Starting phenix.real_space_refine (version: dev) on Mon Feb 20 14:48:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmp_30766/02_2023/7dmp_30766.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmp_30766/02_2023/7dmp_30766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmp_30766/02_2023/7dmp_30766.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmp_30766/02_2023/7dmp_30766.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmp_30766/02_2023/7dmp_30766.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmp_30766/02_2023/7dmp_30766.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Process input model Symmetric amino acids flipped Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B GLU 369": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B ARG 438": "NH1" <-> "NH2" Residue "B GLU 528": "OE1" <-> "OE2" Residue "B GLU 643": "OE1" <-> "OE2" Residue "b GLU 316": "OE1" <-> "OE2" Residue "b GLU 362": "OE1" <-> "OE2" Residue "b GLU 420": "OE1" <-> "OE2" Residue "b ARG 422": "NH1" <-> "NH2" Residue "b ARG 438": "NH1" <-> "NH2" Residue "b GLU 528": "OE1" <-> "OE2" Residue "b PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 643": "OE1" <-> "OE2" Residue "b GLU 675": "OE1" <-> "OE2" Residue "b GLU 687": "OE1" <-> "OE2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a GLU 45": "OE1" <-> "OE2" Residue "a GLU 49": "OE1" <-> "OE2" Residue "a TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 200": "OE1" <-> "OE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 40": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "c GLU 11": "OE1" <-> "OE2" Residue "c ARG 37": "NH1" <-> "NH2" Residue "c ARG 40": "NH1" <-> "NH2" Residue "c ARG 43": "NH1" <-> "NH2" Residue "c GLU 65": "OE1" <-> "OE2" Residue "c ARG 71": "NH1" <-> "NH2" Residue "c GLU 81": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c GLU 110": "OE1" <-> "OE2" Residue "c ARG 139": "NH1" <-> "NH2" Residue "c ARG 156": "NH1" <-> "NH2" Residue "c ARG 171": "NH1" <-> "NH2" Residue "c ARG 191": "NH1" <-> "NH2" Residue "c GLU 267": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12308 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2704 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 31, 'TRANS': 304} Chain breaks: 4 Chain: "b" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2704 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 31, 'TRANS': 304} Chain breaks: 4 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1521 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "a" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1521 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "C" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1929 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 12, 'TRANS': 229} Chain breaks: 2 Chain: "c" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1929 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 12, 'TRANS': 229} Chain breaks: 2 Time building chain proxies: 7.28, per 1000 atoms: 0.59 Number of scatterers: 12308 At special positions: 0 Unit cell: (110.16, 84.66, 223.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 2314 8.00 N 2090 7.00 C 7866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 4.55 Conformation dependent library (CDL) restraints added in 1.9 seconds 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2780 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 16 sheets defined 17.1% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.720A pdb=" N GLU B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALA B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.652A pdb=" N TYR B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.576A pdb=" N ASP B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 492 removed outlier: 3.769A pdb=" N ARG B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 538 removed outlier: 3.551A pdb=" N LEU B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 removed outlier: 3.963A pdb=" N GLU B 598 " --> pdb=" O PRO B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 688 removed outlier: 3.542A pdb=" N GLU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing helix chain 'b' and resid 278 through 285 removed outlier: 3.551A pdb=" N THR b 285 " --> pdb=" O GLU b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 286 through 289 Processing helix chain 'b' and resid 314 through 325 Processing helix chain 'b' and resid 334 through 345 Processing helix chain 'b' and resid 479 through 494 removed outlier: 3.589A pdb=" N LEU b 483 " --> pdb=" O GLU b 479 " (cutoff:3.500A) Processing helix chain 'b' and resid 533 through 538 removed outlier: 3.647A pdb=" N SER b 538 " --> pdb=" O ASP b 534 " (cutoff:3.500A) Processing helix chain 'b' and resid 595 through 599 removed outlier: 4.077A pdb=" N GLU b 598 " --> pdb=" O PRO b 595 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP b 599 " --> pdb=" O ILE b 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 595 through 599' Processing helix chain 'b' and resid 683 through 690 removed outlier: 3.561A pdb=" N PHE b 690 " --> pdb=" O GLU b 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 24 through 39 removed outlier: 4.150A pdb=" N MET C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 removed outlier: 3.785A pdb=" N ALA C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 135 through 149 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.580A pdb=" N GLU C 180 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 181 " --> pdb=" O LEU C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'c' and resid 24 through 39 removed outlier: 3.504A pdb=" N LEU c 28 " --> pdb=" O ARG c 24 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET c 33 " --> pdb=" O LEU c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 64 through 68 removed outlier: 4.050A pdb=" N GLN c 67 " --> pdb=" O SER c 64 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU c 68 " --> pdb=" O GLU c 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 64 through 68' Processing helix chain 'c' and resid 89 through 96 removed outlier: 3.912A pdb=" N ILE c 96 " --> pdb=" O MET c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 136 through 151 Processing helix chain 'c' and resid 183 through 187 removed outlier: 3.627A pdb=" N SER c 186 " --> pdb=" O LYS c 183 " (cutoff:3.500A) Processing helix chain 'c' and resid 271 through 276 Processing sheet with id=AA1, first strand: chain 'B' and resid 441 through 442 removed outlier: 5.839A pdb=" N GLU B 369 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE B 354 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TRP B 355 " --> pdb=" O ASN B 644 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 637 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 623 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 496 through 498 Processing sheet with id=AA3, first strand: chain 'b' and resid 441 through 442 removed outlier: 3.614A pdb=" N PHE b 431 " --> pdb=" O ALA b 368 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU b 369 " --> pdb=" O PHE b 354 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N PHE b 354 " --> pdb=" O GLU b 369 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLU b 371 " --> pdb=" O CYS b 352 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS b 352 " --> pdb=" O GLU b 371 " (cutoff:3.500A) removed outlier: 15.264A pdb=" N PHE b 642 " --> pdb=" O ARG b 351 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N ARG b 353 " --> pdb=" O PHE b 642 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N ASN b 644 " --> pdb=" O ARG b 353 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TRP b 355 " --> pdb=" O ASN b 644 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR b 646 " --> pdb=" O TRP b 355 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA b 633 " --> pdb=" O SER b 627 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 497 through 498 Processing sheet with id=AA5, first strand: chain 'A' and resid 19 through 20 removed outlier: 5.854A pdb=" N GLN A 56 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 49 " --> pdb=" O HIS A 54 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS A 54 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLN A 79 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 72 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS A 77 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG A 89 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 104 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU A 91 " --> pdb=" O GLN A 102 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLN A 102 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU A 93 " --> pdb=" O HIS A 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 114 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 127 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU A 116 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 125 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 19 through 20 removed outlier: 5.854A pdb=" N GLN A 56 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 49 " --> pdb=" O HIS A 54 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS A 54 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLN A 79 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 72 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS A 77 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG A 89 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 104 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU A 91 " --> pdb=" O GLN A 102 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLN A 102 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU A 93 " --> pdb=" O HIS A 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 114 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 127 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU A 116 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 125 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU A 197 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 34 through 37 removed outlier: 3.574A pdb=" N SER a 47 " --> pdb=" O GLN a 56 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN a 56 " --> pdb=" O SER a 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU a 49 " --> pdb=" O HIS a 54 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS a 54 " --> pdb=" O GLU a 49 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN a 79 " --> pdb=" O ASP a 70 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL a 72 " --> pdb=" O HIS a 77 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS a 77 " --> pdb=" O VAL a 72 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLN a 102 " --> pdb=" O GLU a 93 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA a 95 " --> pdb=" O HIS a 100 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS a 100 " --> pdb=" O ALA a 95 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN a 125 " --> pdb=" O GLU a 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 34 through 37 removed outlier: 3.574A pdb=" N SER a 47 " --> pdb=" O GLN a 56 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN a 56 " --> pdb=" O SER a 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU a 49 " --> pdb=" O HIS a 54 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS a 54 " --> pdb=" O GLU a 49 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN a 79 " --> pdb=" O ASP a 70 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL a 72 " --> pdb=" O HIS a 77 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS a 77 " --> pdb=" O VAL a 72 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLN a 102 " --> pdb=" O GLU a 93 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA a 95 " --> pdb=" O HIS a 100 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS a 100 " --> pdb=" O ALA a 95 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN a 125 " --> pdb=" O GLU a 116 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N CYS a 180 " --> pdb=" O PHE a 176 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU a 181 " --> pdb=" O GLU a 198 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU a 198 " --> pdb=" O GLU a 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 163 through 164 Processing sheet with id=AB1, first strand: chain 'C' and resid 44 through 48 removed outlier: 6.670A pdb=" N ILE C 59 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 72 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR C 75 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 83 " --> pdb=" O TYR C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AB3, first strand: chain 'C' and resid 226 through 230 removed outlier: 5.109A pdb=" N LEU C 247 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 43 through 48 removed outlier: 5.442A pdb=" N VAL c 44 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU c 63 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE c 46 " --> pdb=" O GLN c 61 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN c 61 " --> pdb=" O PHE c 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 110 through 113 Processing sheet with id=AB6, first strand: chain 'c' and resid 153 through 154 Processing sheet with id=AB7, first strand: chain 'c' and resid 226 through 230 removed outlier: 4.815A pdb=" N LEU c 247 " --> pdb=" O SER c 241 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1203 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: 3.99 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3461 1.33 - 1.45: 2386 1.45 - 1.57: 6734 1.57 - 1.69: 1 1.69 - 1.81: 64 Bond restraints: 12646 Sorted by residual: bond pdb=" C ILE C 221 " pdb=" N PRO C 222 " ideal model delta sigma weight residual 1.332 1.372 -0.040 8.20e-03 1.49e+04 2.38e+01 bond pdb=" C ILE c 221 " pdb=" N PRO c 222 " ideal model delta sigma weight residual 1.337 1.376 -0.039 1.24e-02 6.50e+03 9.85e+00 bond pdb=" C TRP b 630 " pdb=" O TRP b 630 " ideal model delta sigma weight residual 1.246 1.225 0.021 9.20e-03 1.18e+04 5.37e+00 bond pdb=" C VAL B 314 " pdb=" O VAL B 314 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.17e-02 7.31e+03 4.17e+00 bond pdb=" C SER c 21 " pdb=" N PRO c 22 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.82e+00 ... (remaining 12641 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.80: 484 106.80 - 113.60: 6392 113.60 - 120.41: 4857 120.41 - 127.22: 5241 127.22 - 134.03: 178 Bond angle restraints: 17152 Sorted by residual: angle pdb=" N VAL a 27 " pdb=" CA VAL a 27 " pdb=" C VAL a 27 " ideal model delta sigma weight residual 113.71 109.11 4.60 9.50e-01 1.11e+00 2.34e+01 angle pdb=" C ALA a 95 " pdb=" N ASP a 96 " pdb=" CA ASP a 96 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C ILE b 617 " pdb=" N PRO b 618 " pdb=" CA PRO b 618 " ideal model delta sigma weight residual 119.05 124.17 -5.12 1.11e+00 8.12e-01 2.13e+01 angle pdb=" C ASN B 478 " pdb=" N GLU B 479 " pdb=" CA GLU B 479 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.89e+01 angle pdb=" N TYR b 620 " pdb=" CA TYR b 620 " pdb=" C TYR b 620 " ideal model delta sigma weight residual 109.11 115.08 -5.97 1.42e+00 4.96e-01 1.77e+01 ... (remaining 17147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 6672 18.01 - 36.01: 603 36.01 - 54.02: 100 54.02 - 72.03: 29 72.03 - 90.03: 22 Dihedral angle restraints: 7426 sinusoidal: 3038 harmonic: 4388 Sorted by residual: dihedral pdb=" CA SER C 21 " pdb=" C SER C 21 " pdb=" N PRO C 22 " pdb=" CA PRO C 22 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" C ASN a 165 " pdb=" N ASN a 165 " pdb=" CA ASN a 165 " pdb=" CB ASN a 165 " ideal model delta harmonic sigma weight residual -122.60 -133.48 10.88 0 2.50e+00 1.60e-01 1.90e+01 dihedral pdb=" CA PRO C 22 " pdb=" C PRO C 22 " pdb=" N ASP C 23 " pdb=" CA ASP C 23 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 7423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1502 0.072 - 0.144: 244 0.144 - 0.217: 16 0.217 - 0.289: 3 0.289 - 0.361: 1 Chirality restraints: 1766 Sorted by residual: chirality pdb=" CA ASN a 165 " pdb=" N ASN a 165 " pdb=" C ASN a 165 " pdb=" CB ASN a 165 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA LYS a 166 " pdb=" N LYS a 166 " pdb=" C LYS a 166 " pdb=" CB LYS a 166 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ASP a 96 " pdb=" N ASP a 96 " pdb=" C ASP a 96 " pdb=" CB ASP a 96 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1763 not shown) Planarity restraints: 2248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 435 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO B 436 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 436 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 436 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA c 69 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO c 70 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO c 70 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO c 70 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER c 21 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO c 22 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO c 22 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO c 22 " 0.030 5.00e-02 4.00e+02 ... (remaining 2245 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 1 1.80 - 2.57: 111 2.57 - 3.35: 14164 3.35 - 4.12: 31027 4.12 - 4.90: 55617 Nonbonded interactions: 100920 Sorted by model distance: nonbonded pdb=" OH TYR b 634 " pdb=" CG GLN c 18 " model vdw 1.020 3.440 nonbonded pdb=" OH TYR b 634 " pdb=" CD GLN c 18 " model vdw 1.948 3.270 nonbonded pdb=" OD1 ASN b 615 " pdb=" OD2 ASP c 23 " model vdw 1.987 3.040 nonbonded pdb=" CG2 VAL b 326 " pdb=" CE1 TYR b 634 " model vdw 2.052 3.760 nonbonded pdb=" OE2 GLU B 316 " pdb=" NZ LYS B 641 " model vdw 2.119 2.520 ... (remaining 100915 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 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 7866 2.51 5 N 2090 2.21 5 O 2314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.690 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: 0.010 Extract box with map and model: 16.900 Check model and map are aligned: 0.170 Process input model: 33.690 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.110 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 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 0.046 12646 Z= 0.217 Angle : 0.758 9.135 17152 Z= 0.438 Chirality : 0.052 0.361 1766 Planarity : 0.006 0.060 2248 Dihedral : 14.924 90.032 4646 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -4.33 (0.17), residues: 1492 helix: -3.09 (0.24), residues: 218 sheet: -2.68 (0.23), residues: 372 loop : -3.01 (0.16), residues: 902 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 297 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 314 average time/residue: 0.3094 time to fit residues: 131.3949 Evaluate side-chains 199 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1230 time to fit residues: 4.6801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 GLN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS B 541 ASN ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 495 HIS ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 619 GLN ** b 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 HIS A 110 ASN A 156 ASN ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN a 123 HIS ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 189 HIS c 251 HIS c 257 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.053 12646 Z= 0.499 Angle : 0.819 9.772 17152 Z= 0.419 Chirality : 0.050 0.224 1766 Planarity : 0.006 0.057 2248 Dihedral : 5.359 24.586 1692 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.24 % Favored : 91.69 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.78 (0.18), residues: 1492 helix: -1.88 (0.28), residues: 232 sheet: -2.85 (0.23), residues: 360 loop : -2.62 (0.17), residues: 900 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 1.417 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 30 residues processed: 246 average time/residue: 0.2697 time to fit residues: 92.9618 Evaluate side-chains 209 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1156 time to fit residues: 8.3737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 46 optimal weight: 0.0070 chunk 109 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 680 ASN ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 12646 Z= 0.258 Angle : 0.624 10.850 17152 Z= 0.314 Chirality : 0.044 0.165 1766 Planarity : 0.004 0.042 2248 Dihedral : 4.872 22.725 1692 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.36 (0.19), residues: 1492 helix: -1.50 (0.30), residues: 250 sheet: -2.75 (0.24), residues: 358 loop : -2.26 (0.18), residues: 884 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 1.502 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 223 average time/residue: 0.2587 time to fit residues: 82.7636 Evaluate side-chains 188 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 173 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1111 time to fit residues: 4.7805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 GLN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 12646 Z= 0.303 Angle : 0.639 8.307 17152 Z= 0.322 Chirality : 0.045 0.192 1766 Planarity : 0.004 0.043 2248 Dihedral : 4.861 22.308 1692 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.11 (0.20), residues: 1492 helix: -1.18 (0.31), residues: 250 sheet: -2.66 (0.24), residues: 360 loop : -2.08 (0.19), residues: 882 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 1.474 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 207 average time/residue: 0.2725 time to fit residues: 79.6891 Evaluate side-chains 192 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 1.270 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1106 time to fit residues: 5.9626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.3980 chunk 82 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 123 optimal weight: 0.0980 chunk 100 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 HIS ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 12646 Z= 0.235 Angle : 0.603 8.846 17152 Z= 0.304 Chirality : 0.044 0.208 1766 Planarity : 0.004 0.055 2248 Dihedral : 4.739 22.122 1692 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.89 (0.20), residues: 1492 helix: -1.00 (0.32), residues: 250 sheet: -2.53 (0.24), residues: 368 loop : -1.92 (0.19), residues: 874 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 200 time to evaluate : 1.373 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 217 average time/residue: 0.2459 time to fit residues: 76.6484 Evaluate side-chains 189 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1215 time to fit residues: 4.9870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 145 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.0050 chunk 12 optimal weight: 0.3980 chunk 76 optimal weight: 0.2980 chunk 139 optimal weight: 0.5980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12646 Z= 0.201 Angle : 0.594 8.662 17152 Z= 0.297 Chirality : 0.044 0.228 1766 Planarity : 0.004 0.049 2248 Dihedral : 4.644 21.534 1692 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.74 (0.20), residues: 1492 helix: -0.86 (0.33), residues: 250 sheet: -2.44 (0.24), residues: 368 loop : -1.83 (0.19), residues: 874 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 1.304 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 208 average time/residue: 0.2567 time to fit residues: 76.0724 Evaluate side-chains 190 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 177 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1220 time to fit residues: 4.8126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.3980 chunk 82 optimal weight: 0.0980 chunk 105 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 89 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 GLN ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12646 Z= 0.199 Angle : 0.593 8.872 17152 Z= 0.298 Chirality : 0.044 0.209 1766 Planarity : 0.004 0.045 2248 Dihedral : 4.609 21.882 1692 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.62 (0.20), residues: 1492 helix: -0.77 (0.33), residues: 250 sheet: -2.29 (0.24), residues: 388 loop : -1.75 (0.20), residues: 854 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 1.503 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 203 average time/residue: 0.2706 time to fit residues: 77.5400 Evaluate side-chains 190 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 1.394 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1161 time to fit residues: 4.3772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 131 optimal weight: 0.4980 chunk 138 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 12646 Z= 0.260 Angle : 0.627 10.544 17152 Z= 0.314 Chirality : 0.045 0.204 1766 Planarity : 0.004 0.051 2248 Dihedral : 4.743 22.557 1692 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.65 (0.20), residues: 1492 helix: -0.80 (0.33), residues: 250 sheet: -2.34 (0.24), residues: 386 loop : -1.75 (0.20), residues: 856 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 1.478 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 193 average time/residue: 0.2877 time to fit residues: 77.7713 Evaluate side-chains 182 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 1.480 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1190 time to fit residues: 4.4543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 138 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 121 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 142 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 GLN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS c 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 12646 Z= 0.299 Angle : 0.650 10.673 17152 Z= 0.326 Chirality : 0.045 0.184 1766 Planarity : 0.004 0.054 2248 Dihedral : 4.866 22.168 1692 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.70 (0.20), residues: 1492 helix: -0.88 (0.32), residues: 250 sheet: -2.42 (0.24), residues: 376 loop : -1.77 (0.20), residues: 866 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 182 time to evaluate : 1.417 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 190 average time/residue: 0.2965 time to fit residues: 79.0311 Evaluate side-chains 179 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1223 time to fit residues: 3.8161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 12646 Z= 0.291 Angle : 0.659 10.589 17152 Z= 0.330 Chirality : 0.045 0.187 1766 Planarity : 0.004 0.048 2248 Dihedral : 4.921 23.046 1692 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.66 (0.20), residues: 1492 helix: -0.87 (0.32), residues: 250 sheet: -2.35 (0.25), residues: 366 loop : -1.77 (0.20), residues: 876 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 186 time to evaluate : 1.508 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 190 average time/residue: 0.3044 time to fit residues: 79.9302 Evaluate side-chains 173 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.419 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1157 time to fit residues: 2.1886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 15 optimal weight: 0.1980 chunk 21 optimal weight: 0.4980 chunk 104 optimal weight: 0.3980 chunk 6 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN c 67 GLN c 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.135077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.105061 restraints weight = 18374.877| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.65 r_work: 0.3410 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 12646 Z= 0.206 Angle : 0.631 10.088 17152 Z= 0.319 Chirality : 0.044 0.258 1766 Planarity : 0.004 0.053 2248 Dihedral : 4.805 21.907 1692 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.51 (0.21), residues: 1492 helix: -0.72 (0.33), residues: 248 sheet: -2.25 (0.24), residues: 378 loop : -1.66 (0.20), residues: 866 =============================================================================== Job complete usr+sys time: 3234.13 seconds wall clock time: 59 minutes 37.34 seconds (3577.34 seconds total)