Starting phenix.real_space_refine on Mon Sep 14 01:39:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uy5_26863/09_2026/7uy5_26863.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uy5_26863/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7uy5_26863/09_2026/7uy5_26863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uy5_26863/09_2026/7uy5_26863.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uy5_26863/09_2026/7uy5_26863.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uy5_26863/09_2026/7uy5_26863.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uy5_26863/09_2026/7uy5_26863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uy5_26863/09_2026/7uy5_26863.map" } 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-2.2.1-6174/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: {'RNAv2': 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: 5.16, per 1000 atoms: 0.20 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: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 2.94 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: 6.06 Time building geometry restraints manager: 2.56 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: 35625 1.60 - 3.20: 798 3.20 - 4.80: 164 4.80 - 6.40: 48 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 - 34.63: 15069 34.63 - 69.26: 621 69.26 - 103.89: 85 103.89 - 138.52: 0 138.52 - 173.15: 1 Dihedral angle restraints: 15776 sinusoidal: 7744 harmonic: 8032 Sorted by residual: dihedral pdb=" C4' U B 137 " pdb=" C3' U B 137 " pdb=" C2' U B 137 " pdb=" C1' U B 137 " ideal model delta sinusoidal sigma weight residual 36.35 -36.87 73.21 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' C B 75 " pdb=" C3' C B 75 " pdb=" C2' C B 75 " pdb=" C1' C B 75 " ideal model delta sinusoidal sigma weight residual 36.34 -36.34 72.69 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' U B 13 " pdb=" C3' U B 13 " pdb=" C2' U B 13 " pdb=" C1' U B 13 " ideal model delta sinusoidal sigma weight residual 36.34 -36.32 72.67 1 3.10e+00 1.04e-01 7.01e+02 ... (remaining 15773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3450 0.059 - 0.117: 467 0.117 - 0.176: 28 0.176 - 0.234: 100 0.234 - 0.293: 130 Chirality restraints: 4175 Sorted by residual: chirality pdb=" P C B 75 " pdb=" OP1 C B 75 " pdb=" OP2 C B 75 " pdb=" O5' C B 75 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C3' C B 75 " pdb=" C4' C B 75 " pdb=" O3' C B 75 " pdb=" C2' C B 75 " both_signs ideal model delta sigma weight residual False -2.50 -2.79 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C2' U B 13 " pdb=" C3' U B 13 " pdb=" O2' U B 13 " pdb=" C1' U B 13 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.270 Find NCS groups from input model: 0.140 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- 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= 0.130 Angle : 0.604 7.997 36650 Z= 0.294 Chirality : 0.068 0.293 4175 Planarity : 0.003 0.057 4061 Dihedral : 17.711 173.149 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 0.00241 / 0.13 (26608) covalent geometry : angle 0.60039 / 0.29 (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 : 0.913 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: 0.1596 time to fit residues: 72.9112 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 : 0.961 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.158690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.123387 restraints weight = 44182.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123350 restraints weight = 59055.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.124151 restraints weight = 57784.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.124792 restraints weight = 35527.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.126077 restraints weight = 30214.533| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26616 Z= 0.218 Angle : 1.079 24.679 36650 Z= 0.453 Chirality : 0.104 1.454 4175 Planarity : 0.004 0.047 4061 Dihedral : 14.367 162.334 4889 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.06 % Allowed : 7.81 % Favored : 91.13 % 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: -0.31 (0.23), residues: 509 loop : -0.99 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 812 TYR 0.017 0.002 TYR E 167 PHE 0.015 0.002 PHE A 866 TRP 0.014 0.002 TRP A 496 HIS 0.006 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (26608) covalent geometry : angle 1.07640 / 0.45 (36638) hydrogen bonds : bond 0.05496 / 3.86 ( 1070) hydrogen bonds : angle 5.38675 / 3.78 ( 3052) metal coordination : bond 0.00723 / 0.43 ( 8) metal coordination : angle 4.52599 / 3.28 ( 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: 26 poor density : 231 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: H 513 TYR cc_start: 0.4463 (OUTLIER) cc_final: 0.4153 (t80) REVERT: E 105 MET cc_start: 0.5880 (ppp) cc_final: 0.4731 (ptp) REVERT: G 44 ASP cc_start: 0.7293 (t0) cc_final: 0.7091 (t0) REVERT: G 178 LEU cc_start: 0.8249 (tt) cc_final: 0.7903 (mt) REVERT: I 447 ASP cc_start: 0.7832 (t0) cc_final: 0.7524 (t0) REVERT: K 147 MET cc_start: 0.6460 (mtt) cc_final: 0.6102 (mtt) REVERT: K 160 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6970 (tm-30) outliers start: 26 outliers final: 19 residues processed: 247 average time/residue: 0.1597 time to fit residues: 65.3473 Evaluate side-chains 222 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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: 2.9990 chunk 265 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 140 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 472 GLN ** H 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 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 = 0.4191 r_free = 0.4191 target = 0.158488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.122964 restraints weight = 44152.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.122350 restraints weight = 57196.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.123385 restraints weight = 57448.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124084 restraints weight = 34738.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.125398 restraints weight = 30059.827| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26616 Z= 0.174 Angle : 0.825 20.973 36650 Z= 0.361 Chirality : 0.073 1.160 4175 Planarity : 0.004 0.053 4061 Dihedral : 15.113 163.494 4889 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.91 % Allowed : 10.62 % Favored : 87.47 % 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: 0.37 (0.17), residues: 2654 helix: 1.87 (0.17), residues: 1037 sheet: -0.34 (0.23), residues: 510 loop : -1.03 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 102 TYR 0.026 0.002 TYR E 167 PHE 0.024 0.001 PHE H 521 TRP 0.015 0.002 TRP A 496 HIS 0.005 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (26608) covalent geometry : angle 0.82109 / 0.36 (36638) hydrogen bonds : bond 0.05111 / 3.53 ( 1070) hydrogen bonds : angle 5.02510 / 3.54 ( 3052) metal coordination : bond 0.00688 / 0.41 ( 8) metal coordination : angle 4.24864 / 3.10 ( 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 276 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 229 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 380 LEU cc_start: 0.5482 (OUTLIER) cc_final: 0.5082 (pp) REVERT: G 44 ASP cc_start: 0.7362 (t0) cc_final: 0.7050 (t0) REVERT: G 177 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7662 (mm-40) REVERT: I 17 LYS cc_start: 0.6262 (tppt) cc_final: 0.6049 (tptt) REVERT: I 24 ASP cc_start: 0.6056 (p0) cc_final: 0.5799 (p0) REVERT: I 102 ARG cc_start: 0.4854 (mpt180) cc_final: 0.4581 (mpt180) REVERT: I 447 ASP cc_start: 0.7840 (t0) cc_final: 0.7540 (t0) REVERT: K 147 MET cc_start: 0.6502 (mtt) cc_final: 0.6107 (mtt) REVERT: K 160 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6976 (tm-30) outliers start: 47 outliers final: 27 residues processed: 259 average time/residue: 0.1632 time to fit residues: 70.0604 Evaluate side-chains 238 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 506 GLU Chi-restraints excluded: chain H residue 509 ASN 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 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 1085 LEU Chi-restraints excluded: chain D residue 696 ASN 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 G residue 34 GLN Chi-restraints excluded: chain G residue 42 VAL 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 406 THR Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 127 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 239 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 259 optimal weight: 9.9990 chunk 4 optimal weight: 0.4980 chunk 55 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 193 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 472 GLN H 488 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.160494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125001 restraints weight = 43812.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.124711 restraints weight = 51946.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.125491 restraints weight = 59376.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.126030 restraints weight = 35669.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127674 restraints weight = 30203.275| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 26616 Z= 0.118 Angle : 0.723 19.240 36650 Z= 0.321 Chirality : 0.064 1.082 4175 Planarity : 0.003 0.051 4061 Dihedral : 15.070 176.563 4889 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.83 % Allowed : 11.92 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.17), residues: 2654 helix: 2.08 (0.17), residues: 1030 sheet: -0.33 (0.24), residues: 492 loop : -0.96 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 60 TYR 0.025 0.001 TYR E 167 PHE 0.014 0.001 PHE A 866 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 / 0.12 (26608) covalent geometry : angle 0.71987 / 0.32 (36638) hydrogen bonds : bond 0.04098 / 2.85 ( 1070) hydrogen bonds : angle 4.67127 / 3.27 ( 3052) metal coordination : bond 0.00511 / 0.30 ( 8) metal coordination : angle 3.73361 / 2.81 ( 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 279 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 380 LEU cc_start: 0.5516 (OUTLIER) cc_final: 0.4977 (pp) REVERT: H 497 ASP cc_start: 0.2973 (m-30) cc_final: 0.2769 (m-30) REVERT: E 34 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7173 (pp) REVERT: I 17 LYS cc_start: 0.6549 (tppt) cc_final: 0.6270 (tptt) REVERT: I 23 PHE cc_start: 0.8181 (m-80) cc_final: 0.7917 (m-80) REVERT: I 447 ASP cc_start: 0.7822 (t0) cc_final: 0.7501 (t0) REVERT: I 614 LEU cc_start: 0.7531 (tt) cc_final: 0.6933 (mt) REVERT: K 147 MET cc_start: 0.6668 (mtt) cc_final: 0.6249 (mtt) REVERT: K 160 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6803 (tm-30) REVERT: J 38 GLU cc_start: 0.5128 (tm-30) cc_final: 0.4511 (tm-30) outliers start: 45 outliers final: 22 residues processed: 267 average time/residue: 0.1650 time to fit residues: 72.5317 Evaluate side-chains 236 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU 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 899 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 144 LEU 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 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 98 ILE 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: 0.1980 chunk 255 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 152 optimal weight: 0.1980 chunk 113 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 143 optimal weight: 0.0030 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 472 GLN A 554 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.158935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.124044 restraints weight = 43954.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.123648 restraints weight = 60482.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.125082 restraints weight = 53512.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.125388 restraints weight = 34610.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.128141 restraints weight = 29713.403| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26616 Z= 0.151 Angle : 0.716 17.443 36650 Z= 0.323 Chirality : 0.061 0.902 4175 Planarity : 0.003 0.054 4061 Dihedral : 15.090 176.567 4889 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.99 % Allowed : 13.18 % 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: 0.39 (0.17), residues: 2654 helix: 1.99 (0.17), residues: 1035 sheet: -0.49 (0.23), residues: 504 loop : -1.04 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 102 TYR 0.022 0.001 TYR A 325 PHE 0.017 0.001 PHE H 521 TRP 0.013 0.002 TRP A 496 HIS 0.004 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (26608) covalent geometry : angle 0.71260 / 0.32 (36638) hydrogen bonds : bond 0.04433 / 3.07 ( 1070) hydrogen bonds : angle 4.63320 / 3.26 ( 3052) metal coordination : bond 0.00578 / 0.36 ( 8) metal coordination : angle 3.91225 / 2.94 ( 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 268 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: H 380 LEU cc_start: 0.5663 (OUTLIER) cc_final: 0.4960 (pp) REVERT: A 846 ASN cc_start: 0.7636 (t0) cc_final: 0.7431 (t0) REVERT: E 34 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7275 (pp) REVERT: E 85 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6707 (mt) REVERT: G 178 LEU cc_start: 0.8707 (tp) cc_final: 0.8086 (mt) REVERT: I 17 LYS cc_start: 0.6365 (tppt) cc_final: 0.6113 (tptt) REVERT: I 447 ASP cc_start: 0.7845 (t0) cc_final: 0.7542 (t0) REVERT: K 147 MET cc_start: 0.6653 (mtt) cc_final: 0.6205 (mtt) REVERT: K 160 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6802 (tm-30) outliers start: 49 outliers final: 34 residues processed: 257 average time/residue: 0.1631 time to fit residues: 69.2588 Evaluate side-chains 251 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU 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 899 ILE Chi-restraints excluded: chain A residue 907 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 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 144 LEU Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 116 ILE 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 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 138 ILE Chi-restraints excluded: chain J residue 15 SER 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: 3.9990 chunk 133 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN E 121 GLN F 80 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.158175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122756 restraints weight = 44018.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.122506 restraints weight = 59842.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.123957 restraints weight = 52763.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124078 restraints weight = 35494.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.126477 restraints weight = 30331.460| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26616 Z= 0.161 Angle : 0.707 15.575 36650 Z= 0.322 Chirality : 0.059 0.752 4175 Planarity : 0.004 0.063 4061 Dihedral : 15.059 178.439 4889 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.28 % Allowed : 13.63 % Favored : 84.09 % 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: 0.29 (0.17), residues: 2654 helix: 1.91 (0.17), residues: 1035 sheet: -0.54 (0.23), residues: 501 loop : -1.10 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 102 TYR 0.021 0.002 TYR I 19 PHE 0.017 0.001 PHE A1059 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 0.00374 / 0.16 (26608) covalent geometry : angle 0.70331 / 0.32 (36638) hydrogen bonds : bond 0.04526 / 3.15 ( 1070) hydrogen bonds : angle 4.60650 / 3.24 ( 3052) metal coordination : bond 0.00609 / 0.38 ( 8) metal coordination : angle 3.80825 / 2.86 ( 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 280 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 224 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 380 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.4988 (pp) REVERT: H 471 GLU cc_start: 0.2390 (tt0) cc_final: 0.1711 (tt0) REVERT: A 846 ASN cc_start: 0.7685 (t0) cc_final: 0.7479 (t0) REVERT: A 961 MET cc_start: 0.8163 (mtt) cc_final: 0.7844 (mtm) REVERT: E 34 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7313 (pp) REVERT: I 17 LYS cc_start: 0.6526 (tppt) cc_final: 0.6251 (tptt) REVERT: I 23 PHE cc_start: 0.8107 (m-80) cc_final: 0.7868 (m-80) REVERT: I 447 ASP cc_start: 0.7740 (t0) cc_final: 0.7364 (t0) REVERT: K 147 MET cc_start: 0.6597 (mtt) cc_final: 0.6189 (mtt) REVERT: K 160 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6771 (tm-30) outliers start: 56 outliers final: 40 residues processed: 268 average time/residue: 0.1588 time to fit residues: 71.2936 Evaluate side-chains 246 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 395 VAL 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 461 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 505 VAL 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 899 ILE Chi-restraints excluded: chain A residue 907 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 117 LEU Chi-restraints excluded: chain G residue 26 TYR 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 144 LEU Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 116 ILE 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 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: 0.3980 chunk 14 optimal weight: 7.9990 chunk 246 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN ** 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 = 0.4197 r_free = 0.4197 target = 0.159111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124181 restraints weight = 43767.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.123659 restraints weight = 57697.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.124741 restraints weight = 54921.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.125249 restraints weight = 35577.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126841 restraints weight = 30626.724| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26616 Z= 0.131 Angle : 0.688 13.843 36650 Z= 0.314 Chirality : 0.057 0.632 4175 Planarity : 0.003 0.060 4061 Dihedral : 15.046 178.344 4889 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.12 % Allowed : 14.04 % 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: 0.35 (0.17), residues: 2654 helix: 1.98 (0.17), residues: 1036 sheet: -0.56 (0.23), residues: 504 loop : -1.07 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 75 TYR 0.014 0.001 TYR A 325 PHE 0.021 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 0.00294 / 0.13 (26608) covalent geometry : angle 0.68453 / 0.31 (36638) hydrogen bonds : bond 0.04258 / 2.97 ( 1070) hydrogen bonds : angle 4.51260 / 3.17 ( 3052) metal coordination : bond 0.00522 / 0.33 ( 8) metal coordination : angle 3.72591 / 2.79 ( 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 274 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: H 380 LEU cc_start: 0.5764 (OUTLIER) cc_final: 0.5033 (pp) REVERT: H 471 GLU cc_start: 0.2340 (tt0) cc_final: 0.1683 (tt0) REVERT: A 816 ASP cc_start: 0.6629 (m-30) cc_final: 0.6377 (m-30) REVERT: A 846 ASN cc_start: 0.7833 (t0) cc_final: 0.7613 (t0) REVERT: E 34 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7277 (pp) REVERT: I 17 LYS cc_start: 0.6615 (tppt) cc_final: 0.6272 (tptt) REVERT: I 447 ASP cc_start: 0.7706 (t0) cc_final: 0.7343 (t0) REVERT: K 147 MET cc_start: 0.6571 (mtt) cc_final: 0.6163 (mtt) REVERT: K 160 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6846 (tm-30) outliers start: 52 outliers final: 42 residues processed: 260 average time/residue: 0.1584 time to fit residues: 68.6690 Evaluate side-chains 255 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 395 VAL 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 505 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 32 VAL 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 G residue 144 LEU Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 116 ILE 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 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 134 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 175 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 247 optimal weight: 8.9990 chunk 228 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.159119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.123836 restraints weight = 43747.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.123595 restraints weight = 56323.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.124539 restraints weight = 55310.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.125268 restraints weight = 35386.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.126698 restraints weight = 30282.816| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26616 Z= 0.131 Angle : 0.682 12.983 36650 Z= 0.311 Chirality : 0.056 0.572 4175 Planarity : 0.003 0.060 4061 Dihedral : 15.015 178.734 4889 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.12 % Allowed : 14.65 % Favored : 83.24 % 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: 1.99 (0.17), residues: 1035 sheet: -0.56 (0.23), residues: 499 loop : -1.07 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 74 TYR 0.022 0.001 TYR I 19 PHE 0.014 0.001 PHE A1059 TRP 0.014 0.001 TRP A 496 HIS 0.004 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (26608) covalent geometry : angle 0.67871 / 0.31 (36638) hydrogen bonds : bond 0.04184 / 2.93 ( 1070) hydrogen bonds : angle 4.46472 / 3.14 ( 3052) metal coordination : bond 0.00473 / 0.29 ( 8) metal coordination : angle 3.67837 / 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 275 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 380 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5069 (pp) REVERT: H 471 GLU cc_start: 0.2467 (tt0) cc_final: 0.1803 (tt0) REVERT: A 816 ASP cc_start: 0.6625 (m-30) cc_final: 0.6410 (m-30) REVERT: E 34 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7278 (pp) REVERT: G 26 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6695 (m-80) REVERT: G 177 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7614 (mm-40) REVERT: I 17 LYS cc_start: 0.6616 (tppt) cc_final: 0.6306 (tptt) REVERT: I 447 ASP cc_start: 0.7611 (t0) cc_final: 0.7197 (t0) REVERT: I 614 LEU cc_start: 0.7534 (tt) cc_final: 0.7061 (mt) REVERT: K 147 MET cc_start: 0.6568 (mtt) cc_final: 0.6174 (mtt) REVERT: K 160 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6935 (tm-30) outliers start: 52 outliers final: 44 residues processed: 261 average time/residue: 0.1599 time to fit residues: 69.6047 Evaluate side-chains 261 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 513 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 284 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 461 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 907 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 18 MET Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 221 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 245 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 191 optimal weight: 9.9990 chunk 96 optimal weight: 0.0870 chunk 57 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.159900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.124755 restraints weight = 43955.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.124411 restraints weight = 56427.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.125519 restraints weight = 53780.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126112 restraints weight = 35053.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.127432 restraints weight = 30280.850| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26616 Z= 0.116 Angle : 0.670 12.076 36650 Z= 0.308 Chirality : 0.055 0.507 4175 Planarity : 0.003 0.066 4061 Dihedral : 14.985 178.733 4889 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.03 % Allowed : 14.97 % Favored : 82.99 % 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: 0.41 (0.17), residues: 2654 helix: 2.05 (0.17), residues: 1029 sheet: -0.56 (0.23), residues: 499 loop : -1.03 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 60 TYR 0.022 0.001 TYR J 116 PHE 0.022 0.001 PHE H 521 TRP 0.014 0.001 TRP A 496 HIS 0.004 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (26608) covalent geometry : angle 0.66736 / 0.31 (36638) hydrogen bonds : bond 0.03958 / 2.79 ( 1070) hydrogen bonds : angle 4.38570 / 3.09 ( 3052) metal coordination : bond 0.00430 / 0.26 ( 8) metal coordination : angle 3.59022 / 2.70 ( 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 277 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 380 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5051 (pp) REVERT: H 471 GLU cc_start: 0.2459 (tt0) cc_final: 0.1832 (tt0) REVERT: A 816 ASP cc_start: 0.6576 (m-30) cc_final: 0.6369 (m-30) REVERT: A 1048 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7224 (m-40) REVERT: E 34 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7219 (pp) REVERT: G 26 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.6634 (m-80) REVERT: G 177 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7658 (mm-40) REVERT: I 17 LYS cc_start: 0.6581 (tppt) cc_final: 0.6272 (tptt) REVERT: I 447 ASP cc_start: 0.7602 (t0) cc_final: 0.7184 (t0) REVERT: I 614 LEU cc_start: 0.7515 (tt) cc_final: 0.7083 (mt) REVERT: K 22 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7186 (mm-40) REVERT: K 147 MET cc_start: 0.6545 (mtt) cc_final: 0.6142 (mtt) REVERT: K 160 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6908 (tm-30) outliers start: 50 outliers final: 38 residues processed: 263 average time/residue: 0.1611 time to fit residues: 70.1587 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 : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 395 VAL 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 505 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1048 ASN 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 F residue 54 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 116 ILE 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 22 GLN 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 159 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 270 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 chunk 226 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 509 ASN A 218 GLN A 439 ASN A 702 GLN A 841 ASN A 926 ASN E 40 ASN F 7 GLN F 93 GLN I 119 ASN ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 290 GLN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.155784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.120939 restraints weight = 43986.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.120168 restraints weight = 60809.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.121574 restraints weight = 55412.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.121877 restraints weight = 36957.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125122 restraints weight = 31227.304| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 26616 Z= 0.281 Angle : 0.815 13.712 36650 Z= 0.382 Chirality : 0.061 0.655 4175 Planarity : 0.004 0.072 4061 Dihedral : 15.101 179.541 4889 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.24 % Allowed : 15.42 % Favored : 82.34 % 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: -0.13 (0.16), residues: 2654 helix: 1.53 (0.16), residues: 1028 sheet: -0.78 (0.23), residues: 500 loop : -1.27 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 769 TYR 0.022 0.002 TYR A 474 PHE 0.027 0.002 PHE A1059 TRP 0.012 0.002 TRP A 496 HIS 0.006 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.28 (26608) covalent geometry : angle 0.81044 / 0.38 (36638) hydrogen bonds : bond 0.05534 / 3.88 ( 1070) hydrogen bonds : angle 4.81931 / 3.41 ( 3052) metal coordination : bond 0.00957 / 0.64 ( 8) metal coordination : angle 4.64355 / 3.37 ( 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 275 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 380 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5000 (pp) REVERT: H 471 GLU cc_start: 0.2526 (tt0) cc_final: 0.1823 (tt0) REVERT: A 816 ASP cc_start: 0.6970 (m-30) cc_final: 0.6725 (m-30) REVERT: A 1048 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7498 (m-40) REVERT: A 1075 GLN cc_start: 0.5150 (mt0) cc_final: 0.4226 (mp10) REVERT: E 34 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7325 (pp) REVERT: G 26 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.6648 (m-80) REVERT: I 102 ARG cc_start: 0.3703 (mpt180) cc_final: 0.3180 (mpt180) REVERT: I 614 LEU cc_start: 0.7642 (tt) cc_final: 0.7165 (mt) REVERT: K 147 MET cc_start: 0.6541 (mtt) cc_final: 0.6265 (mtt) REVERT: K 160 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6910 (tm-30) outliers start: 55 outliers final: 42 residues processed: 264 average time/residue: 0.1598 time to fit residues: 70.4357 Evaluate side-chains 258 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 513 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1048 ASN 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 121 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain I residue 108 PHE Chi-restraints excluded: chain I residue 116 ILE 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 290 GLN 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 22 GLN 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: 0.6980 chunk 134 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.155864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.120619 restraints weight = 43759.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120027 restraints weight = 58481.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.121204 restraints weight = 54779.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.121635 restraints weight = 35834.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.123106 restraints weight = 30908.520| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 26616 Z= 0.260 Angle : 0.910 59.199 36650 Z= 0.457 Chirality : 0.060 0.652 4175 Planarity : 0.004 0.072 4061 Dihedral : 15.101 179.498 4889 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.91 % Allowed : 16.03 % Favored : 82.06 % Cbeta Deviations : 0.04 % 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: -0.16 (0.16), residues: 2654 helix: 1.51 (0.16), residues: 1028 sheet: -0.81 (0.23), residues: 500 loop : -1.28 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 769 TYR 0.032 0.002 TYR F 10 PHE 0.025 0.002 PHE A1059 TRP 0.013 0.002 TRP A 496 HIS 0.006 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.26 (26608) covalent geometry : angle 0.90630 / 0.46 (36638) hydrogen bonds : bond 0.05431 / 3.81 ( 1070) hydrogen bonds : angle 4.81459 / 3.41 ( 3052) metal coordination : bond 0.00830 / 0.53 ( 8) metal coordination : angle 4.64743 / 3.37 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3796.15 seconds wall clock time: 66 minutes 55.37 seconds (4015.37 seconds total)