna3p_pyr': 57} Link IDs: {'rna2p': 36, 'rna3p': 119} Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "I" Number of atoms: 4424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4424 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 13, 'TRANS': 514} Chain breaks: 3 Chain: "K" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1315 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "J" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1081 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10290 SG CYS D 555 144.344 100.472 81.639 1.00 38.97 S ATOM 10303 SG CYS D 557 143.158 97.786 83.876 1.00 45.04 S ATOM 10423 SG CYS D 572 140.666 99.664 81.601 1.00 54.57 S ATOM 10444 SG CYS D 575 142.154 101.463 84.591 1.00 47.21 S ATOM 21879 SG CYS I 398 85.547 85.639 61.191 1.00 8.07 S ATOM 21901 SG CYS I 401 88.373 84.985 63.781 1.00 6.39 S ATOM 21991 SG CYS I 412 87.563 88.479 62.556 1.00 6.72 S ATOM 22013 SG CYS I 415 89.232 85.684 60.305 1.00 6.49 S Time building chain proxies: 5.32, per 1000 atoms: 0.21 Number of scatterers: 25772 At special positions: 0 Unit cell: (216.24, 187.68, 118.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 89 16.00 P 170 15.00 O 5269 8.00 N 4315 7.00 C 15927 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: 2.02 Conformation dependent library (CDL) restraints added in 964.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 900 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 555 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 572 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 557 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 575 " pdb=" ZN I 900 " pdb="ZN ZN I 900 " - pdb=" SG CYS I 401 " pdb="ZN ZN I 900 " - pdb=" SG CYS I 415 " pdb="ZN ZN I 900 " - pdb=" SG CYS I 398 " pdb="ZN ZN I 900 " - pdb=" SG CYS I 412 " Number of angles added : 12 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5222 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 26 sheets defined 44.1% alpha, 24.4% beta 23 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'H' and resid 115 through 130 Processing helix chain 'H' and resid 131 through 139 Processing helix chain 'H' and resid 139 through 148 removed outlier: 3.888A pdb=" N GLY H 143 " --> pdb=" O SER H 139 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE H 144 " --> pdb=" O TYR H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 160 Processing helix chain 'H' and resid 162 through 167 Processing helix chain 'H' and resid 203 through 216 removed outlier: 4.679A pdb=" N GLU H 216 " --> pdb=" O ASP H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 391 through 400 Processing helix chain 'H' and resid 401 through 403 No H-bonds generated for 'chain 'H' and resid 401 through 403' Processing helix chain 'H' and resid 468 through 480 removed outlier: 4.104A pdb=" N GLN H 472 " --> pdb=" O ASN H 468 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG H 473 " --> pdb=" O SER H 469 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN H 477 " --> pdb=" O ARG H 473 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS H 478 " --> pdb=" O LEU H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 530 Processing helix chain 'A' and resid 19 through 26 Processing helix chain 'A' and resid 36 through 43 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.972A pdb=" N TYR A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.811A pdb=" N SER A 179 " --> pdb=" O GLN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.565A pdb=" N GLN A 228 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 251 removed outlier: 3.705A pdb=" N SER A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 300 through 319 removed outlier: 3.686A pdb=" N ARG A 304 " --> pdb=" O CYS A 300 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 331 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.525A pdb=" N ILE A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 removed outlier: 3.907A pdb=" N LYS A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.815A pdb=" N TYR A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 475 removed outlier: 3.514A pdb=" N TYR A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ILE A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.992A pdb=" N GLU A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 528 removed outlier: 3.642A pdb=" N PHE A 525 " --> pdb=" O PRO A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 565 through 582 removed outlier: 3.987A pdb=" N ASP A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.887A pdb=" N ILE A 626 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.606A pdb=" N LYS A 717 " --> pdb=" O GLN A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 793 removed outlier: 3.518A pdb=" N LEU A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 804 removed outlier: 4.033A pdb=" N LYS A 798 " --> pdb=" O THR A 794 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN A 799 " --> pdb=" O GLN A 795 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLN A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 842 Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.663A pdb=" N GLN A 901 " --> pdb=" O GLN A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 925 Processing helix chain 'A' and resid 938 through 966 removed outlier: 3.930A pdb=" N MET A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) Proline residue: A 959 - end of helix Processing helix chain 'A' and resid 972 through 980 removed outlier: 4.370A pdb=" N GLN A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1009 Processing helix chain 'A' and resid 1014 through 1038 removed outlier: 3.563A pdb=" N LYS A1018 " --> pdb=" O ASN A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1044 Processing helix chain 'A' and resid 1045 through 1074 removed outlier: 4.167A pdb=" N LYS A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A1050 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A1070 " --> pdb=" O CYS A1066 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1102 through 1109 removed outlier: 4.426A pdb=" N LYS A1106 " --> pdb=" O THR A1102 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1109 " --> pdb=" O PRO A1105 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 526 Processing helix chain 'D' and resid 603 through 615 Processing helix chain 'D' and resid 622 through 634 removed outlier: 3.794A pdb=" N GLY D 634 " --> pdb=" O CYS D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 Processing helix chain 'D' and resid 680 through 697 Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 110 through 124 removed outlier: 4.207A pdb=" N TYR E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 175 removed outlier: 3.716A pdb=" N SER E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 22 removed outlier: 4.293A pdb=" N GLN F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 111 removed outlier: 3.998A pdb=" N TYR F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 119 removed outlier: 3.845A pdb=" N PHE F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.823A pdb=" N LYS G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 41 Processing helix chain 'G' and resid 87 through 94 removed outlier: 3.976A pdb=" N LEU G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 156 Processing helix chain 'G' and resid 158 through 161 Processing helix chain 'G' and resid 162 through 184 Processing helix chain 'G' and resid 186 through 197 removed outlier: 3.925A pdb=" N SER G 190 " --> pdb=" O ASP G 186 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU G 191 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU G 192 " --> pdb=" O TYR G 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 32 Processing helix chain 'I' and resid 101 through 107 removed outlier: 3.997A pdb=" N PHE I 107 " --> pdb=" O GLU I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.666A pdb=" N LEU I 176 " --> pdb=" O THR I 172 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER I 177 " --> pdb=" O LEU I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 197 removed outlier: 4.190A pdb=" N GLN I 194 " --> pdb=" O ASN I 190 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN I 197 " --> pdb=" O ILE I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 208 removed outlier: 3.627A pdb=" N PHE I 207 " --> pdb=" O ASN I 203 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS I 208 " --> pdb=" O THR I 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 203 through 208' Processing helix chain 'I' and resid 231 through 236 Processing helix chain 'I' and resid 275 through 286 Processing helix chain 'I' and resid 303 through 305 No H-bonds generated for 'chain 'I' and resid 303 through 305' Processing helix chain 'I' and resid 322 through 328 Processing helix chain 'I' and resid 342 through 351 Processing helix chain 'I' and resid 352 through 359 removed outlier: 4.048A pdb=" N SER I 356 " --> pdb=" O ASP I 352 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS I 359 " --> pdb=" O LYS I 355 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 369 Processing helix chain 'I' and resid 446 through 453 Processing helix chain 'I' and resid 456 through 470 Processing helix chain 'I' and resid 485 through 498 Processing helix chain 'I' and resid 601 through 622 Processing helix chain 'K' and resid 15 through 23 removed outlier: 4.151A pdb=" N ASP K 20 " --> pdb=" O ASP K 16 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N PHE K 21 " --> pdb=" O LYS K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 61 removed outlier: 4.175A pdb=" N ASN K 61 " --> pdb=" O ASP K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 87 removed outlier: 3.698A pdb=" N ALA K 68 " --> pdb=" O SER K 64 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU K 76 " --> pdb=" O ILE K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 164 removed outlier: 3.507A pdb=" N LEU K 155 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 70 removed outlier: 3.531A pdb=" N GLN J 70 " --> pdb=" O LYS J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 136 removed outlier: 3.832A pdb=" N GLU J 112 " --> pdb=" O SER J 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 152 through 153 removed outlier: 4.212A pdb=" N LYS H 230 " --> pdb=" O LYS H 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 407 through 408 removed outlier: 3.516A pdb=" N TYR H 407 " --> pdb=" O ARG H 465 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP H 497 " --> pdb=" O ILE H 384 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.598A pdb=" N TYR A 32 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 166 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASN A 733 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLN A 168 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.598A pdb=" N TYR A 32 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 166 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASN A 733 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLN A 168 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 112 through 115 Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 Processing sheet with id=AA8, first strand: chain 'A' and resid 808 through 813 Processing sheet with id=AA9, first strand: chain 'A' and resid 874 through 876 Processing sheet with id=AB1, first strand: chain 'D' and resid 532 through 537 removed outlier: 3.777A pdb=" N LYS D 533 " --> pdb=" O PHE D 657 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 657 " --> pdb=" O LYS D 533 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 537 " --> pdb=" O PHE D 653 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N ARG D 650 " --> pdb=" O LYS D 677 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS D 677 " --> pdb=" O ARG D 650 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE D 652 " --> pdb=" O ILE D 675 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE D 675 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU D 654 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 669 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 13.085A pdb=" N THR D 597 " --> pdb=" O ILE D 668 " (cutoff:3.500A) removed outlier: 10.161A pdb=" N TYR D 670 " --> pdb=" O THR D 597 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL D 672 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET D 601 " --> pdb=" O VAL D 672 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N LYS D 674 " --> pdb=" O MET D 601 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG D 588 " --> pdb=" O GLN D 545 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE D 590 " --> pdb=" O SER D 543 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER D 543 " --> pdb=" O PHE D 590 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN D 592 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU D 541 " --> pdb=" O GLN D 592 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA D 649 " --> pdb=" O LEU D 541 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 551 through 553 Processing sheet with id=AB3, first strand: chain 'D' and resid 562 through 563 removed outlier: 3.571A pdb=" N LEU D 563 " --> pdb=" O PHE D 571 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE D 571 " --> pdb=" O LEU D 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.961A pdb=" N VAL E 32 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N THR E 70 " --> pdb=" O VAL E 32 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.961A pdb=" N VAL E 32 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N THR E 70 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS E 135 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU E 144 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 99 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TYR E 146 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N GLN E 101 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 14.649A pdb=" N SER E 148 " --> pdb=" O GLN E 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 87 through 91 removed outlier: 3.777A pdb=" N THR F 89 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU F 72 " --> pdb=" O THR F 89 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL F 83 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL F 55 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 54 " --> pdb=" O ILE F 43 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL F 26 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL F 71 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 46 through 51 removed outlier: 7.528A pdb=" N LEU G 46 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N TYR G 116 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE G 48 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER G 103 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE G 58 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE G 62 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR G 75 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA G 64 " --> pdb=" O GLN G 73 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL G 79 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS G 80 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 46 through 51 removed outlier: 7.528A pdb=" N LEU G 46 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N TYR G 116 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE G 48 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SER G 103 " --> pdb=" O ASP G 134 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP G 134 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL G 105 " --> pdb=" O CYS G 132 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS G 132 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE G 107 " --> pdb=" O MET G 130 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET G 130 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN G 109 " --> pdb=" O ASP G 128 " (cutoff:3.500A) removed outlier: 21.422A pdb=" N LYS G 80 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 16.311A pdb=" N ILE G 123 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 10.662A pdb=" N ILE G 82 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU G 125 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS G 80 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AC1, first strand: chain 'I' and resid 52 through 57 removed outlier: 5.594A pdb=" N THR I 52 " --> pdb=" O ASN I 119 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU I 54 " --> pdb=" O MET I 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 60 through 68 removed outlier: 7.337A pdb=" N ASN I 61 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLN I 79 " --> pdb=" O ASN I 61 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR I 63 " --> pdb=" O ILE I 77 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE I 78 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N TYR I 153 " --> pdb=" O GLN I 90 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASN I 92 " --> pdb=" O TYR I 153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 188 through 189 Processing sheet with id=AC4, first strand: chain 'I' and resid 335 through 337 removed outlier: 9.436A pdb=" N GLN I 296 " --> pdb=" O PHE I 312 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE I 312 " --> pdb=" O GLN I 296 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU I 298 " --> pdb=" O ILE I 310 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N PHE I 264 " --> pdb=" O LEU I 307 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N MET I 309 " --> pdb=" O PHE I 264 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU I 266 " --> pdb=" O MET I 309 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N SER I 311 " --> pdb=" O GLU I 266 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR I 268 " --> pdb=" O SER I 311 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N PHE I 313 " --> pdb=" O TYR I 268 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL I 270 " --> pdb=" O PHE I 313 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR I 251 " --> pdb=" O LEU I 269 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR I 271 " --> pdb=" O ARG I 249 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE I 252 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL I 225 " --> pdb=" O ILE I 252 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYS I 254 " --> pdb=" O LEU I 223 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL I 221 " --> pdb=" O ALA I 256 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL I 214 " --> pdb=" O LEU I 298 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU I 298 " --> pdb=" O VAL I 214 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN I 216 " --> pdb=" O GLN I 296 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 473 through 476 removed outlier: 4.221A pdb=" N PHE I 392 " --> pdb=" O LEU I 476 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N CYS I 503 " --> pdb=" O VAL I 594 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL I 594 " --> pdb=" O CYS I 503 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL I 505 " --> pdb=" O MET I 592 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N CYS I 588 " --> pdb=" O PHE I 509 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N LEU I 589 " --> pdb=" O GLN I 439 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR I 441 " --> pdb=" O LEU I 589 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL I 591 " --> pdb=" O TYR I 441 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR I 443 " --> pdb=" O VAL I 591 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N TYR I 593 " --> pdb=" O TYR I 443 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN I 427 " --> pdb=" O TYR I 391 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR I 391 " --> pdb=" O GLN I 427 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU I 429 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL I 389 " --> pdb=" O LEU I 429 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLN I 431 " --> pdb=" O LYS I 387 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS I 387 " --> pdb=" O GLN I 431 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 569 through 571 Processing sheet with id=AC7, first strand: chain 'K' and resid 112 through 113 removed outlier: 3.554A pdb=" N ARG K 128 " --> pdb=" O GLN K 140 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN K 126 " --> pdb=" O HIS K 142 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL K 144 " --> pdb=" O PHE K 124 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE K 124 " --> pdb=" O VAL K 144 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP K 121 " --> pdb=" O PHE K 43 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU K 137 " --> pdb=" O GLN K 103 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE K 105 " --> pdb=" O LEU K 137 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU K 139 " --> pdb=" O ILE K 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 6 through 7 removed outlier: 7.090A pdb=" N ALA J 78 " --> pdb=" O ILE J 105 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE J 105 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR J 80 " --> pdb=" O PHE J 103 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE J 103 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE J 82 " --> pdb=" O GLU J 101 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N GLU J 58 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N CYS J 96 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL J 100 " --> pdb=" O PHE J 62 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE J 49 " --> pdb=" O PHE J 31 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE J 31 " --> pdb=" O ILE J 49 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE J 51 " --> pdb=" O LEU J 29 " (cutoff:3.500A) 1033 hydrogen bonds defined for protein. 2946 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 6.23 Time building geometry restraints manager: 2.76 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: 7409 1.34 - 1.46: 5476 1.46 - 1.58: 13252 1.58 - 1.70: 339 1.70 - 1.82: 132 Bond restraints: 26608 Sorted by residual: bond pdb=" C3' DT C 26 " pdb=" C2' DT C 26 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.79e+00 bond pdb=" C3' DT C 20 " pdb=" C2' DT C 20 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.69e+00 bond pdb=" C1' DT C 21 " pdb=" N1 DT C 21 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.89e+00 bond pdb=" C3' DG C 25 " pdb=" C2' DG C 25 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.84e+00 bond pdb=" C1' DT C 20 " pdb=" N1 DT C 20 " ideal model delta sigma weight residual 1.468 1.495 -0.027 1.40e-02 5.10e+03 3.76e+00 ... (remaining 26603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 36165 1.60 - 3.20: 387 3.20 - 4.80: 54 4.80 - 6.40: 29 6.40 - 8.00: 3 Bond angle restraints: 36638 Sorted by residual: angle pdb=" N GLU H 520 " pdb=" CA GLU H 520 " pdb=" CB GLU H 520 " ideal model delta sigma weight residual 110.40 117.11 -6.71 1.63e+00 3.76e-01 1.69e+01 angle pdb=" N3 DT C 27 " pdb=" C4 DT C 27 " pdb=" O4 DT C 27 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT C 26 " pdb=" C4 DT C 26 " pdb=" O4 DT C 26 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT C 21 " pdb=" C4 DT C 21 " pdb=" O4 DT C 21 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT C 20 " pdb=" C4 DT C 20 " pdb=" O4 DT C 20 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 ... (remaining 36633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 15343 36.00 - 72.00: 380 72.00 - 107.99: 45 107.99 - 143.99: 0 143.99 - 179.99: 8 Dihedral angle restraints: 15776 sinusoidal: 7744 harmonic: 8032 Sorted by residual: dihedral pdb=" O4' C B 43 " pdb=" C1' C B 43 " pdb=" N1 C B 43 " pdb=" C2 C B 43 " ideal model delta sinusoidal sigma weight residual 200.00 42.20 157.80 1 1.50e+01 4.44e-03 8.22e+01 dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual 200.00 53.51 146.49 1 1.50e+01 4.44e-03 7.82e+01 dihedral pdb=" O4' U B 138 " pdb=" C1' U B 138 " pdb=" N1 U B 138 " pdb=" C2 U B 138 " ideal model delta sinusoidal sigma weight residual -128.00 51.99 -179.99 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3017 0.033 - 0.066: 770 0.066 - 0.099: 256 0.099 - 0.132: 124 0.132 - 0.164: 8 Chirality restraints: 4175 Sorted by residual: chirality pdb=" CA ASN I 304 " pdb=" N ASN I 304 " pdb=" C ASN I 304 " pdb=" CB ASN I 304 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA VAL J 45 " pdb=" N VAL J 45 " pdb=" C VAL J 45 " pdb=" CB VAL J 45 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CB VAL I 430 " pdb=" CA VAL I 430 " pdb=" CG1 VAL I 430 " pdb=" CG2 VAL I 430 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 4172 not shown) Planarity restraints: 4061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE H 386 " 0.037 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO H 387 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO H 387 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 387 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET I 198 " 0.028 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO I 199 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 199 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 199 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 109 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO E 110 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 110 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 110 " -0.019 5.00e-02 4.00e+02 ... (remaining 4058 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1183 2.73 - 3.27: 24823 3.27 - 3.81: 41335 3.81 - 4.36: 49797 4.36 - 4.90: 83868 Nonbonded interactions: 201006 Sorted by model distance: nonbonded pdb=" OD1 ASP E 91 " pdb=" N SER E 92 " model vdw 2.182 3.120 nonbonded pdb=" OD1 ASN J 129 " pdb=" NE2 GLN J 133 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR A1061 " pdb=" O2' G B 61 " model vdw 2.211 3.040 nonbonded pdb=" NE2 GLN A 26 " pdb=" O LEU A 661 " model vdw 2.228 3.120 nonbonded pdb=" OH TYR A 650 " pdb=" OE2 GLU A 721 " model vdw 2.247 3.040 ... (remaining 201001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 29.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 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 : 0.002 0.058 26616 Z= 0.120 Angle : 0.465 7.997 36650 Z= 0.257 Chirality : 0.037 0.164 4175 Planarity : 0.003 0.057 4061 Dihedral : 16.217 179.991 10554 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.04 % Allowed : 0.16 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2654 helix: 2.08 (0.17), residues: 1018 sheet: -0.18 (0.24), residues: 485 loop : -0.81 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 102 TYR 0.012 0.001 TYR K 79 PHE 0.020 0.001 PHE A 965 TRP 0.013 0.001 TRP A 496 HIS 0.003 0.001 HIS K 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 (26608) covalent geometry : angle 0.46108 / 0.26 (36638) hydrogen bonds : bond 0.19412 / 13.22 ( 1070) hydrogen bonds : angle 7.30503 / 5.13 ( 3052) metal coordination : bond 0.00326 / 0.20 ( 8) metal coordination : angle 3.48818 / 2.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.975 Fit side-chains REVERT: I 447 ASP cc_start: 0.7627 (t0) cc_final: 0.7417 (t0) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.1564 time to fit residues: 71.2917 Evaluate side-chains 200 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 472 GLN ** H 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 466 HIS I 470 ASN K 102 HIS K 110 ASN J 132 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.158544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.123086 restraints weight = 44025.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.122765 restraints weight = 55158.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.123617 restraints weight = 56089.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.124273 restraints weight = 34664.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.125538 restraints weight = 29647.792| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26616 Z= 0.185 Angle : 0.589 8.554 36650 Z= 0.308 Chirality : 0.041 0.206 4175 Planarity : 0.004 0.050 4061 Dihedral : 13.179 179.084 4889 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.10 % Allowed : 7.81 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2654 helix: 1.90 (0.17), residues: 1040 sheet: -0.32 (0.23), residues: 509 loop : -0.98 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 921 TYR 0.019 0.002 TYR E 167 PHE 0.014 0.002 PHE I 107 TRP 0.014 0.002 TRP A 496 HIS 0.005 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (26608) covalent geometry : angle 0.58325 / 0.31 (36638) hydrogen bonds : bond 0.05334 / 3.69 ( 1070) hydrogen bonds : angle 5.37392 / 3.77 ( 3052) metal coordination : bond 0.00701 / 0.40 ( 8) metal coordination : angle 4.51660 / 3.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: H 513 TYR cc_start: 0.4463 (OUTLIER) cc_final: 0.4178 (t80) REVERT: E 105 MET cc_start: 0.5892 (ppp) cc_final: 0.4727 (ptp) REVERT: G 44 ASP cc_start: 0.7316 (t0) cc_final: 0.7107 (t0) REVERT: I 447 ASP cc_start: 0.7839 (t0) cc_final: 0.7532 (t0) REVERT: K 147 MET cc_start: 0.6450 (mtt) cc_final: 0.6089 (mtt) REVERT: K 160 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6986 (tm-30) REVERT: J 129 ASN cc_start: 0.8321 (t0) cc_final: 0.8104 (t0) outliers start: 27 outliers final: 19 residues processed: 246 average time/residue: 0.1581 time to fit residues: 64.3647 Evaluate side-chains 221 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 509 ASN Chi-restraints excluded: chain H residue 513 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 350 CYS Chi-restraints excluded: chain I residue 516 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 134 HIS Chi-restraints excluded: chain J residue 15 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 210 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 236 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 41 optimal weight: 0.0070 chunk 88 optimal weight: 0.3980 chunk 140 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 472 GLN ** H 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.160615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.126064 restraints weight = 43950.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125847 restraints weight = 57175.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.126759 restraints weight = 56324.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.127355 restraints weight = 36701.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.128391 restraints weight = 31272.703| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26616 Z= 0.105 Angle : 0.504 12.132 36650 Z= 0.265 Chirality : 0.039 0.160 4175 Planarity : 0.003 0.052 4061 Dihedral : 13.221 179.198 4889 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.14 % Allowed : 10.41 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.17), residues: 2654 helix: 2.04 (0.17), residues: 1040 sheet: -0.28 (0.24), residues: 501 loop : -0.91 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 102 TYR 0.030 0.001 TYR E 167 PHE 0.022 0.001 PHE H 521 TRP 0.013 0.001 TRP A 496 HIS 0.004 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (26608) covalent geometry : angle 0.49958 / 0.26 (36638) hydrogen bonds : bond 0.04358 / 3.02 ( 1070) hydrogen bonds : angle 4.92133 / 3.45 ( 3052) metal coordination : bond 0.00532 / 0.31 ( 8) metal coordination : angle 3.78593 / 2.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 513 TYR cc_start: 0.4420 (OUTLIER) cc_final: 0.4145 (t80) REVERT: G 44 ASP cc_start: 0.7247 (t0) cc_final: 0.6974 (t0) REVERT: I 17 LYS cc_start: 0.6534 (tppt) cc_final: 0.6323 (tptt) REVERT: I 447 ASP cc_start: 0.7806 (t0) cc_final: 0.7486 (t0) REVERT: K 147 MET cc_start: 0.6647 (mtt) cc_final: 0.6226 (mtt) REVERT: K 160 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6932 (tm-30) outliers start: 28 outliers final: 16 residues processed: 245 average time/residue: 0.1674 time to fit residues: 67.3059 Evaluate side-chains 228 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 513 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 350 CYS Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 589 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 134 HIS Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 133 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 239 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 259 optimal weight: 7.9990 chunk 4 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 193 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 243 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 472 GLN H 488 GLN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.160097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.125966 restraints weight = 43660.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.125066 restraints weight = 58350.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126072 restraints weight = 58683.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.126914 restraints weight = 37507.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128090 restraints weight = 31479.446| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26616 Z= 0.113 Angle : 0.503 8.788 36650 Z= 0.263 Chirality : 0.039 0.172 4175 Planarity : 0.003 0.053 4061 Dihedral : 13.244 179.112 4889 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.87 % Allowed : 10.86 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.54 (0.17), residues: 2654 helix: 2.03 (0.17), residues: 1041 sheet: -0.29 (0.24), residues: 494 loop : -0.95 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 102 TYR 0.021 0.001 TYR E 167 PHE 0.019 0.001 PHE H 521 TRP 0.013 0.001 TRP A 496 HIS 0.004 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (26608) covalent geometry : angle 0.49872 / 0.26 (36638) hydrogen bonds : bond 0.04098 / 2.85 ( 1070) hydrogen bonds : angle 4.74326 / 3.32 ( 3052) metal coordination : bond 0.00535 / 0.32 ( 8) metal coordination : angle 3.79321 / 2.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: E 34 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7112 (pp) REVERT: G 44 ASP cc_start: 0.7391 (t0) cc_final: 0.7060 (t0) REVERT: I 17 LYS cc_start: 0.6514 (tppt) cc_final: 0.6298 (tptt) REVERT: I 447 ASP cc_start: 0.7831 (t0) cc_final: 0.7504 (t0) REVERT: K 147 MET cc_start: 0.6666 (mtt) cc_final: 0.6243 (mtt) REVERT: K 160 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6771 (tm-30) outliers start: 46 outliers final: 28 residues processed: 254 average time/residue: 0.1629 time to fit residues: 68.0793 Evaluate side-chains 235 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 350 CYS Chi-restraints excluded: chain I residue 406 THR Chi-restraints excluded: chain I residue 516 ILE Chi-restraints excluded: chain I residue 589 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 127 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 38 optimal weight: 4.9990 chunk 255 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 263 optimal weight: 20.0000 chunk 173 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 143 optimal weight: 0.0020 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 472 GLN A 702 GLN E 29 GLN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.160446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.124960 restraints weight = 43736.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.124838 restraints weight = 51557.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.125529 restraints weight = 56512.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.125801 restraints weight = 37536.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128742 restraints weight = 30990.127| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26616 Z= 0.104 Angle : 0.490 8.341 36650 Z= 0.257 Chirality : 0.039 0.168 4175 Planarity : 0.003 0.055 4061 Dihedral : 13.265 179.141 4889 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.75 % Allowed : 12.08 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2654 helix: 2.11 (0.17), residues: 1034 sheet: -0.35 (0.23), residues: 504 loop : -0.96 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 102 TYR 0.014 0.001 TYR E 167 PHE 0.013 0.001 PHE J 9 TRP 0.013 0.001 TRP A 496 HIS 0.004 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (26608) covalent geometry : angle 0.48612 / 0.26 (36638) hydrogen bonds : bond 0.03948 / 2.75 ( 1070) hydrogen bonds : angle 4.61423 / 3.23 ( 3052) metal coordination : bond 0.00473 / 0.28 ( 8) metal coordination : angle 3.58876 / 2.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7126 (pp) REVERT: G 44 ASP cc_start: 0.7347 (t0) cc_final: 0.7007 (t0) REVERT: I 17 LYS cc_start: 0.6629 (tppt) cc_final: 0.6350 (tptt) REVERT: I 447 ASP cc_start: 0.7788 (t0) cc_final: 0.7469 (t0) REVERT: K 147 MET cc_start: 0.6638 (mtt) cc_final: 0.6211 (mtt) REVERT: K 160 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6767 (tm-30) outliers start: 43 outliers final: 28 residues processed: 250 average time/residue: 0.1587 time to fit residues: 65.4570 Evaluate side-chains 231 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 231 ILE Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 406 THR Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 589 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 127 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 205 optimal weight: 4.9990 chunk 133 optimal weight: 0.0040 chunk 123 optimal weight: 0.8980 chunk 159 optimal weight: 0.0570 chunk 257 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 overall best weight: 0.5712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 472 GLN A 702 GLN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.160590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125130 restraints weight = 43947.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.124907 restraints weight = 51614.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.125567 restraints weight = 57421.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.125912 restraints weight = 37646.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129794 restraints weight = 31184.164| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26616 Z= 0.099 Angle : 0.481 7.783 36650 Z= 0.252 Chirality : 0.039 0.167 4175 Planarity : 0.003 0.056 4061 Dihedral : 13.285 179.382 4889 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.87 % Allowed : 12.45 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.17), residues: 2654 helix: 2.15 (0.17), residues: 1034 sheet: -0.39 (0.24), residues: 498 loop : -0.93 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 102 TYR 0.021 0.001 TYR I 19 PHE 0.019 0.001 PHE H 521 TRP 0.013 0.001 TRP A 496 HIS 0.004 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (26608) covalent geometry : angle 0.47646 / 0.25 (36638) hydrogen bonds : bond 0.03773 / 2.64 ( 1070) hydrogen bonds : angle 4.46083 / 3.13 ( 3052) metal coordination : bond 0.00429 / 0.25 ( 8) metal coordination : angle 3.48634 / 2.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: H 467 GLN cc_start: 0.3980 (pt0) cc_final: 0.3670 (pt0) REVERT: H 471 GLU cc_start: 0.2159 (tt0) cc_final: 0.1600 (tt0) REVERT: H 472 GLN cc_start: 0.2728 (OUTLIER) cc_final: 0.2521 (mm-40) REVERT: A 395 LYS cc_start: 0.7510 (mmtt) cc_final: 0.7270 (tppt) REVERT: A 816 ASP cc_start: 0.6696 (m-30) cc_final: 0.6482 (m-30) REVERT: E 34 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7117 (pp) REVERT: E 85 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6738 (mt) REVERT: F 56 ILE cc_start: 0.5379 (mp) cc_final: 0.5161 (mm) REVERT: I 17 LYS cc_start: 0.6620 (tppt) cc_final: 0.6384 (tptt) REVERT: I 23 PHE cc_start: 0.8194 (m-80) cc_final: 0.7919 (m-80) REVERT: I 24 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.6031 (p0) REVERT: I 447 ASP cc_start: 0.7771 (t0) cc_final: 0.7458 (t0) REVERT: K 147 MET cc_start: 0.6687 (mtt) cc_final: 0.6259 (mtt) REVERT: K 160 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6861 (tm-30) outliers start: 46 outliers final: 31 residues processed: 255 average time/residue: 0.1575 time to fit residues: 66.3565 Evaluate side-chains 235 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 472 GLN Chi-restraints excluded: chain H residue 513 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain I residue 24 ASP Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 231 ILE Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 406 THR Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 516 ILE Chi-restraints excluded: chain I residue 589 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 127 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 214 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 233 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 209 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 702 GLN E 121 GLN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.159212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.123699 restraints weight = 43627.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123726 restraints weight = 53470.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.124343 restraints weight = 56551.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.124974 restraints weight = 35159.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126548 restraints weight = 29563.769| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26616 Z= 0.140 Angle : 0.509 7.623 36650 Z= 0.266 Chirality : 0.040 0.196 4175 Planarity : 0.003 0.080 4061 Dihedral : 13.329 179.014 4889 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.87 % Allowed : 12.65 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2654 helix: 2.08 (0.17), residues: 1028 sheet: -0.47 (0.23), residues: 508 loop : -1.01 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 102 TYR 0.012 0.001 TYR A 293 PHE 0.014 0.001 PHE A1059 TRP 0.012 0.001 TRP A 496 HIS 0.005 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (26608) covalent geometry : angle 0.50482 / 0.27 (36638) hydrogen bonds : bond 0.04067 / 2.85 ( 1070) hydrogen bonds : angle 4.49571 / 3.16 ( 3052) metal coordination : bond 0.00539 / 0.34 ( 8) metal coordination : angle 3.56969 / 2.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 467 GLN cc_start: 0.3954 (OUTLIER) cc_final: 0.3675 (pt0) REVERT: H 471 GLU cc_start: 0.2270 (tt0) cc_final: 0.1891 (tt0) REVERT: E 34 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7158 (pp) REVERT: E 85 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6824 (mt) REVERT: F 56 ILE cc_start: 0.5677 (mp) cc_final: 0.5433 (mm) REVERT: I 17 LYS cc_start: 0.6475 (tppt) cc_final: 0.6232 (tptt) REVERT: I 23 PHE cc_start: 0.8131 (m-80) cc_final: 0.7899 (m-80) REVERT: I 24 ASP cc_start: 0.6388 (OUTLIER) cc_final: 0.6079 (p0) REVERT: I 102 ARG cc_start: 0.3844 (mpt180) cc_final: 0.3375 (mpt180) REVERT: I 447 ASP cc_start: 0.7807 (t0) cc_final: 0.7511 (t0) REVERT: K 147 MET cc_start: 0.6701 (mtt) cc_final: 0.6265 (mtt) REVERT: K 160 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6885 (tm-30) outliers start: 46 outliers final: 34 residues processed: 247 average time/residue: 0.1548 time to fit residues: 63.0973 Evaluate side-chains 244 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 467 GLN Chi-restraints excluded: chain H residue 513 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain I residue 24 ASP Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 231 ILE Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 406 THR Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 516 ILE Chi-restraints excluded: chain I residue 589 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 127 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 175 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 702 GLN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.158422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.123274 restraints weight = 43684.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123390 restraints weight = 56086.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124065 restraints weight = 55453.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.124624 restraints weight = 34615.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126517 restraints weight = 29524.568| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26616 Z= 0.152 Angle : 0.533 7.837 36650 Z= 0.279 Chirality : 0.040 0.175 4175 Planarity : 0.003 0.053 4061 Dihedral : 13.428 178.777 4889 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.79 % Allowed : 13.38 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2654 helix: 1.98 (0.17), residues: 1033 sheet: -0.56 (0.23), residues: 506 loop : -1.06 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 102 TYR 0.021 0.001 TYR I 19 PHE 0.036 0.001 PHE H 521 TRP 0.012 0.001 TRP A 496 HIS 0.005 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (26608) covalent geometry : angle 0.52864 / 0.28 (36638) hydrogen bonds : bond 0.04260 / 2.98 ( 1070) hydrogen bonds : angle 4.51545 / 3.18 ( 3052) metal coordination : bond 0.00599 / 0.38 ( 8) metal coordination : angle 3.71666 / 2.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 471 GLU cc_start: 0.2449 (tt0) cc_final: 0.1838 (tt0) REVERT: A 961 MET cc_start: 0.8190 (mtt) cc_final: 0.7853 (mtm) REVERT: E 34 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7276 (pp) REVERT: I 17 LYS cc_start: 0.6687 (tppt) cc_final: 0.6406 (tptt) REVERT: I 24 ASP cc_start: 0.6367 (OUTLIER) cc_final: 0.6082 (p0) REVERT: I 102 ARG cc_start: 0.3424 (mpt180) cc_final: 0.3002 (mpt180) REVERT: I 447 ASP cc_start: 0.7716 (t0) cc_final: 0.7355 (t0) REVERT: K 147 MET cc_start: 0.6516 (mtt) cc_final: 0.6070 (mtt) REVERT: K 160 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6874 (tm-30) outliers start: 44 outliers final: 33 residues processed: 246 average time/residue: 0.1645 time to fit residues: 66.8297 Evaluate side-chains 241 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 513 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain I residue 24 ASP Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 231 ILE Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 350 CYS Chi-restraints excluded: chain I residue 406 THR Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 516 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 127 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 245 optimal weight: 0.0010 chunk 61 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 191 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 128 optimal weight: 0.4980 chunk 257 optimal weight: 4.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN A 702 GLN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.160183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.125714 restraints weight = 43756.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.125249 restraints weight = 57702.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.126128 restraints weight = 58190.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.126892 restraints weight = 37371.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.128096 restraints weight = 31491.429| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 26616 Z= 0.101 Angle : 0.512 9.830 36650 Z= 0.265 Chirality : 0.039 0.202 4175 Planarity : 0.003 0.052 4061 Dihedral : 13.428 179.011 4889 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.55 % Allowed : 14.04 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.17), residues: 2654 helix: 2.13 (0.17), residues: 1027 sheet: -0.52 (0.23), residues: 496 loop : -0.96 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 60 TYR 0.020 0.001 TYR J 116 PHE 0.019 0.001 PHE H 524 TRP 0.015 0.001 TRP A 496 HIS 0.005 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (26608) covalent geometry : angle 0.50779 / 0.26 (36638) hydrogen bonds : bond 0.03799 / 2.66 ( 1070) hydrogen bonds : angle 4.38868 / 3.09 ( 3052) metal coordination : bond 0.00437 / 0.28 ( 8) metal coordination : angle 3.49897 / 2.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 467 GLN cc_start: 0.3901 (pt0) cc_final: 0.3649 (pt0) REVERT: H 471 GLU cc_start: 0.2373 (tt0) cc_final: 0.1805 (tt0) REVERT: E 34 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7160 (pp) REVERT: I 17 LYS cc_start: 0.6580 (tppt) cc_final: 0.6293 (tptt) REVERT: I 102 ARG cc_start: 0.3819 (mpt180) cc_final: 0.3320 (mpt180) REVERT: I 447 ASP cc_start: 0.7678 (t0) cc_final: 0.7303 (t0) REVERT: K 102 HIS cc_start: 0.4776 (OUTLIER) cc_final: 0.4431 (m90) REVERT: K 147 MET cc_start: 0.6464 (mtt) cc_final: 0.6011 (mtt) REVERT: K 160 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6943 (tm-30) outliers start: 38 outliers final: 28 residues processed: 254 average time/residue: 0.1620 time to fit residues: 68.0311 Evaluate side-chains 245 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 513 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 231 ILE Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 516 ILE Chi-restraints excluded: chain I residue 589 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 102 HIS Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 127 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 159 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 270 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 260 optimal weight: 0.0770 chunk 226 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 472 GLN A 702 GLN A 841 ASN F 93 GLN I 119 ASN ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.156868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.122055 restraints weight = 43873.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.121428 restraints weight = 59682.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.122649 restraints weight = 55142.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.122955 restraints weight = 35316.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.126075 restraints weight = 30082.338| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26616 Z= 0.210 Angle : 0.602 8.772 36650 Z= 0.313 Chirality : 0.043 0.226 4175 Planarity : 0.004 0.062 4061 Dihedral : 13.571 178.849 4889 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.51 % Allowed : 14.52 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2654 helix: 1.81 (0.17), residues: 1031 sheet: -0.63 (0.23), residues: 514 loop : -1.15 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 60 TYR 0.018 0.002 TYR A 474 PHE 0.028 0.002 PHE H 521 TRP 0.013 0.002 TRP H 511 HIS 0.005 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (26608) covalent geometry : angle 0.59713 / 0.31 (36638) hydrogen bonds : bond 0.04800 / 3.38 ( 1070) hydrogen bonds : angle 4.63642 / 3.27 ( 3052) metal coordination : bond 0.00684 / 0.41 ( 8) metal coordination : angle 4.23246 / 3.09 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: H 471 GLU cc_start: 0.2766 (tt0) cc_final: 0.2160 (tt0) REVERT: E 34 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7345 (pp) REVERT: F 56 ILE cc_start: 0.5860 (mm) cc_final: 0.5559 (mm) REVERT: I 17 LYS cc_start: 0.6474 (tppt) cc_final: 0.6168 (tptt) REVERT: I 102 ARG cc_start: 0.3535 (mpt180) cc_final: 0.3272 (mpt180) REVERT: I 447 ASP cc_start: 0.7670 (t0) cc_final: 0.7244 (t0) REVERT: K 147 MET cc_start: 0.6575 (mtt) cc_final: 0.6197 (mtt) REVERT: K 160 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6953 (tm-30) outliers start: 37 outliers final: 29 residues processed: 235 average time/residue: 0.1405 time to fit residues: 55.0314 Evaluate side-chains 227 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 513 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain D residue 601 MET Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 231 ILE Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 350 CYS Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 516 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 127 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 222 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 270 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 171 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 230 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 472 GLN ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.158665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.123971 restraints weight = 43449.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.123315 restraints weight = 59383.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.124789 restraints weight = 53578.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.125208 restraints weight = 34520.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.127117 restraints weight = 29589.062| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26616 Z= 0.127 Angle : 0.537 8.309 36650 Z= 0.281 Chirality : 0.040 0.222 4175 Planarity : 0.003 0.053 4061 Dihedral : 13.572 179.482 4889 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.38 % Allowed : 14.77 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2654 helix: 1.96 (0.17), residues: 1026 sheet: -0.70 (0.23), residues: 507 loop : -1.06 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 812 TYR 0.019 0.001 TYR I 19 PHE 0.019 0.001 PHE H 524 TRP 0.015 0.001 TRP A 496 HIS 0.005 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (26608) covalent geometry : angle 0.53295 / 0.28 (36638) hydrogen bonds : bond 0.04166 / 2.92 ( 1070) hydrogen bonds : angle 4.48853 / 3.16 ( 3052) metal coordination : bond 0.00510 / 0.31 ( 8) metal coordination : angle 3.72532 / 2.75 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3774.22 seconds wall clock time: 66 minutes 31.77 seconds (3991.77 seconds total)