Starting phenix.real_space_refine on Thu Dec 7 23:54:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/12_2023/7ux2_26846_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/12_2023/7ux2_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_26846/12_2023/7ux2_26846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/12_2023/7ux2_26846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/12_2023/7ux2_26846_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/12_2023/7ux2_26846_trim_updated.pdb" } 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 27147 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 128": "OD1" <-> "OD2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 57": "OD1" <-> "OD2" Residue "E ASP 75": "OD1" <-> "OD2" Residue "F PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 39": "OD1" <-> "OD2" Residue "I GLU 143": "OE1" <-> "OE2" Residue "I ASP 166": "OD1" <-> "OD2" Residue "J ASP 170": "OD1" <-> "OD2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 4": "OD1" <-> "OD2" Residue "N GLU 45": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 10": "OE1" <-> "OE2" Residue "O GLU 40": "OE1" <-> "OE2" Residue "O ASP 61": "OD1" <-> "OD2" Residue "O GLU 68": "OE1" <-> "OE2" Residue "P TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 54396 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.53, per 1000 atoms: 0.32 Number of scatterers: 54396 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 27147 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 - 3.50 Amino acid : False - 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: 33.47 Conformation dependent library (CDL) restraints added in 4.2 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... running ksdssp... Secondary structure from input PDB file: 107 helices and 25 sheets defined 40.9% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.94 Creating SS restraints... Processing helix chain 'A' and resid 33 through 36 No H-bonds generated for 'chain 'A' and resid 33 through 36' Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 179 through 185 Processing helix chain 'A' and resid 199 through 217 Processing helix chain 'A' and resid 262 through 268 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 294 through 297 Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 341 through 360 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) removed outlier: 3.968A pdb=" N TYR A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 391 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 408 through 425 removed outlier: 3.622A pdb=" N MET A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 446 through 459 removed outlier: 3.895A pdb=" N LEU A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 473 through 481 removed outlier: 3.697A pdb=" N LEU A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 499 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.503A pdb=" N ALA A 507 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 509 " --> pdb=" O GLN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 523 Processing helix chain 'A' and resid 532 through 542 Processing helix chain 'A' and resid 547 through 555 Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 571 through 584 Processing helix chain 'A' and resid 589 through 597 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 606 through 609 removed outlier: 3.644A pdb=" N SER A 609 " --> pdb=" O SER A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 609' Processing helix chain 'A' and resid 613 through 625 Processing helix chain 'A' and resid 635 through 651 removed outlier: 3.730A pdb=" N GLN A 650 " --> pdb=" O MET A 646 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU A 651 " --> pdb=" O MET A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 673 Processing helix chain 'A' and resid 675 through 691 removed outlier: 4.068A pdb=" N LYS A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 788 Processing helix chain 'A' and resid 807 through 819 Processing helix chain 'A' and resid 824 through 842 Processing helix chain 'A' and resid 959 through 966 removed outlier: 3.541A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR A 966 " --> pdb=" O TRP A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1007 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 20 through 29 Processing helix chain 'B' and resid 33 through 38 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 67 through 75 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 101 through 116 Processing helix chain 'B' and resid 134 through 151 removed outlier: 4.458A pdb=" N ASP B 138 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 139 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 147 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 150 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 151 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 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 184 through 198 Processing helix chain 'B' and resid 227 through 245 removed outlier: 3.641A pdb=" N LYS B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 300 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) removed outlier: 5.003A pdb=" N LEU B 300 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 81 Processing helix chain 'C' and resid 151 through 167 Processing helix chain 'C' and resid 185 through 205 Processing helix chain 'C' and resid 224 through 234 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 279 through 299 Processing helix chain 'C' and resid 345 through 367 removed outlier: 3.788A pdb=" N ARG C 348 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY C 350 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 367 " --> pdb=" O HIS C 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 64 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 98 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 115 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 128 through 145 removed outlier: 3.804A pdb=" N SER D 144 " --> pdb=" O TYR D 140 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 14 removed outlier: 3.563A pdb=" N GLN E 13 " --> pdb=" O GLN E 9 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA E 14 " --> pdb=" O VAL E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 63 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 101 through 123 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 11 Processing helix chain 'F' and resid 42 through 45 Processing helix chain 'F' and resid 47 through 62 removed outlier: 3.962A pdb=" N THR F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU F 55 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS F 62 " --> pdb=" O ASP F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 120 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) Processing helix chain 'G' and resid 38 through 52 removed outlier: 4.394A pdb=" N GLY G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 13 Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 43 through 52 removed outlier: 3.794A pdb=" N ALA H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 28 Processing helix chain 'I' and resid 34 through 37 Processing helix chain 'I' and resid 67 through 75 Processing helix chain 'I' and resid 78 through 81 No H-bonds generated for 'chain 'I' and resid 78 through 81' Processing helix chain 'I' and resid 99 through 116 Processing helix chain 'I' and resid 129 through 131 No H-bonds generated for 'chain 'I' and resid 129 through 131' Processing helix chain 'I' and resid 137 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.627A pdb=" N ALA I 172 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP I 173 " --> pdb=" O TYR I 170 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL I 177 " --> pdb=" O SER I 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR I 178 " --> pdb=" O SER I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 197 Processing helix chain 'I' and resid 228 through 244 Processing helix chain 'I' and resid 283 through 300 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) removed outlier: 4.465A pdb=" N LEU I 300 " --> pdb=" O HIS I 296 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 81 Processing helix chain 'J' and resid 151 through 167 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 185 through 203 removed outlier: 3.909A pdb=" N LYS J 188 " --> pdb=" O ASP J 185 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR J 191 " --> pdb=" O LYS J 188 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE J 195 " --> pdb=" O GLN J 192 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU J 203 " --> pdb=" O ASN J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 235 removed outlier: 3.898A pdb=" N LYS J 235 " --> pdb=" O LYS J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 254 Processing helix chain 'J' and resid 279 through 299 Processing helix chain 'J' and resid 345 through 367 removed outlier: 3.543A pdb=" N ARG J 348 " --> pdb=" O SER J 345 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLY J 350 " --> pdb=" O GLU J 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 64 Processing helix chain 'K' and resid 68 through 71 Processing helix chain 'K' and resid 78 through 98 Processing helix chain 'K' and resid 116 through 119 No H-bonds generated for 'chain 'K' and resid 116 through 119' Processing helix chain 'K' and resid 126 through 145 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 4 through 14 removed outlier: 4.252A pdb=" N ALA L 14 " --> pdb=" O VAL L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 63 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 101 through 123 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 42 through 45 Processing helix chain 'M' and resid 47 through 62 removed outlier: 4.433A pdb=" N THR M 52 " --> pdb=" O GLY M 48 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE M 53 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA M 54 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU M 55 " --> pdb=" O SER M 51 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 116 Proline residue: M 112 - end of helix Processing helix chain 'M' and resid 118 through 121 No H-bonds generated for 'chain 'M' and resid 118 through 121' Processing helix chain 'N' and resid 6 through 9 No H-bonds generated for 'chain 'N' and resid 6 through 9' Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 41 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 3 through 13 Processing helix chain 'O' and resid 43 through 55 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) removed outlier: 4.028A pdb=" N LEU O 55 " --> pdb=" O GLN O 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 40 Processing helix chain 'P' and resid 81 through 100 Processing sheet with id= A, first strand: chain 'A' and resid 118 through 123 removed outlier: 7.891A pdb=" N ARG A 145 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL A 60 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A 147 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU A 62 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS A 149 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU A 64 " --> pdb=" O HIS A 149 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN A 151 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 241 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N TYR A 194 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 243 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 163 through 166 Processing sheet with id= C, 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= D, first strand: chain 'A' and resid 1070 through 1076 removed outlier: 6.636A pdb=" N ALA A1087 " --> pdb=" O THR A1071 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET A1073 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A1085 " --> pdb=" O MET A1073 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TYR A1075 " --> pdb=" O LEU A1083 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A1083 " --> pdb=" O TYR A1075 " (cutoff:3.500A) 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= E, 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= F, first strand: chain 'A' and resid 1169 through 1175 removed outlier: 6.466A pdb=" N GLY A1184 " --> pdb=" O THR A1170 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A1172 " --> pdb=" O VAL A1182 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A1182 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N CYS A1174 " --> pdb=" O LEU A1180 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU A1180 " --> pdb=" O CYS A1174 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A1205 " --> pdb=" O VAL A1192 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1227 through 1229 Processing sheet with id= H, first strand: chain 'A' and resid 1258 through 1261 removed outlier: 3.792A pdb=" N ALA A1258 " --> pdb=" O GLY A1271 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A1277 " --> pdb=" O ILE A1290 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A1288 " --> pdb=" O ILE A1279 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN A1281 " --> pdb=" O LEU A1286 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A1286 " --> pdb=" O ASN A1281 " (cutoff:3.500A) Processing sheet with id= I, 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) Processing sheet with id= J, first strand: chain 'B' and resid 157 through 161 removed outlier: 6.833A pdb=" N ILE B 122 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE B 160 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N CYS B 124 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 58 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ARG B 51 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 60 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N HIS B 49 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP B 62 " --> pdb=" O HIS B 47 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N HIS B 47 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 251 through 255 Processing sheet with id= L, first strand: chain 'C' and resid 110 through 114 removed outlier: 8.113A pdb=" N GLN C 113 " --> pdb=" O PRO C 62 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 64 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA C 139 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N MET C 67 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C 141 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN C 172 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N TYR C 142 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU C 174 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE C 144 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE C 176 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 258 through 263 Processing sheet with id= N, first strand: chain 'E' and resid 71 through 76 removed outlier: 3.516A pdb=" N GLY E 79 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER E 21 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 70 through 74 Processing sheet with id= P, 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) Processing sheet with id= Q, first strand: chain 'H' and resid 65 through 68 removed outlier: 4.829A pdb=" N ASN H 73 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 121 through 127 Processing sheet with id= S, first strand: chain 'I' and resid 213 through 218 removed outlier: 6.909A pdb=" N LEU I 205 " --> pdb=" O ILE I 214 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N HIS I 216 " --> pdb=" O VAL I 203 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL I 203 " --> pdb=" O HIS I 216 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR I 270 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL I 272 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE I 265 " --> pdb=" O VAL I 272 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL I 274 " --> pdb=" O ILE I 263 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE I 263 " --> pdb=" O VAL I 274 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N MET I 276 " --> pdb=" O ALA I 261 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ALA I 261 " --> pdb=" O MET I 276 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 111 through 114 removed outlier: 6.520A pdb=" N ASN J 172 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TYR J 142 " --> pdb=" O ASN J 172 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU J 174 " --> pdb=" O TYR J 142 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE J 144 " --> pdb=" O GLU J 174 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE J 176 " --> pdb=" O ILE J 144 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 258 through 263 removed outlier: 3.733A pdb=" N THR J 324 " --> pdb=" O LEU J 320 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 72 through 76 removed outlier: 3.719A pdb=" N GLY L 79 " --> pdb=" O CYS L 76 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS L 92 " --> pdb=" O LEU L 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'M' and resid 70 through 74 removed outlier: 3.857A pdb=" N VAL M 90 " --> pdb=" O PHE M 83 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 66 through 69 removed outlier: 3.559A pdb=" N VAL N 68 " --> pdb=" O LEU N 75 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR N 74 " --> pdb=" O ARG N 89 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 75 through 78 removed outlier: 3.713A pdb=" N GLY O 32 " --> pdb=" O CYS O 23 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3264 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: 19.25 Time building geometry restraints manager: 35.31 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: 27080 1.03 - 1.23: 104 1.23 - 1.42: 11496 1.42 - 1.62: 15991 1.62 - 1.81: 247 Bond restraints: 54918 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 54913 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.58: 489 105.58 - 113.28: 65248 113.28 - 120.97: 21571 120.97 - 128.67: 11669 128.67 - 136.37: 258 Bond angle restraints: 99235 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 99230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.00: 24750 33.00 - 65.99: 463 65.99 - 98.99: 38 98.99 - 131.99: 1 131.99 - 164.99: 3 Dihedral angle restraints: 25255 sinusoidal: 13569 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 25252 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: 8069 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 8066 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 5454 2.23 - 2.83: 124251 2.83 - 3.42: 148908 3.42 - 4.01: 207748 4.01 - 4.60: 317122 Nonbonded interactions: 803483 Sorted by model distance: nonbonded pdb=" OD1 ASP C 202 " pdb="HH12 ARG K 86 " model vdw 1.644 1.850 nonbonded pdb=" OE1 GLN I 133 " pdb=" H GLN I 133 " model vdw 1.650 1.850 nonbonded pdb="HH21 ARG J 70 " pdb=" O1B GDP J 401 " model vdw 1.654 1.850 nonbonded pdb=" O TRP A 325 " pdb="HH22 ARG A 330 " model vdw 1.667 1.850 nonbonded pdb=" O ASP A 568 " pdb="HH11 ARG A 574 " model vdw 1.667 1.850 ... (remaining 803478 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.260 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: 0.630 Extract box with map and model: 8.570 Check model and map are aligned: 0.610 Set scattering table: 0.350 Process input model: 133.210 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.830 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 533 time to evaluate : 3.153 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 outliers start: 0 outliers final: 0 residues processed: 533 average time/residue: 2.6726 time to fit residues: 1651.8045 Evaluate side-chains 419 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 3.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0622 ------------------------------------------------------------------------------- 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: 4.9990 chunk 253 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 304 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27771 Z= 0.293 Angle : 0.575 7.982 37619 Z= 0.299 Chirality : 0.043 0.163 4288 Planarity : 0.005 0.073 4805 Dihedral : 7.377 167.282 3731 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.16 % Allowed : 8.74 % Favored : 90.10 % 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: 0.16 (0.15), residues: 3361 helix: 1.26 (0.14), residues: 1432 sheet: -0.77 (0.21), residues: 609 loop : -0.65 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 585 HIS 0.007 0.001 HIS G 73 PHE 0.016 0.002 PHE I 238 TYR 0.014 0.001 TYR D 140 ARG 0.010 0.001 ARG D 86 *********************** 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 479 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 444 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 459 average time/residue: 2.6348 time to fit residues: 1428.6824 Evaluate side-chains 439 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 420 time to evaluate : 3.158 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 11 residues processed: 10 average time/residue: 1.1267 time to fit residues: 19.9716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 253 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 304 optimal weight: 0.7980 chunk 329 optimal weight: 5.9990 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: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN L 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27771 Z= 0.280 Angle : 0.556 7.603 37619 Z= 0.287 Chirality : 0.042 0.156 4288 Planarity : 0.004 0.069 4805 Dihedral : 7.356 166.089 3731 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.53 % Allowed : 11.10 % Favored : 87.37 % 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: 0.09 (0.15), residues: 3361 helix: 1.20 (0.14), residues: 1437 sheet: -0.92 (0.20), residues: 626 loop : -0.62 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 585 HIS 0.007 0.001 HIS G 73 PHE 0.017 0.001 PHE B 266 TYR 0.014 0.001 TYR L 94 ARG 0.008 0.000 ARG A1066 *********************** 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 486 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 440 time to evaluate : 3.257 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 outliers start: 46 outliers final: 32 residues processed: 460 average time/residue: 2.5838 time to fit residues: 1389.0673 Evaluate side-chains 452 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 420 time to evaluate : 3.197 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 18 residues processed: 17 average time/residue: 1.2841 time to fit residues: 33.0888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 158 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 204 optimal weight: 30.0000 chunk 305 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 289 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN J 113 GLN J 197 GLN L 62 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 27771 Z= 0.243 Angle : 0.540 6.933 37619 Z= 0.278 Chirality : 0.042 0.154 4288 Planarity : 0.004 0.083 4805 Dihedral : 7.295 165.624 3731 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.43 % Allowed : 11.96 % Favored : 86.61 % 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: 0.12 (0.15), residues: 3361 helix: 1.27 (0.14), residues: 1439 sheet: -0.94 (0.20), residues: 624 loop : -0.63 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 576 HIS 0.006 0.001 HIS G 73 PHE 0.013 0.001 PHE B 266 TYR 0.013 0.001 TYR L 94 ARG 0.008 0.000 ARG D 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 470 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 427 time to evaluate : 3.194 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 outliers start: 43 outliers final: 25 residues processed: 449 average time/residue: 2.5785 time to fit residues: 1358.7046 Evaluate side-chains 436 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 411 time to evaluate : 3.212 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 18 residues processed: 10 average time/residue: 1.2595 time to fit residues: 20.9880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 4 optimal weight: 3.9990 chunk 241 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 253 ASN L 62 GLN N 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 27771 Z= 0.310 Angle : 0.562 8.695 37619 Z= 0.290 Chirality : 0.043 0.157 4288 Planarity : 0.005 0.077 4805 Dihedral : 7.370 166.320 3731 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.63 % Allowed : 13.33 % Favored : 85.04 % 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: 0.01 (0.15), residues: 3361 helix: 1.18 (0.14), residues: 1439 sheet: -1.07 (0.20), residues: 638 loop : -0.63 (0.19), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 576 HIS 0.006 0.001 HIS G 73 PHE 0.017 0.002 PHE B 266 TYR 0.016 0.001 TYR L 94 ARG 0.014 0.001 ARG K 86 *********************** 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 472 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 423 time to evaluate : 3.205 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 outliers start: 49 outliers final: 26 residues processed: 449 average time/residue: 2.5910 time to fit residues: 1360.0979 Evaluate side-chains 439 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 413 time to evaluate : 3.195 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 16 residues processed: 11 average time/residue: 1.4159 time to fit residues: 24.3632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 324 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN L 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27771 Z= 0.317 Angle : 0.572 8.452 37619 Z= 0.295 Chirality : 0.043 0.160 4288 Planarity : 0.005 0.084 4805 Dihedral : 7.426 167.209 3731 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.86 % Allowed : 13.96 % Favored : 84.18 % 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: -0.03 (0.15), residues: 3361 helix: 1.13 (0.14), residues: 1439 sheet: -1.10 (0.20), residues: 636 loop : -0.63 (0.19), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 576 HIS 0.005 0.001 HIS G 73 PHE 0.028 0.002 PHE I 211 TYR 0.017 0.001 TYR L 94 ARG 0.020 0.001 ARG D 134 *********************** 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 474 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 418 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 37 residues processed: 450 average time/residue: 2.5018 time to fit residues: 1324.3212 Evaluate side-chains 445 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 408 time to evaluate : 3.182 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 23 residues processed: 15 average time/residue: 1.2382 time to fit residues: 29.0291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 322 optimal weight: 3.9990 chunk 202 optimal weight: 30.0000 chunk 196 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN A 956 GLN J 248 ASN L 13 GLN L 62 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27771 Z= 0.278 Angle : 0.561 7.642 37619 Z= 0.288 Chirality : 0.042 0.158 4288 Planarity : 0.005 0.102 4805 Dihedral : 7.408 167.499 3731 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.36 % Allowed : 14.99 % Favored : 83.65 % 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: 0.01 (0.15), residues: 3361 helix: 1.17 (0.14), residues: 1440 sheet: -1.12 (0.19), residues: 638 loop : -0.60 (0.19), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 576 HIS 0.005 0.001 HIS G 73 PHE 0.015 0.001 PHE B 238 TYR 0.019 0.001 TYR I 73 ARG 0.019 0.001 ARG J 70 *********************** REFINEMENT MACRO_CYCLE 7 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 453 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 412 time to evaluate : 3.294 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 outliers start: 41 outliers final: 31 residues processed: 437 average time/residue: 2.5690 time to fit residues: 1314.8113 Evaluate side-chains 434 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 403 time to evaluate : 3.176 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 23 residues processed: 10 average time/residue: 1.2181 time to fit residues: 20.4950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 199 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 205 optimal weight: 10.0000 chunk 219 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN L 62 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27771 Z= 0.261 Angle : 0.556 7.670 37619 Z= 0.286 Chirality : 0.042 0.160 4288 Planarity : 0.005 0.109 4805 Dihedral : 7.369 167.360 3731 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.46 % Allowed : 15.15 % Favored : 83.38 % 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: 0.04 (0.15), residues: 3361 helix: 1.21 (0.14), residues: 1440 sheet: -1.15 (0.19), residues: 642 loop : -0.59 (0.19), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 576 HIS 0.005 0.001 HIS G 73 PHE 0.014 0.001 PHE B 238 TYR 0.019 0.001 TYR I 73 ARG 0.015 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 8 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 454 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 410 time to evaluate : 3.294 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 outliers start: 44 outliers final: 36 residues processed: 436 average time/residue: 2.5371 time to fit residues: 1297.8474 Evaluate side-chains 439 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 403 time to evaluate : 3.185 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 24 residues processed: 13 average time/residue: 1.2758 time to fit residues: 26.1343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 293 optimal weight: 1.9990 chunk 309 optimal weight: 5.9990 chunk 282 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 299 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27771 Z= 0.286 Angle : 0.569 8.205 37619 Z= 0.292 Chirality : 0.042 0.162 4288 Planarity : 0.005 0.088 4805 Dihedral : 7.374 167.797 3731 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.96 % Allowed : 15.89 % Favored : 83.15 % 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: 0.01 (0.15), residues: 3361 helix: 1.19 (0.14), residues: 1443 sheet: -1.15 (0.19), residues: 642 loop : -0.61 (0.19), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 115 HIS 0.005 0.001 HIS G 73 PHE 0.015 0.001 PHE B 238 TYR 0.019 0.001 TYR I 73 ARG 0.012 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 9 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 430 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 401 time to evaluate : 3.948 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 outliers start: 29 outliers final: 27 residues processed: 425 average time/residue: 2.5320 time to fit residues: 1270.0879 Evaluate side-chains 422 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 395 time to evaluate : 3.189 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 5 average time/residue: 1.1855 time to fit residues: 12.2265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 0.8980 chunk 318 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 333 optimal weight: 6.9990 chunk 307 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 205 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27771 Z= 0.258 Angle : 0.562 8.028 37619 Z= 0.288 Chirality : 0.042 0.161 4288 Planarity : 0.005 0.089 4805 Dihedral : 7.343 167.515 3731 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.03 % Allowed : 15.99 % Favored : 82.98 % 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: 0.05 (0.15), residues: 3361 helix: 1.25 (0.14), residues: 1444 sheet: -1.16 (0.19), residues: 642 loop : -0.61 (0.19), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 115 HIS 0.005 0.001 HIS G 73 PHE 0.014 0.001 PHE B 238 TYR 0.020 0.001 TYR I 73 ARG 0.013 0.001 ARG A1012 ********************** REFINEMENT MACRO_CYCLE 10 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 434 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 403 time to evaluate : 3.212 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 outliers start: 31 outliers final: 26 residues processed: 427 average time/residue: 2.6342 time to fit residues: 1330.8993 Evaluate side-chains 425 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 399 time to evaluate : 3.473 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 5 average time/residue: 1.2974 time to fit residues: 13.0737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 211 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 245 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 266 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 273 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 GLN L 62 GLN ** N 90 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 = 0.3765 r_free = 0.3765 target = 0.154849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113264 restraints weight = 95173.119| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.04 r_work: 0.3012 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27771 Z= 0.212 Angle : 0.555 11.588 37619 Z= 0.282 Chirality : 0.041 0.160 4288 Planarity : 0.004 0.085 4805 Dihedral : 7.252 166.197 3731 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.93 % Allowed : 16.09 % Favored : 82.98 % 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: 1.35 (0.14), residues: 1444 sheet: -1.11 (0.19), residues: 642 loop : -0.59 (0.19), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 115 HIS 0.006 0.001 HIS O 79 PHE 0.013 0.001 PHE B 238 TYR 0.022 0.001 TYR I 73 ARG 0.012 0.000 ARG F 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19440.04 seconds wall clock time: 333 minutes 55.10 seconds (20035.10 seconds total)