Starting phenix.real_space_refine on Wed Nov 20 07:12:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/11_2024/7ux2_26846_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/11_2024/7ux2_26846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/11_2024/7ux2_26846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/11_2024/7ux2_26846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/11_2024/7ux2_26846_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/11_2024/7ux2_26846_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.017 sd= 1.412 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 157 5.16 5 C 17270 2.51 5 N 4696 2.21 5 O 5114 1.98 5 H 27167 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 54416 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 17564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 17564 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 58, 'TRANS': 1044} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4882 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 4523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4523 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 6, 'TRANS': 274} Chain breaks: 2 Chain: "D" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1738 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain breaks: 1 Chain: "E" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1888 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1892 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "G" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1294 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain breaks: 1 Chain: "H" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1311 Classifications: {'peptide': 89} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "I" Number of atoms: 4882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4882 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4447 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 5, 'TRANS': 271} Chain breaks: 2 Chain: "K" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1791 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "L" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1888 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "M" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1892 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "N" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1294 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain breaks: 1 Chain: "O" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1311 Classifications: {'peptide': 89} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "P" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1677 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 9, 'TRANS': 94} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.62, per 1000 atoms: 0.45 Number of scatterers: 54416 At special positions: 0 Unit cell: (116.55, 172.2, 223.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 157 16.00 P 10 15.00 Mg 2 11.99 O 5114 8.00 N 4696 7.00 C 17270 6.00 H 27167 1.00 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: 14.76 Conformation dependent library (CDL) restraints added in 4.0 seconds 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6534 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 21 sheets defined 46.4% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 32 through 37 Processing helix chain 'A' and resid 89 through 93 removed outlier: 4.066A pdb=" N MET A 93 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 114 removed outlier: 4.119A pdb=" N TRP A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 179 through 186 Processing helix chain 'A' and resid 198 through 218 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.874A pdb=" N ILE A 298 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 328 Processing helix chain 'A' and resid 329 through 338 removed outlier: 3.578A pdb=" N ARG A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 359 removed outlier: 3.761A pdb=" N LEU A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 392 removed outlier: 3.841A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN A 392 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 407 through 423 removed outlier: 3.622A pdb=" N MET A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 445 through 458 Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 471 through 480 removed outlier: 4.549A pdb=" N TYR A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 removed outlier: 4.753A pdb=" N LEU A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 504 No H-bonds generated for 'chain 'A' and resid 502 through 504' Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 514 through 524 removed outlier: 3.507A pdb=" N PHE A 518 " --> pdb=" O GLY A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 544 Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 570 through 585 removed outlier: 3.711A pdb=" N TRP A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 598 Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 606 through 610 removed outlier: 3.644A pdb=" N SER A 609 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 634 through 649 Processing helix chain 'A' and resid 650 through 652 No H-bonds generated for 'chain 'A' and resid 650 through 652' Processing helix chain 'A' and resid 656 through 674 Processing helix chain 'A' and resid 674 through 690 removed outlier: 4.068A pdb=" N LYS A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 789 removed outlier: 3.699A pdb=" N ARG A 789 " --> pdb=" O ASP A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 820 Processing helix chain 'A' and resid 823 through 843 Processing helix chain 'A' and resid 958 through 965 removed outlier: 3.541A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 969 Processing helix chain 'A' and resid 982 through 1008 removed outlier: 3.801A pdb=" N GLU A 987 " --> pdb=" O GLN A 983 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A1003 " --> pdb=" O ARG A 999 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.816A pdb=" N ASN B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 39 removed outlier: 3.547A pdb=" N ARG B 37 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 38 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 100 through 117 Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 136 through 152 Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.621A pdb=" N GLN B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 226 through 243 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 282 through 299 removed outlier: 4.072A pdb=" N THR B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 82 Processing helix chain 'C' and resid 150 through 168 Processing helix chain 'C' and resid 184 through 206 Processing helix chain 'C' and resid 223 through 235 removed outlier: 3.557A pdb=" N GLU C 227 " --> pdb=" O HIS C 223 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 235 " --> pdb=" O LYS C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 255 Processing helix chain 'C' and resid 278 through 300 Processing helix chain 'C' and resid 344 through 347 Processing helix chain 'C' and resid 348 through 368 Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.941A pdb=" N ALA D 52 " --> pdb=" O THR D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 99 removed outlier: 3.899A pdb=" N SER D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 120 removed outlier: 3.629A pdb=" N ALA D 120 " --> pdb=" O HIS D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 144 removed outlier: 3.939A pdb=" N GLN D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER D 144 " --> pdb=" O TYR D 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.563A pdb=" N GLN E 13 " --> pdb=" O GLN E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 64 removed outlier: 3.655A pdb=" N THR E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA E 47 " --> pdb=" O ARG E 43 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 124 removed outlier: 3.542A pdb=" N TYR E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Proline residue: E 118 - end of helix Processing helix chain 'F' and resid 4 through 12 Processing helix chain 'F' and resid 41 through 45 Processing helix chain 'F' and resid 46 through 51 Processing helix chain 'F' and resid 51 through 61 removed outlier: 4.034A pdb=" N LEU F 55 " --> pdb=" O SER F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 122 Proline residue: F 112 - end of helix removed outlier: 3.508A pdb=" N GLU F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN F 119 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 51 Processing helix chain 'H' and resid 2 through 14 Processing helix chain 'H' and resid 38 through 41 Processing helix chain 'H' and resid 42 through 51 Processing helix chain 'I' and resid 19 through 28 Processing helix chain 'I' and resid 33 through 38 Processing helix chain 'I' and resid 66 through 75 Processing helix chain 'I' and resid 77 through 82 Processing helix chain 'I' and resid 98 through 117 Processing helix chain 'I' and resid 128 through 132 Processing helix chain 'I' and resid 135 through 152 removed outlier: 4.512A pdb=" N LEU I 139 " --> pdb=" O ASP I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.508A pdb=" N LYS I 171 " --> pdb=" O GLU I 167 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 198 Processing helix chain 'I' and resid 227 through 245 Processing helix chain 'I' and resid 282 through 299 removed outlier: 3.794A pdb=" N THR I 286 " --> pdb=" O PRO I 282 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS I 295 " --> pdb=" O ARG I 291 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N HIS I 296 " --> pdb=" O ASN I 292 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS I 299 " --> pdb=" O LYS I 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 82 Processing helix chain 'J' and resid 150 through 168 removed outlier: 3.552A pdb=" N THR J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE J 159 " --> pdb=" O THR J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 185 removed outlier: 3.896A pdb=" N SER J 184 " --> pdb=" O ASP J 181 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP J 185 " --> pdb=" O GLY J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 204 removed outlier: 4.009A pdb=" N ALA J 204 " --> pdb=" O ASN J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 234 Processing helix chain 'J' and resid 239 through 255 removed outlier: 3.618A pdb=" N LEU J 243 " --> pdb=" O GLN J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 300 Processing helix chain 'J' and resid 344 through 347 Processing helix chain 'J' and resid 348 through 368 Processing helix chain 'K' and resid 48 through 65 removed outlier: 3.820A pdb=" N ALA K 52 " --> pdb=" O THR K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 77 through 99 Processing helix chain 'K' and resid 115 through 120 removed outlier: 3.836A pdb=" N ALA K 120 " --> pdb=" O HIS K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 145 removed outlier: 3.590A pdb=" N LEU K 129 " --> pdb=" O PRO K 125 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER K 144 " --> pdb=" O TYR K 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN K 145 " --> pdb=" O SER K 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 13 Processing helix chain 'L' and resid 41 through 64 removed outlier: 3.555A pdb=" N THR L 45 " --> pdb=" O ASP L 41 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA L 47 " --> pdb=" O ARG L 43 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ILE L 48 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA L 49 " --> pdb=" O THR L 45 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN L 62 " --> pdb=" O ARG L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 124 removed outlier: 5.075A pdb=" N GLU L 117 " --> pdb=" O GLN L 113 " (cutoff:3.500A) Proline residue: L 118 - end of helix Processing helix chain 'M' and resid 4 through 12 Processing helix chain 'M' and resid 41 through 45 Processing helix chain 'M' and resid 46 through 51 Processing helix chain 'M' and resid 51 through 61 removed outlier: 3.911A pdb=" N LEU M 55 " --> pdb=" O SER M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 110 Processing helix chain 'M' and resid 110 through 117 Processing helix chain 'M' and resid 117 through 122 removed outlier: 4.051A pdb=" N VAL M 121 " --> pdb=" O LEU M 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 10 Processing helix chain 'N' and resid 36 through 39 Processing helix chain 'N' and resid 40 through 52 removed outlier: 3.683A pdb=" N GLY N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 14 Processing helix chain 'O' and resid 38 through 41 Processing helix chain 'O' and resid 42 through 54 removed outlier: 3.629A pdb=" N ALA O 53 " --> pdb=" O ALA O 49 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS O 54 " --> pdb=" O GLN O 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 41 Processing helix chain 'P' and resid 80 through 101 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 123 removed outlier: 6.768A pdb=" N VAL A 58 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LYS A 120 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 60 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N SER A 122 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 62 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 59 " --> pdb=" O ARG A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA3, first strand: chain 'A' and resid 1015 through 1021 removed outlier: 3.505A pdb=" N ILE A1017 " --> pdb=" O VAL A1327 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A1327 " --> pdb=" O ILE A1017 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU A1019 " --> pdb=" O ILE A1325 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE A1325 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A1317 " --> pdb=" O LEU A1307 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU A1307 " --> pdb=" O ALA A1317 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY A1319 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1028 through 1031 removed outlier: 3.642A pdb=" N ASP A1058 " --> pdb=" O PHE A1048 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1070 through 1076 removed outlier: 4.362A pdb=" N ALA A1092 " --> pdb=" O THR A1088 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A1110 " --> pdb=" O VAL A1095 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS A1097 " --> pdb=" O MET A1108 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N MET A1108 " --> pdb=" O LYS A1097 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1127 through 1132 removed outlier: 4.971A pdb=" N GLY A1142 " --> pdb=" O ILE A1146 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A1146 " --> pdb=" O GLY A1142 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A1159 " --> pdb=" O ILE A1149 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP A1151 " --> pdb=" O LYS A1157 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LYS A1157 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1169 through 1175 removed outlier: 3.582A pdb=" N LEU A1180 " --> pdb=" O ASP A1175 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A1205 " --> pdb=" O VAL A1192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1214 through 1216 removed outlier: 3.978A pdb=" N LYS A1216 " --> pdb=" O VAL A1230 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N HIS A1226 " --> pdb=" O GLN A1220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1214 through 1216 removed outlier: 3.978A pdb=" N LYS A1216 " --> pdb=" O VAL A1230 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A1231 " --> pdb=" O ASP A1235 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP A1235 " --> pdb=" O SER A1231 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A1238 " --> pdb=" O ASN A1248 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A1248 " --> pdb=" O ILE A1238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1256 through 1261 removed outlier: 3.792A pdb=" N ALA A1258 " --> pdb=" O GLY A1271 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A1277 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASN A1289 " --> pdb=" O THR A1277 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE A1279 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A1285 " --> pdb=" O ASN A1281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 46 through 53 removed outlier: 6.765A pdb=" N LEU B 56 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N MET B 6 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN B 59 " --> pdb=" O MET B 6 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS B 8 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TRP B 61 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 10 " --> pdb=" O TRP B 61 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N VAL B 87 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS B 9 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE B 89 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU B 11 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL B 91 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N MET B 13 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASP B 93 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU B 88 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B 125 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR B 90 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N HIS B 127 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE B 92 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 215 through 217 removed outlier: 9.136A pdb=" N GLN B 250 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS C 319 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET B 252 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 317 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL B 254 " --> pdb=" O MET C 315 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET C 315 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA C 259 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR C 272 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU C 261 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.534A pdb=" N ARG C 63 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE C 141 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU C 65 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL C 143 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N MET C 67 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ASP C 145 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU C 140 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE C 176 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR C 142 " --> pdb=" O PHE C 176 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS C 178 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE C 144 " --> pdb=" O HIS C 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 31 through 36 removed outlier: 3.605A pdb=" N SER E 21 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY E 79 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG E 85 " --> pdb=" O LYS E 70 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LYS E 70 " --> pdb=" O ARG E 85 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS F 69 " --> pdb=" O ASN F 84 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP F 26 " --> pdb=" O PRO F 31 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 17 through 22 removed outlier: 3.643A pdb=" N GLY G 17 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS G 88 " --> pdb=" O GLY G 17 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE G 85 " --> pdb=" O THR G 78 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR G 78 " --> pdb=" O PHE G 85 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN H 73 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA H 85 " --> pdb=" O VAL H 21 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL H 21 " --> pdb=" O ALA H 85 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N HIS H 87 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL H 21 " --> pdb=" O CYS H 33 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N CYS H 33 " --> pdb=" O VAL H 21 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS H 23 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 46 through 51 removed outlier: 6.322A pdb=" N MET I 6 " --> pdb=" O VAL I 57 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN I 59 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS I 8 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TRP I 61 " --> pdb=" O LYS I 8 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL I 10 " --> pdb=" O TRP I 61 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N VAL I 87 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS I 9 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE I 89 " --> pdb=" O LYS I 9 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU I 11 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL I 91 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET I 13 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N ASP I 93 " --> pdb=" O MET I 13 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 213 through 218 removed outlier: 7.142A pdb=" N VAL I 213 " --> pdb=" O GLU I 207 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU I 207 " --> pdb=" O VAL I 213 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER I 215 " --> pdb=" O LEU I 205 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR I 270 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE I 265 " --> pdb=" O GLN I 250 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N GLN I 250 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS J 319 " --> pdb=" O GLN I 250 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET I 252 " --> pdb=" O ILE J 317 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE J 317 " --> pdb=" O MET I 252 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR J 324 " --> pdb=" O LEU J 320 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 111 through 114 removed outlier: 7.228A pdb=" N ARG J 63 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE J 141 " --> pdb=" O ARG J 63 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU J 65 " --> pdb=" O ILE J 141 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL J 143 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET J 67 " --> pdb=" O VAL J 143 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ASP J 145 " --> pdb=" O MET J 67 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU J 140 " --> pdb=" O GLU J 174 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE J 176 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR J 142 " --> pdb=" O PHE J 176 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N HIS J 178 " --> pdb=" O TYR J 142 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE J 144 " --> pdb=" O HIS J 178 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 31 through 36 removed outlier: 3.688A pdb=" N CYS L 92 " --> pdb=" O LEU L 23 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY L 79 " --> pdb=" O CYS L 76 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG L 85 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N LYS L 70 " --> pdb=" O ARG L 85 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS M 69 " --> pdb=" O ASN M 84 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL M 90 " --> pdb=" O PHE M 83 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N HIS M 20 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA M 36 " --> pdb=" O HIS M 20 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE M 22 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LYS M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL M 24 " --> pdb=" O VAL M 32 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 30 through 31 removed outlier: 6.000A pdb=" N LYS N 88 " --> pdb=" O LEU N 16 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR N 18 " --> pdb=" O VAL N 86 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL N 86 " --> pdb=" O TYR N 18 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR N 74 " --> pdb=" O ARG N 89 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL N 68 " --> pdb=" O LEU N 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 30 through 34 removed outlier: 5.931A pdb=" N CYS O 23 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N CYS O 33 " --> pdb=" O VAL O 21 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL O 21 " --> pdb=" O CYS O 33 " (cutoff:3.500A) 1391 hydrogen bonds defined for protein. 3996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.39 Time building geometry restraints manager: 17.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 27088 1.03 - 1.23: 116 1.23 - 1.42: 11496 1.42 - 1.62: 15991 1.62 - 1.81: 247 Bond restraints: 54938 Sorted by residual: bond pdb=" CB ARG A1123 " pdb=" CG ARG A1123 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.21e+00 bond pdb=" CE LYS I 239 " pdb=" NZ LYS I 239 " ideal model delta sigma weight residual 1.489 1.446 0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CB GLU A 782 " pdb=" CG GLU A 782 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CD LYS J 361 " pdb=" CE LYS J 361 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" CB ASP K 72 " pdb=" CG ASP K 72 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.60e+00 ... (remaining 54933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 97794 1.88 - 3.77: 1308 3.77 - 5.65: 155 5.65 - 7.54: 17 7.54 - 9.42: 3 Bond angle restraints: 99277 Sorted by residual: angle pdb=" CA LYS I 239 " pdb=" CB LYS I 239 " pdb=" CG LYS I 239 " ideal model delta sigma weight residual 114.10 123.52 -9.42 2.00e+00 2.50e-01 2.22e+01 angle pdb=" CA ARG A1123 " pdb=" CB ARG A1123 " pdb=" CG ARG A1123 " ideal model delta sigma weight residual 114.10 122.11 -8.01 2.00e+00 2.50e-01 1.60e+01 angle pdb=" N LYS I 239 " pdb=" CA LYS I 239 " pdb=" CB LYS I 239 " ideal model delta sigma weight residual 110.01 115.53 -5.52 1.45e+00 4.76e-01 1.45e+01 angle pdb=" C LYS I 239 " pdb=" CA LYS I 239 " pdb=" CB LYS I 239 " ideal model delta sigma weight residual 110.88 105.43 5.45 1.57e+00 4.06e-01 1.21e+01 angle pdb=" CB LYS I 239 " pdb=" CG LYS I 239 " pdb=" CD LYS I 239 " ideal model delta sigma weight residual 111.30 103.62 7.68 2.30e+00 1.89e-01 1.11e+01 ... (remaining 99272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.00: 25101 33.00 - 65.99: 618 65.99 - 98.99: 38 98.99 - 131.99: 1 131.99 - 164.99: 3 Dihedral angle restraints: 25761 sinusoidal: 14075 harmonic: 11686 Sorted by residual: dihedral pdb=" CA ARG M 85 " pdb=" C ARG M 85 " pdb=" N LEU M 86 " pdb=" CA LEU M 86 " ideal model delta harmonic sigma weight residual -180.00 -143.14 -36.86 0 5.00e+00 4.00e-02 5.44e+01 dihedral pdb=" C8 GTP B 401 " pdb=" C1' GTP B 401 " pdb=" N9 GTP B 401 " pdb=" O4' GTP B 401 " ideal model delta sinusoidal sigma weight residual 104.59 -60.39 164.99 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP I 401 " pdb=" C1' GTP I 401 " pdb=" N9 GTP I 401 " pdb=" O4' GTP I 401 " ideal model delta sinusoidal sigma weight residual 104.59 -57.15 161.74 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 25758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2894 0.035 - 0.070: 952 0.070 - 0.106: 260 0.106 - 0.141: 160 0.141 - 0.176: 22 Chirality restraints: 4288 Sorted by residual: chirality pdb=" CA VAL E 86 " pdb=" N VAL E 86 " pdb=" C VAL E 86 " pdb=" CB VAL E 86 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA LYS J 361 " pdb=" N LYS J 361 " pdb=" C LYS J 361 " pdb=" CB LYS J 361 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA ILE K 124 " pdb=" N ILE K 124 " pdb=" C ILE K 124 " pdb=" CB ILE K 124 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 4285 not shown) Planarity restraints: 8071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 585 " 0.030 2.00e-02 2.50e+03 2.38e-02 2.27e+01 pdb=" CG TRP A 585 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP A 585 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 585 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 585 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 585 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 585 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 585 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 585 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 TRP A 585 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP A 585 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 585 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 585 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 585 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 585 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 428 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO A 429 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 683 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C LEU A 683 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU A 683 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN A 684 " -0.014 2.00e-02 2.50e+03 ... (remaining 8068 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 5307 2.23 - 2.83: 124195 2.83 - 3.42: 148890 3.42 - 4.01: 207550 4.01 - 4.60: 317128 Nonbonded interactions: 803070 Sorted by model distance: nonbonded pdb=" OD1 ASP C 202 " pdb="HH12 ARG K 86 " model vdw 1.644 2.450 nonbonded pdb=" OE1 GLN I 133 " pdb=" H GLN I 133 " model vdw 1.650 2.450 nonbonded pdb="HH21 ARG J 70 " pdb=" O1B GDP J 401 " model vdw 1.654 2.450 nonbonded pdb=" O TRP A 325 " pdb="HH22 ARG A 330 " model vdw 1.667 2.450 nonbonded pdb=" O ASP A 568 " pdb="HH11 ARG A 574 " model vdw 1.667 2.450 ... (remaining 803065 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'I' } ncs_group { reference = (chain 'C' and (resid 59 through 83 or resid 106 through 116 or (resid 131 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name O \ E1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or r \ esid 132 through 371 or resid 401)) selection = (chain 'J' and (resid 59 through 177 or (resid 178 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 179 through 371 or resid 401)) } ncs_group { reference = chain 'D' selection = (chain 'K' and (resid 47 through 72 or (resid 77 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3)) or resid 78 through 161)) } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.900 Extract box with map and model: 1.940 Check model and map are aligned: 0.360 Set scattering table: 0.460 Process input model: 109.560 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.330 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: 0.030 Load rotamer database and sin/cos tables:10.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27771 Z= 0.230 Angle : 0.636 9.421 37619 Z= 0.326 Chirality : 0.043 0.176 4288 Planarity : 0.005 0.106 4805 Dihedral : 14.236 164.986 10290 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3361 helix: 1.37 (0.14), residues: 1412 sheet: -0.73 (0.21), residues: 611 loop : -0.63 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP A 585 HIS 0.007 0.001 HIS A1310 PHE 0.021 0.001 PHE B 266 TYR 0.026 0.001 TYR I 73 ARG 0.021 0.001 ARG I 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Evaluate side-chains 533 residues out of total 3014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 4.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ARG cc_start: 0.7158 (mpp-170) cc_final: 0.6891 (mpp-170) REVERT: B 201 ASP cc_start: 0.7885 (t70) cc_final: 0.7577 (t0) REVERT: H 34 ARG cc_start: 0.7796 (mmt-90) cc_final: 0.7511 (mmt-90) REVERT: J 198 ARG cc_start: 0.6977 (ttm170) cc_final: 0.6546 (ttp-170) REVERT: K 60 LYS cc_start: 0.8221 (tttm) cc_final: 0.7830 (ttmt) outliers start: 0 outliers final: 0 residues processed: 533 average time/residue: 3.2744 time to fit residues: 2022.6711 Evaluate side-chains 420 residues out of total 3014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 4.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 304 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 443 GLN A1016 GLN A1020 ASN B 107 GLN D 131 GLN ** G 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN J 83 HIS J 113 GLN L 62 GLN M 76 ASN N 90 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 27771 Z= 0.299 Angle : 0.602 7.115 37619 Z= 0.317 Chirality : 0.044 0.160 4288 Planarity : 0.005 0.074 4805 Dihedral : 7.539 165.498 3731 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.20 % Allowed : 9.01 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3361 helix: 1.42 (0.14), residues: 1431 sheet: -0.94 (0.20), residues: 609 loop : -0.73 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 585 HIS 0.008 0.001 HIS J 178 PHE 0.018 0.002 PHE B 266 TYR 0.014 0.001 TYR B 170 ARG 0.009 0.001 ARG G 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Evaluate side-chains 494 residues out of total 3014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 458 time to evaluate : 4.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1180 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7768 (tm) REVERT: A 1235 ASP cc_start: 0.8056 (p0) cc_final: 0.7840 (p0) REVERT: A 1287 ILE cc_start: 0.8267 (mm) cc_final: 0.8008 (mt) REVERT: B 201 ASP cc_start: 0.7961 (t70) cc_final: 0.7634 (t0) REVERT: J 71 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7162 (mtp85) REVERT: J 145 ASP cc_start: 0.7159 (p0) cc_final: 0.6906 (t0) outliers start: 36 outliers final: 20 residues processed: 472 average time/residue: 3.1601 time to fit residues: 1753.2684 Evaluate side-chains 449 residues out of total 3014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 428 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 266 SER Chi-restraints excluded: chain J residue 321 ASN Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 30 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 253 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 83 optimal weight: 0.0370 chunk 304 optimal weight: 1.9990 chunk 329 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 HIS L 62 GLN P 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27771 Z= 0.263 Angle : 0.570 6.551 37619 Z= 0.297 Chirality : 0.042 0.156 4288 Planarity : 0.004 0.065 4805 Dihedral : 7.523 165.312 3731 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.36 % Allowed : 11.83 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3361 helix: 1.49 (0.14), residues: 1433 sheet: -1.19 (0.20), residues: 622 loop : -0.74 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 585 HIS 0.007 0.001 HIS J 178 PHE 0.017 0.001 PHE B 266 TYR 0.013 0.001 TYR B 170 ARG 0.008 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Evaluate side-chains 490 residues out of total 3014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 449 time to evaluate : 4.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1235 ASP cc_start: 0.8233 (p0) cc_final: 0.7895 (p0) REVERT: A 1287 ILE cc_start: 0.8281 (mm) cc_final: 0.8036 (mt) REVERT: B 201 ASP cc_start: 0.8013 (t70) cc_final: 0.7645 (t0) REVERT: J 71 ARG cc_start: 0.7428 (mtp85) cc_final: 0.7198 (mtp85) REVERT: K 91 ARG cc_start: 0.7575 (mtt180) cc_final: 0.7284 (mtt180) outliers start: 41 outliers final: 22 residues processed: 466 average time/residue: 3.0867 time to fit residues: 1675.3072 Evaluate side-chains 445 residues out of total 3014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 423 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1226 HIS Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 348 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain J residue 266 SER Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain P residue 30 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 145 optimal weight: 0.2980 chunk 204 optimal weight: 30.0000 chunk 305 optimal weight: 0.7980 chunk 323 optimal weight: 0.4980 chunk 159 optimal weight: 0.9990 chunk 289 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 ASN J 113 GLN K 87 GLN L 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27771 Z= 0.165 Angle : 0.538 6.570 37619 Z= 0.279 Chirality : 0.041 0.162 4288 Planarity : 0.004 0.077 4805 Dihedral : 7.307 163.445 3731 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.23 % Allowed : 12.56 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3361 helix: 1.69 (0.14), residues: 1435 sheet: -1.19 (0.20), residues: 615 loop : -0.72 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 576 HIS 0.004 0.001 HIS H 8 PHE 0.015 0.001 PHE I 211 TYR 0.013 0.001 TYR D 140 ARG 0.010 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Evaluate side-chains 475 residues out of total 3014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 438 time to evaluate : 4.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ARG cc_start: 0.7273 (mpp-170) cc_final: 0.6984 (mpp-170) REVERT: A 1235 ASP cc_start: 0.8197 (p0) cc_final: 0.7829 (p0) REVERT: A 1287 ILE cc_start: 0.8257 (mm) cc_final: 0.8054 (mt) REVERT: B 139 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8138 (pt) REVERT: B 201 ASP cc_start: 0.8026 (t70) cc_final: 0.7666 (t0) REVERT: C 63 ARG cc_start: 0.7686 (tpt-90) cc_final: 0.7460 (mmm160) REVERT: D 68 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7707 (t) REVERT: K 86 ARG cc_start: 0.7936 (ttt-90) cc_final: 0.7728 (ttt90) REVERT: K 91 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7243 (mtt180) outliers start: 37 outliers final: 17 residues processed: 450 average time/residue: 3.2439 time to fit residues: 1708.4738 Evaluate side-chains 439 residues out of total 3014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 420 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1229 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 348 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 30 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN H 50 GLN K 87 GLN L 62 GLN N 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 27771 Z= 0.338 Angle : 0.587 6.631 37619 Z= 0.306 Chirality : 0.043 0.160 4288 Planarity : 0.005 0.077 4805 Dihedral : 7.592 165.587 3731 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.50 % Allowed : 13.49 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3361 helix: 1.52 (0.14), residues: 1436 sheet: -1.36 (0.19), residues: 636 loop : -0.74 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 576 HIS 0.006 0.001 HIS J 178 PHE 0.021 0.002 PHE B 266 TYR 0.017 0.001 TYR L 94 ARG 0.008 0.000 ARG M 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Evaluate side-chains 474 residues out of total 3014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 429 time to evaluate : 4.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: A 1139 MET cc_start: 0.7960 (mtm) cc_final: 0.7488 (mtm) REVERT: A 1235 ASP cc_start: 0.8272 (p0) cc_final: 0.7880 (p0) REVERT: B 79 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: B 139 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8165 (pt) REVERT: B 201 ASP cc_start: 0.8107 (t70) cc_final: 0.7742 (t0) REVERT: C 63 ARG cc_start: 0.7763 (tpt-90) cc_final: 0.7553 (mmm160) REVERT: C 174 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: D 147 ARG cc_start: 0.8049 (ppt170) cc_final: 0.7766 (ppt90) REVERT: J 171 MET cc_start: 0.7767 (ttm) cc_final: 0.7557 (ttp) REVERT: K 80 GLU cc_start: 0.7881 (tp30) cc_final: 0.7676 (tp30) REVERT: N 64 LYS cc_start: 0.8392 (pttt) cc_final: 0.8123 (pttp) outliers start: 45 outliers final: 31 residues processed: 452 average time/residue: 3.2608 time to fit residues: 1731.3925 Evaluate side-chains 446 residues out of total 3014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 411 time to evaluate : 4.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1229 SER Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 348 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain F residue 11 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain J residue 266 SER Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 32 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 324 optimal weight: 4.9990 chunk 269 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN A1020 ASN J 113 GLN K 87 GLN L 62 GLN N 90 GLN P 73 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27771 Z= 0.198 Angle : 0.548 7.569 37619 Z= 0.284 Chirality : 0.041 0.156 4288 Planarity : 0.004 0.075 4805 Dihedral : 7.434 164.827 3731 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.43 % Allowed : 14.36 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3361 helix: 1.70 (0.14), residues: 1429 sheet: -1.29 (0.19), residues: 633 loop : -0.70 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 576 HIS 0.006 0.001 HIS G 73 PHE 0.012 0.001 PHE B 238 TYR 0.014 0.001 TYR I 73 ARG 0.012 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 683 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Evaluate side-chains 467 residues out of total 3014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 424 time to evaluate : 4.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: A 306 ARG cc_start: 0.7338 (mpp-170) cc_final: 0.7035 (mpp-170) REVERT: A 411 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: A 1235 ASP cc_start: 0.8207 (p0) cc_final: 0.7808 (p0) REVERT: B 201 ASP cc_start: 0.8122 (t70) cc_final: 0.7765 (t0) REVERT: C 151 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.6824 (ttp) REVERT: C 174 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7865 (mm-30) REVERT: D 58 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8461 (mp) REVERT: D 147 ARG cc_start: 0.8035 (ppt170) cc_final: 0.7754 (ppt90) REVERT: J 63 ARG cc_start: 0.6897 (mmm160) cc_final: 0.6644 (mmm160) REVERT: J 171 MET cc_start: 0.7735 (ttm) cc_final: 0.7532 (ttp) REVERT: K 86 ARG cc_start: 0.7936 (ttt-90) cc_final: 0.7706 (ttt90) REVERT: P 34 MET cc_start: 0.7661 (mmm) cc_final: 0.7350 (tpp) outliers start: 43 outliers final: 30 residues processed: 442 average time/residue: 3.1807 time to fit residues: 1637.2889 Evaluate side-chains 443 residues out of total 3014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 408 time to evaluate : 4.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1229 SER Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 348 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain F residue 11 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain K residue 130 GLN Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 32 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: