Starting phenix.real_space_refine on Wed Jan 17 19:48:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/01_2024/7ux2_26846_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/01_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_26846/01_2024/7ux2_26846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/01_2024/7ux2_26846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/01_2024/7ux2_26846_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux2_26846/01_2024/7ux2_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 17.70, per 1000 atoms: 0.33 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: 34.79 Conformation dependent library (CDL) restraints added in 4.1 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: 6.38 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: 18.48 Time building geometry restraints manager: 36.65 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: 24946 33.00 - 65.99: 463 65.99 - 98.99: 38 98.99 - 131.99: 1 131.99 - 164.99: 3 Dihedral angle restraints: 25451 sinusoidal: 13765 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 25448 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: 1.390 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: 0.610 Extract box with map and model: 8.830 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 133.980 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.290 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:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.090 ------------------------------------------------------------------------------- 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 : 3.333 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: 2.6652 time to fit residues: 1644.6201 Evaluate side-chains 420 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 3.293 ------------------------------------------------------------------------------- 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: 0.7756 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27771 Z= 0.293 Angle : 0.576 8.017 37619 Z= 0.299 Chirality : 0.043 0.162 4288 Planarity : 0.005 0.072 4805 Dihedral : 7.375 167.135 3731 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.16 % Allowed : 8.71 % Favored : 90.13 % 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: 0.15 (0.15), residues: 3361 helix: 1.25 (0.14), residues: 1432 sheet: -0.76 (0.21), residues: 609 loop : -0.65 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 585 HIS 0.007 0.001 HIS G 73 PHE 0.016 0.001 PHE B 266 TYR 0.014 0.001 TYR D 140 ARG 0.009 0.001 ARG J 70 *********************** 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 481 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 446 time to evaluate : 3.405 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 534 MET cc_start: 0.8541 (mtm) cc_final: 0.8298 (mtm) REVERT: A 1051 TRP cc_start: 0.8337 (p-90) cc_final: 0.8081 (p-90) REVERT: B 201 ASP cc_start: 0.8013 (t70) cc_final: 0.7669 (t0) REVERT: H 22 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7612 (pt) outliers start: 35 outliers final: 20 residues processed: 461 average time/residue: 2.6670 time to fit residues: 1455.1680 Evaluate side-chains 441 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 420 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 90 THR 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 22 LEU 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 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: 0.2980 chunk 253 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 304 optimal weight: 0.6980 chunk 329 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.7764 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27771 Z= 0.259 Angle : 0.547 7.018 37619 Z= 0.282 Chirality : 0.042 0.156 4288 Planarity : 0.004 0.065 4805 Dihedral : 7.318 165.702 3731 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.36 % Allowed : 11.07 % Favored : 87.57 % 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: 0.11 (0.15), residues: 3361 helix: 1.24 (0.14), residues: 1435 sheet: -0.90 (0.20), residues: 618 loop : -0.63 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 585 HIS 0.006 0.001 HIS G 73 PHE 0.014 0.001 PHE B 238 TYR 0.014 0.001 TYR D 140 ARG 0.009 0.000 ARG M 46 *********************** 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 480 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 439 time to evaluate : 3.306 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: 0.7237 (mpp-170) cc_final: 0.6987 (mpp-170) REVERT: B 201 ASP cc_start: 0.8037 (t70) cc_final: 0.7680 (t0) REVERT: C 63 ARG cc_start: 0.7707 (tpt-90) cc_final: 0.7440 (mmm160) REVERT: E 64 PHE cc_start: 0.5783 (t80) cc_final: 0.5549 (t80) REVERT: H 22 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7591 (pt) REVERT: J 145 ASP cc_start: 0.7114 (p0) cc_final: 0.6831 (t0) REVERT: J 198 ARG cc_start: 0.6950 (ttm170) cc_final: 0.6522 (ttm170) REVERT: N 64 LYS cc_start: 0.8402 (pttt) cc_final: 0.8179 (pttp) outliers start: 41 outliers final: 25 residues processed: 455 average time/residue: 2.5892 time to fit residues: 1373.8908 Evaluate side-chains 443 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 417 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 137 THR 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 F residue 117 LEU Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 235 ILE 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 L residue 28 GLU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 11 LYS 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: 2.9990 chunk 229 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 204 optimal weight: 30.0000 chunk 305 optimal weight: 0.9990 chunk 323 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 289 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 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 443 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 ASN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27771 Z= 0.294 Angle : 0.556 8.401 37619 Z= 0.286 Chirality : 0.042 0.156 4288 Planarity : 0.004 0.091 4805 Dihedral : 7.347 166.281 3731 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.69 % Allowed : 11.70 % 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: 0.07 (0.15), residues: 3361 helix: 1.21 (0.14), residues: 1439 sheet: -1.01 (0.20), residues: 632 loop : -0.61 (0.19), residues: 1290 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 0.001 PHE B 266 TYR 0.015 0.001 TYR L 94 ARG 0.012 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 486 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 435 time to evaluate : 3.388 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 32 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7566 (mptt) REVERT: A 306 ARG cc_start: 0.7277 (mpp-170) cc_final: 0.6941 (mpp-170) REVERT: A 565 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: A 1239 PHE cc_start: 0.8490 (m-80) cc_final: 0.8219 (m-80) REVERT: B 139 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7756 (pt) REVERT: B 201 ASP cc_start: 0.8119 (t70) cc_final: 0.7750 (t0) REVERT: C 63 ARG cc_start: 0.7759 (tpt-90) cc_final: 0.7499 (mmm160) REVERT: C 174 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: D 68 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7922 (t) REVERT: D 147 ARG cc_start: 0.8055 (ppt170) cc_final: 0.7774 (ppt90) REVERT: H 22 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7630 (pt) REVERT: I 51 ARG cc_start: 0.7497 (mmm160) cc_final: 0.7279 (mmm160) REVERT: J 145 ASP cc_start: 0.7125 (p0) cc_final: 0.6881 (t0) REVERT: K 82 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7915 (mtt) REVERT: N 64 LYS cc_start: 0.8400 (pttt) cc_final: 0.8179 (pttp) outliers start: 51 outliers final: 29 residues processed: 458 average time/residue: 2.5402 time to fit residues: 1362.8012 Evaluate side-chains 450 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 414 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain B residue 139 LEU 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 174 GLU 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 148 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain H residue 22 LEU 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 I residue 235 ILE 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 324 THR Chi-restraints excluded: chain K residue 82 MET 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 11 LYS Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 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: 1.9990 chunk 290 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 27771 Z= 0.308 Angle : 0.563 8.343 37619 Z= 0.291 Chirality : 0.043 0.157 4288 Planarity : 0.004 0.077 4805 Dihedral : 7.397 166.591 3731 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.99 % Allowed : 13.09 % Favored : 84.91 % 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: 0.00 (0.15), residues: 3361 helix: 1.17 (0.14), residues: 1439 sheet: -1.08 (0.20), residues: 636 loop : -0.63 (0.19), residues: 1286 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 0.018 0.002 PHE B 266 TYR 0.017 0.001 TYR L 94 ARG 0.009 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 485 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 425 time to evaluate : 3.462 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: A 100 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: A 306 ARG cc_start: 0.7300 (mpp-170) cc_final: 0.6947 (mpp-170) REVERT: A 565 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: A 1051 TRP cc_start: 0.8354 (p-90) cc_final: 0.8100 (p-90) REVERT: A 1139 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7487 (mpt) REVERT: A 1239 PHE cc_start: 0.8453 (m-80) cc_final: 0.8252 (m-80) REVERT: B 139 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7540 (pt) REVERT: B 201 ASP cc_start: 0.8238 (t70) cc_final: 0.7856 (t0) REVERT: C 63 ARG cc_start: 0.7788 (tpt-90) cc_final: 0.7541 (mmm160) REVERT: C 174 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: D 145 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7123 (mp10) REVERT: D 147 ARG cc_start: 0.8044 (ppt170) cc_final: 0.7754 (ppt90) REVERT: H 22 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7646 (pt) REVERT: I 51 ARG cc_start: 0.7505 (mmm160) cc_final: 0.7304 (mmm160) REVERT: J 145 ASP cc_start: 0.7148 (p0) cc_final: 0.6921 (t0) REVERT: N 64 LYS cc_start: 0.8396 (pttt) cc_final: 0.8141 (pttp) REVERT: P 17 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7007 (mm110) REVERT: P 34 MET cc_start: 0.7644 (mmm) cc_final: 0.7416 (tpp) outliers start: 60 outliers final: 38 residues processed: 455 average time/residue: 2.5138 time to fit residues: 1337.0450 Evaluate side-chains 462 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 416 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1229 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 132 MET 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 90 THR Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 235 ILE 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 324 THR 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 M residue 77 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 50 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 190 optimal weight: 0.0770 chunk 79 optimal weight: 0.6980 chunk 324 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 112 ASN A 443 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN J 197 GLN L 13 GLN L 62 GLN N 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27771 Z= 0.180 Angle : 0.527 6.760 37619 Z= 0.271 Chirality : 0.041 0.155 4288 Planarity : 0.004 0.072 4805 Dihedral : 7.241 165.172 3731 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.60 % Allowed : 14.09 % Favored : 84.31 % 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: 0.18 (0.15), residues: 3361 helix: 1.36 (0.14), residues: 1442 sheet: -1.04 (0.20), residues: 634 loop : -0.57 (0.19), residues: 1285 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 0.012 0.001 PHE I 238 TYR 0.014 0.001 TYR I 73 ARG 0.013 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 470 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 422 time to evaluate : 3.304 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 100 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: A 306 ARG cc_start: 0.7313 (mpp-170) cc_final: 0.6946 (mpp-170) REVERT: A 411 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: A 565 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: A 1139 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7523 (mpt) REVERT: A 1235 ASP cc_start: 0.8211 (p0) cc_final: 0.7856 (p0) REVERT: A 1239 PHE cc_start: 0.8464 (m-80) cc_final: 0.8257 (m-80) REVERT: B 139 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7502 (pt) REVERT: B 201 ASP cc_start: 0.8247 (t70) cc_final: 0.7885 (t0) REVERT: C 63 ARG cc_start: 0.7706 (tpt-90) cc_final: 0.7476 (mmm160) REVERT: C 151 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6796 (ttp) REVERT: C 174 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: C 327 TYR cc_start: 0.8687 (t80) cc_final: 0.8468 (t80) REVERT: D 58 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8485 (mp) REVERT: D 68 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.8039 (t) REVERT: D 147 ARG cc_start: 0.8038 (ppt170) cc_final: 0.7750 (ppt90) REVERT: H 22 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7610 (pt) REVERT: N 64 LYS cc_start: 0.8396 (pttt) cc_final: 0.8136 (pttp) REVERT: P 34 MET cc_start: 0.7596 (mmm) cc_final: 0.7347 (tpp) outliers start: 48 outliers final: 29 residues processed: 444 average time/residue: 2.5485 time to fit residues: 1328.7718 Evaluate side-chains 446 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 407 time to evaluate : 3.518 ------------------------------------------------------------------------------- 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 422 MET Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 139 LEU 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 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 129 LEU 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 117 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 235 ILE 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 30 VAL Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain P residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 322 optimal weight: 0.7980 chunk 202 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27771 Z= 0.347 Angle : 0.579 9.867 37619 Z= 0.298 Chirality : 0.043 0.158 4288 Planarity : 0.005 0.098 4805 Dihedral : 7.412 167.462 3731 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.96 % Allowed : 14.29 % Favored : 83.75 % 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: -0.02 (0.15), residues: 3361 helix: 1.16 (0.14), residues: 1439 sheet: -1.13 (0.19), residues: 642 loop : -0.62 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 576 HIS 0.005 0.001 HIS G 73 PHE 0.019 0.002 PHE B 266 TYR 0.019 0.001 TYR I 73 ARG 0.020 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 472 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 413 time to evaluate : 3.385 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: A 32 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7646 (mptt) REVERT: A 100 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: A 304 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6896 (m-30) REVERT: A 306 ARG cc_start: 0.7316 (mpp-170) cc_final: 0.6940 (mpp-170) REVERT: A 411 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: A 565 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8158 (mt0) REVERT: A 1051 TRP cc_start: 0.8387 (p-90) cc_final: 0.8163 (p-90) REVERT: A 1066 ARG cc_start: 0.7486 (ttp-110) cc_final: 0.7202 (ttp80) REVERT: A 1139 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7501 (mpt) REVERT: A 1239 PHE cc_start: 0.8488 (m-80) cc_final: 0.8228 (m-80) REVERT: B 139 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7521 (pt) REVERT: B 201 ASP cc_start: 0.8277 (t70) cc_final: 0.7902 (t0) REVERT: C 63 ARG cc_start: 0.7761 (tpt-90) cc_final: 0.7545 (mmm160) REVERT: C 151 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6850 (ttp) REVERT: C 174 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: C 327 TYR cc_start: 0.8731 (t80) cc_final: 0.8514 (t80) REVERT: D 58 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8483 (mp) REVERT: D 145 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: D 147 ARG cc_start: 0.8048 (ppt170) cc_final: 0.7752 (ppt90) REVERT: K 82 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.7920 (mtt) REVERT: N 64 LYS cc_start: 0.8402 (pttt) cc_final: 0.8140 (pttp) REVERT: O 19 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7511 (p) REVERT: P 34 MET cc_start: 0.7585 (mmm) cc_final: 0.7343 (tpp) outliers start: 59 outliers final: 34 residues processed: 441 average time/residue: 2.6147 time to fit residues: 1355.8287 Evaluate side-chains 456 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 409 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS 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 304 ASP Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1229 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 265 ILE 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 145 GLN Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 84 THR 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 117 LEU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 266 SER Chi-restraints excluded: chain K residue 82 MET 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 19 VAL Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain P residue 50 THR 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: 1.9990 chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 205 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27771 Z= 0.249 Angle : 0.552 7.412 37619 Z= 0.283 Chirality : 0.042 0.162 4288 Planarity : 0.005 0.113 4805 Dihedral : 7.356 166.776 3731 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.76 % Allowed : 14.82 % Favored : 83.42 % 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: 0.07 (0.15), residues: 3361 helix: 1.24 (0.14), residues: 1443 sheet: -1.07 (0.20), residues: 632 loop : -0.62 (0.19), residues: 1286 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 0.018 0.001 TYR I 73 ARG 0.016 0.001 ARG D 134 *********************** 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 467 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 414 time to evaluate : 3.520 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 32 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7564 (mptt) REVERT: A 100 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: A 306 ARG cc_start: 0.7286 (mpp-170) cc_final: 0.6908 (mpp-170) REVERT: A 411 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: A 565 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: A 658 MET cc_start: 0.8962 (ptt) cc_final: 0.8730 (ptt) REVERT: A 1066 ARG cc_start: 0.7507 (ttp-110) cc_final: 0.7223 (ttp80) REVERT: A 1139 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7515 (mpt) REVERT: A 1239 PHE cc_start: 0.8507 (m-80) cc_final: 0.8284 (m-80) REVERT: B 201 ASP cc_start: 0.8281 (t70) cc_final: 0.7893 (t0) REVERT: C 63 ARG cc_start: 0.7735 (tpt-90) cc_final: 0.7526 (mmm160) REVERT: C 151 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.6854 (ttp) REVERT: C 174 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: D 58 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8498 (mp) REVERT: N 64 LYS cc_start: 0.8395 (pttt) cc_final: 0.8133 (pttp) REVERT: O 19 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7541 (p) outliers start: 53 outliers final: 36 residues processed: 444 average time/residue: 2.5225 time to fit residues: 1310.4525 Evaluate side-chains 453 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 408 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS 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 422 MET Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 258 ASN 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 129 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 84 THR 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 117 LEU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 168 THR 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 341 LEU 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 O residue 19 VAL Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain P residue 50 THR 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: 0.7980 chunk 282 optimal weight: 2.9990 chunk 300 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 236 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 284 optimal weight: 0.0070 chunk 299 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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: 0.7765 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27771 Z= 0.176 Angle : 0.534 7.680 37619 Z= 0.273 Chirality : 0.041 0.160 4288 Planarity : 0.005 0.087 4805 Dihedral : 7.171 164.381 3731 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.46 % Allowed : 15.32 % Favored : 83.22 % 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: 1.42 (0.14), residues: 1444 sheet: -1.01 (0.20), residues: 635 loop : -0.57 (0.19), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 115 HIS 0.005 0.001 HIS O 79 PHE 0.011 0.001 PHE B 206 TYR 0.018 0.001 TYR I 73 ARG 0.014 0.000 ARG A1012 *********************** 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 454 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 410 time to evaluate : 4.218 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 100 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: A 306 ARG cc_start: 0.7280 (mpp-170) cc_final: 0.6926 (mpp-170) REVERT: A 411 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: A 658 MET cc_start: 0.8945 (ptt) cc_final: 0.8731 (ptt) REVERT: A 1043 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7921 (tttt) REVERT: A 1066 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7200 (ttp80) REVERT: A 1139 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7546 (mpt) REVERT: A 1239 PHE cc_start: 0.8490 (m-80) cc_final: 0.8283 (m-80) REVERT: B 201 ASP cc_start: 0.8253 (t70) cc_final: 0.7881 (t0) REVERT: C 63 ARG cc_start: 0.7720 (tpt-90) cc_final: 0.7498 (mmm160) REVERT: C 151 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6869 (ttp) REVERT: D 58 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8519 (mp) REVERT: D 147 ARG cc_start: 0.8027 (ppt170) cc_final: 0.7725 (ppt90) REVERT: N 64 LYS cc_start: 0.8389 (pttt) cc_final: 0.8128 (pttp) REVERT: O 19 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7545 (p) outliers start: 44 outliers final: 32 residues processed: 435 average time/residue: 2.6100 time to fit residues: 1335.9508 Evaluate side-chains 444 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 406 time to evaluate : 3.333 ------------------------------------------------------------------------------- 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 483 SER Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 MET 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 148 VAL Chi-restraints excluded: chain E residue 84 THR 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 F residue 117 LEU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain J residue 160 THR 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 19 VAL Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 0.7980 chunk 318 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 333 optimal weight: 5.9990 chunk 307 optimal weight: 0.9990 chunk 265 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2079 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= 0.208 Angle : 0.541 8.110 37619 Z= 0.276 Chirality : 0.041 0.166 4288 Planarity : 0.004 0.088 4805 Dihedral : 7.129 163.907 3731 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.23 % Allowed : 15.72 % Favored : 83.05 % Cbeta Deviations : 0.03 % 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: 1.43 (0.14), residues: 1443 sheet: -0.94 (0.20), residues: 630 loop : -0.59 (0.19), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 115 HIS 0.005 0.001 HIS G 73 PHE 0.012 0.001 PHE I 238 TYR 0.021 0.001 TYR I 73 ARG 0.012 0.001 ARG J 70 ********************** 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 445 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 408 time to evaluate : 3.442 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 100 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: A 306 ARG cc_start: 0.7323 (mpp-170) cc_final: 0.6970 (mpp-170) REVERT: A 411 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: A 658 MET cc_start: 0.8968 (ptt) cc_final: 0.8755 (ptt) REVERT: A 1066 ARG cc_start: 0.7523 (ttp-110) cc_final: 0.7224 (ttp80) REVERT: A 1139 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7548 (mpt) REVERT: A 1239 PHE cc_start: 0.8483 (m-80) cc_final: 0.8279 (m-80) REVERT: B 201 ASP cc_start: 0.8225 (t70) cc_final: 0.7861 (t0) REVERT: C 63 ARG cc_start: 0.7726 (tpt-90) cc_final: 0.7504 (mmm160) REVERT: C 151 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6898 (ttp) REVERT: D 58 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8544 (mp) REVERT: D 147 ARG cc_start: 0.8046 (ppt170) cc_final: 0.7733 (ppt90) REVERT: N 64 LYS cc_start: 0.8396 (pttt) cc_final: 0.8140 (pttp) REVERT: O 19 VAL cc_start: 0.7942 (OUTLIER) cc_final: 0.7559 (p) outliers start: 37 outliers final: 32 residues processed: 428 average time/residue: 2.5426 time to fit residues: 1271.2515 Evaluate side-chains 442 residues out of total 3014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 404 time to evaluate : 3.328 ------------------------------------------------------------------------------- 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 422 MET Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 MET 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 148 VAL Chi-restraints excluded: chain E residue 84 THR 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 117 LEU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain J residue 160 THR 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 19 VAL Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 211 optimal weight: 7.9990 chunk 283 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 245 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 73 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 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 ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.156248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.114955 restraints weight = 95076.045| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.03 r_work: 0.3058 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2112 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= 0.207 Angle : 0.545 8.585 37619 Z= 0.277 Chirality : 0.041 0.157 4288 Planarity : 0.005 0.092 4805 Dihedral : 7.097 163.766 3731 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.33 % Allowed : 15.75 % Favored : 82.92 % Cbeta Deviations : 0.03 % 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: 0.27 (0.15), residues: 3361 helix: 1.45 (0.14), residues: 1442 sheet: -0.95 (0.20), residues: 634 loop : -0.58 (0.19), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 115 HIS 0.006 0.001 HIS O 79 PHE 0.012 0.001 PHE A 781 TYR 0.020 0.001 TYR I 73 ARG 0.016 0.000 ARG A1012 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19321.32 seconds wall clock time: 332 minutes 36.86 seconds (19956.86 seconds total)