Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 02:18:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4s_25687/04_2023/7t4s_25687.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4s_25687/04_2023/7t4s_25687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4s_25687/04_2023/7t4s_25687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4s_25687/04_2023/7t4s_25687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4s_25687/04_2023/7t4s_25687.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4s_25687/04_2023/7t4s_25687.pdb" } resolution = 3.1 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= 0.012 sd= 0.182 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 83 5.16 5 C 10444 2.51 5 N 2813 2.21 5 O 3063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16404 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5034 Classifications: {'peptide': 624} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 591} Chain breaks: 6 Chain: "B" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1804 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 207} Chain breaks: 1 Chain: "C" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 896 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain breaks: 2 Chain: "D" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1359 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 154} Chain breaks: 1 Chain: "E" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 821 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain breaks: 1 Chain: "F" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2883 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 338} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 951 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 924 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "K" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Chain: "I" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 99} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.98, per 1000 atoms: 0.55 Number of scatterers: 16404 At special positions: 0 Unit cell: (202.71, 140.546, 140.546, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 83 16.00 O 3063 8.00 N 2813 7.00 C 10444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 54 " distance=2.04 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 162 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 83 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 207 " distance=2.02 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 277 " - pdb=" SG CYS F 427 " distance=2.03 Simple disulfide: pdb=" SG CYS F 434 " - pdb=" SG CYS F 592 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 55 " " NAG A 802 " - " ASN A 62 " " NAG A 804 " - " ASN A 192 " " NAG D 301 " - " ASN D 201 " " NAG D 302 " - " ASN D 118 " " NAG E 201 " - " ASN E 81 " " NAG F 901 " - " ASN F 157 " " NAG F 902 " - " ASN F 152 " Time building additional restraints: 6.90 Conformation dependent library (CDL) restraints added in 2.4 seconds 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 26 sheets defined 26.9% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.703A pdb=" N ALA A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 99 " --> pdb=" O CYS A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 99' Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.816A pdb=" N ASN A 287 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 327 Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 362 through 385 removed outlier: 3.614A pdb=" N SER A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.740A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.866A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 531 through 537 removed outlier: 3.675A pdb=" N ARG A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 644 through 648 removed outlier: 3.712A pdb=" N ALA A 648 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.526A pdb=" N ARG B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 117 through 127 Processing helix chain 'B' and resid 130 through 143 removed outlier: 3.571A pdb=" N GLU B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 4.201A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 253 removed outlier: 3.981A pdb=" N ARG B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.178A pdb=" N HIS C 82 " --> pdb=" O THR C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.561A pdb=" N LYS C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.960A pdb=" N GLY D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Proline residue: D 126 - end of helix removed outlier: 3.693A pdb=" N ALA D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 35 through 40 Processing helix chain 'E' and resid 45 through 69 Processing helix chain 'E' and resid 73 through 79 removed outlier: 3.820A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG E 79 " --> pdb=" O ASP E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.532A pdb=" N GLN E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 430 through 432 No H-bonds generated for 'chain 'F' and resid 430 through 432' Processing helix chain 'F' and resid 446 through 448 No H-bonds generated for 'chain 'F' and resid 446 through 448' Processing helix chain 'F' and resid 461 through 466 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.610A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.524A pdb=" N ASN J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.587A pdb=" N VAL K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 removed outlier: 5.960A pdb=" N ARG A 50 " --> pdb=" O VAL A 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 removed outlier: 5.979A pdb=" N ALA A 75 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N PHE B 181 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS B 177 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 192 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE B 181 " --> pdb=" O ASN B 190 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN B 190 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU B 183 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 188 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.619A pdb=" N ARG A 136 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG A 223 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 528 removed outlier: 3.572A pdb=" N ARG A 528 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 578 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 637 through 638 removed outlier: 6.908A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER A 652 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N TYR A 668 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 654 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE A 666 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU A 656 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.429A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 155 removed outlier: 5.306A pdb=" N GLY B 161 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ARG D 102 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N ASP B 163 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU D 88 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG D 76 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 90 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE D 74 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR D 92 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.699A pdb=" N ASP C 45 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.271A pdb=" N ARG C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU C 104 " --> pdb=" O ARG C 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 132 through 133 removed outlier: 4.384A pdb=" N ARG D 160 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG D 168 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 122 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 194 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 157 through 161 removed outlier: 6.495A pdb=" N GLY F 259 " --> pdb=" O PHE F 194 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE F 194 " --> pdb=" O GLY F 259 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER F 261 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 174 through 180 Processing sheet with id=AB4, first strand: chain 'F' and resid 279 through 280 removed outlier: 6.219A pdb=" N GLU F 423 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE F 342 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE F 425 " --> pdb=" O THR F 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 279 through 280 removed outlier: 6.219A pdb=" N GLU F 423 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE F 342 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE F 425 " --> pdb=" O THR F 340 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ARG F 405 " --> pdb=" O LEU F 333 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N PHE F 335 " --> pdb=" O LEU F 403 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N LEU F 403 " --> pdb=" O PHE F 335 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N THR F 337 " --> pdb=" O PRO F 401 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N LEU F 339 " --> pdb=" O HIS F 399 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N HIS F 399 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA F 341 " --> pdb=" O LYS F 397 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS F 397 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA F 343 " --> pdb=" O LEU F 395 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU F 395 " --> pdb=" O ALA F 343 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 436 through 437 removed outlier: 6.828A pdb=" N CYS F 592 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL F 498 " --> pdb=" O CYS F 592 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 436 through 437 removed outlier: 6.828A pdb=" N CYS F 592 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL F 498 " --> pdb=" O CYS F 592 " (cutoff:3.500A) removed outlier: 12.701A pdb=" N LEU F 488 " --> pdb=" O GLU F 576 " (cutoff:3.500A) removed outlier: 11.097A pdb=" N GLU F 576 " --> pdb=" O LEU F 488 " (cutoff:3.500A) removed outlier: 12.306A pdb=" N VAL F 490 " --> pdb=" O TYR F 574 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N TYR F 574 " --> pdb=" O VAL F 490 " (cutoff:3.500A) removed outlier: 12.148A pdb=" N LEU F 492 " --> pdb=" O ARG F 572 " (cutoff:3.500A) removed outlier: 12.421A pdb=" N ARG F 572 " --> pdb=" O LEU F 492 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N THR F 494 " --> pdb=" O TYR F 570 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR F 570 " --> pdb=" O THR F 494 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLY F 500 " --> pdb=" O ASP F 564 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N ASP F 564 " --> pdb=" O GLY F 500 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N ILE F 502 " --> pdb=" O ARG F 562 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N ARG F 562 " --> pdb=" O ILE F 502 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N GLN F 504 " --> pdb=" O ILE F 560 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N ILE F 560 " --> pdb=" O GLN F 504 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER F 529 " --> pdb=" O GLN F 569 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL F 571 " --> pdb=" O SER F 527 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER F 527 " --> pdb=" O VAL F 571 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL F 573 " --> pdb=" O LYS F 525 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS F 525 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS F 523 " --> pdb=" O PRO F 575 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ARG F 577 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL F 521 " --> pdb=" O ARG F 577 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.597A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.702A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.932A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU H 106 " --> pdb=" O LEU H 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.470A pdb=" N ILE J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.844A pdb=" N ASP J 112 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.906A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.548A pdb=" N LEU I 11 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1695 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: 5.49 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5282 1.34 - 1.46: 4062 1.46 - 1.58: 7322 1.58 - 1.71: 0 1.71 - 1.83: 120 Bond restraints: 16786 Sorted by residual: bond pdb=" N ASP F 211 " pdb=" CA ASP F 211 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.24e-02 6.50e+03 7.49e+00 bond pdb=" N VAL A 281 " pdb=" CA VAL A 281 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.19e-02 7.06e+03 6.60e+00 bond pdb=" N TYR K 49 " pdb=" CA TYR K 49 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.53e+00 bond pdb=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.44e-02 4.82e+03 6.30e+00 bond pdb=" N ALA K 50 " pdb=" CA ALA K 50 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.31e-02 5.83e+03 6.07e+00 ... (remaining 16781 not shown) Histogram of bond angle deviations from ideal: 95.05 - 102.85: 74 102.85 - 110.65: 5418 110.65 - 118.45: 7565 118.45 - 126.25: 9453 126.25 - 134.05: 285 Bond angle restraints: 22795 Sorted by residual: angle pdb=" C LEU K 47 " pdb=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 123.17 118.18 4.99 1.28e+00 6.10e-01 1.52e+01 angle pdb=" CA ALA K 50 " pdb=" C ALA K 50 " pdb=" O ALA K 50 " ideal model delta sigma weight residual 121.81 117.48 4.33 1.18e+00 7.18e-01 1.35e+01 angle pdb=" CB MET F 253 " pdb=" CG MET F 253 " pdb=" SD MET F 253 " ideal model delta sigma weight residual 112.70 102.77 9.93 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CG ARG F 239 " pdb=" CD ARG F 239 " pdb=" NE ARG F 239 " ideal model delta sigma weight residual 112.00 119.11 -7.11 2.20e+00 2.07e-01 1.04e+01 angle pdb=" C ALA K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 120.38 116.25 4.13 1.37e+00 5.33e-01 9.09e+00 ... (remaining 22790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9204 17.96 - 35.92: 615 35.92 - 53.89: 123 53.89 - 71.85: 31 71.85 - 89.81: 13 Dihedral angle restraints: 9986 sinusoidal: 4016 harmonic: 5970 Sorted by residual: dihedral pdb=" CB CYS C 96 " pdb=" SG CYS C 96 " pdb=" SG CYS C 111 " pdb=" CB CYS C 111 " ideal model delta sinusoidal sigma weight residual 93.00 159.28 -66.28 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS D 57 " pdb=" SG CYS D 57 " pdb=" SG CYS D 83 " pdb=" CB CYS D 83 " ideal model delta sinusoidal sigma weight residual -86.00 -148.39 62.39 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CA MET F 253 " pdb=" C MET F 253 " pdb=" N ALA F 254 " pdb=" CA ALA F 254 " ideal model delta harmonic sigma weight residual -180.00 -151.56 -28.44 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 9983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1824 0.040 - 0.080: 522 0.080 - 0.119: 190 0.119 - 0.159: 37 0.159 - 0.199: 4 Chirality restraints: 2577 Sorted by residual: chirality pdb=" CG LEU C 56 " pdb=" CB LEU C 56 " pdb=" CD1 LEU C 56 " pdb=" CD2 LEU C 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA GLU E 84 " pdb=" N GLU E 84 " pdb=" C GLU E 84 " pdb=" CB GLU E 84 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA VAL A 281 " pdb=" N VAL A 281 " pdb=" C VAL A 281 " pdb=" CB VAL A 281 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 2574 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 226 " -0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C TYR B 226 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR B 226 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN B 227 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 227 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ASN B 227 " 0.066 2.00e-02 2.50e+03 pdb=" O ASN B 227 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 228 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 228 " 0.019 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ALA B 228 " -0.064 2.00e-02 2.50e+03 pdb=" O ALA B 228 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL B 229 " 0.021 2.00e-02 2.50e+03 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1533 2.74 - 3.28: 16536 3.28 - 3.82: 27055 3.82 - 4.36: 33880 4.36 - 4.90: 57289 Nonbonded interactions: 136293 Sorted by model distance: nonbonded pdb=" O SER F 155 " pdb=" OH TYR F 264 " model vdw 2.204 2.440 nonbonded pdb=" OE2 GLU F 197 " pdb="CA CA F 903 " model vdw 2.222 2.510 nonbonded pdb=" OG SER K 7 " pdb=" OG1 THR K 22 " model vdw 2.234 2.440 nonbonded pdb=" OE2 GLU E 84 " pdb=" O5 NAG E 201 " model vdw 2.237 3.040 nonbonded pdb=" OE2 GLU E 26 " pdb=" OH TYR E 36 " model vdw 2.257 2.440 ... (remaining 136288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.690 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: 6.170 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 43.480 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.004 0.056 16786 Z= 0.265 Angle : 0.640 9.928 22795 Z= 0.344 Chirality : 0.044 0.199 2577 Planarity : 0.006 0.078 2901 Dihedral : 13.166 89.808 6078 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % 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: -0.13 (0.19), residues: 1983 helix: 0.42 (0.25), residues: 426 sheet: 0.33 (0.23), residues: 516 loop : -0.45 (0.20), residues: 1041 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.3549 time to fit residues: 226.8920 Evaluate side-chains 397 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.0970 chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 chunk 95 optimal weight: 0.0980 chunk 116 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 502 HIS A 594 GLN B 118 GLN B 203 ASN D 181 HIS F 172 ASN F 276 GLN F 396 ASN F 436 ASN H 84 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 79 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 16786 Z= 0.194 Angle : 0.613 9.384 22795 Z= 0.317 Chirality : 0.044 0.167 2577 Planarity : 0.004 0.044 2901 Dihedral : 4.989 22.159 2239 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % 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: 0.26 (0.19), residues: 1983 helix: 0.87 (0.26), residues: 422 sheet: 0.45 (0.23), residues: 530 loop : -0.18 (0.20), residues: 1031 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 426 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 431 average time/residue: 0.3840 time to fit residues: 229.0726 Evaluate side-chains 413 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 399 time to evaluate : 1.928 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2255 time to fit residues: 7.7656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 0.4980 chunk 56 optimal weight: 0.0970 chunk 151 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 141 GLN A 201 HIS ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN D 181 HIS D 211 ASN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 16786 Z= 0.289 Angle : 0.625 10.495 22795 Z= 0.324 Chirality : 0.045 0.165 2577 Planarity : 0.004 0.044 2901 Dihedral : 5.130 21.310 2239 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % 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: 0.21 (0.19), residues: 1983 helix: 0.80 (0.25), residues: 422 sheet: 0.45 (0.23), residues: 534 loop : -0.23 (0.20), residues: 1027 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 420 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 23 residues processed: 440 average time/residue: 0.3718 time to fit residues: 227.0071 Evaluate side-chains 432 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 409 time to evaluate : 1.937 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1740 time to fit residues: 9.7948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 193 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN B 203 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 GLN J 31 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 16786 Z= 0.264 Angle : 0.611 9.184 22795 Z= 0.316 Chirality : 0.044 0.154 2577 Planarity : 0.004 0.046 2901 Dihedral : 5.084 23.092 2239 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % 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: 0.17 (0.19), residues: 1983 helix: 0.77 (0.25), residues: 422 sheet: 0.53 (0.23), residues: 532 loop : -0.32 (0.20), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 417 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 25 residues processed: 432 average time/residue: 0.3679 time to fit residues: 221.6452 Evaluate side-chains 430 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 405 time to evaluate : 1.905 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2012 time to fit residues: 11.0994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 0.0570 chunk 0 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 273 GLN C 134 ASN D 181 HIS ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 GLN H 111 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16786 Z= 0.212 Angle : 0.589 8.759 22795 Z= 0.303 Chirality : 0.043 0.172 2577 Planarity : 0.004 0.046 2901 Dihedral : 4.929 23.797 2239 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % 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: 0.26 (0.19), residues: 1983 helix: 0.93 (0.26), residues: 417 sheet: 0.52 (0.23), residues: 532 loop : -0.26 (0.20), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 428 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 445 average time/residue: 0.3566 time to fit residues: 221.8611 Evaluate side-chains 429 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 414 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1966 time to fit residues: 7.7553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 101 optimal weight: 0.9980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 273 GLN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN K 79 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 16786 Z= 0.318 Angle : 0.640 8.690 22795 Z= 0.330 Chirality : 0.045 0.172 2577 Planarity : 0.005 0.065 2901 Dihedral : 5.094 26.727 2239 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % 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: 0.14 (0.19), residues: 1983 helix: 0.84 (0.26), residues: 416 sheet: 0.44 (0.23), residues: 534 loop : -0.34 (0.20), residues: 1033 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 420 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 19 residues processed: 431 average time/residue: 0.3701 time to fit residues: 222.7481 Evaluate side-chains 430 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 411 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2403 time to fit residues: 9.7714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 107 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN I 37 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 16786 Z= 0.241 Angle : 0.614 8.176 22795 Z= 0.317 Chirality : 0.044 0.183 2577 Planarity : 0.005 0.061 2901 Dihedral : 5.012 27.575 2239 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % 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: 0.19 (0.19), residues: 1983 helix: 0.91 (0.26), residues: 415 sheet: 0.49 (0.23), residues: 533 loop : -0.33 (0.20), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 421 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 432 average time/residue: 0.3613 time to fit residues: 218.1559 Evaluate side-chains 427 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 413 time to evaluate : 1.988 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1791 time to fit residues: 7.1084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 175 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN I 37 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 16786 Z= 0.260 Angle : 0.621 9.497 22795 Z= 0.320 Chirality : 0.044 0.173 2577 Planarity : 0.005 0.052 2901 Dihedral : 5.025 28.508 2239 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % 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: 0.14 (0.19), residues: 1983 helix: 0.84 (0.26), residues: 416 sheet: 0.49 (0.23), residues: 532 loop : -0.37 (0.20), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 418 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 428 average time/residue: 0.3689 time to fit residues: 219.8510 Evaluate side-chains 423 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 410 time to evaluate : 1.966 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1997 time to fit residues: 6.9424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.9990 chunk 168 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 141 optimal weight: 0.0270 chunk 55 optimal weight: 6.9990 chunk 162 optimal weight: 0.3980 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16786 Z= 0.177 Angle : 0.587 9.326 22795 Z= 0.301 Chirality : 0.043 0.197 2577 Planarity : 0.004 0.045 2901 Dihedral : 4.827 25.891 2239 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % 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: 0.24 (0.19), residues: 1983 helix: 1.02 (0.26), residues: 416 sheet: 0.51 (0.23), residues: 531 loop : -0.32 (0.20), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 420 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 425 average time/residue: 0.3747 time to fit residues: 221.2655 Evaluate side-chains 417 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 411 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2278 time to fit residues: 5.1229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 199 optimal weight: 0.3980 chunk 183 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 169 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN K 79 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16786 Z= 0.198 Angle : 0.595 10.317 22795 Z= 0.304 Chirality : 0.043 0.173 2577 Planarity : 0.004 0.045 2901 Dihedral : 4.792 25.281 2239 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % 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: 0.23 (0.19), residues: 1983 helix: 0.99 (0.26), residues: 417 sheet: 0.45 (0.22), residues: 539 loop : -0.30 (0.20), residues: 1027 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 424 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 426 average time/residue: 0.3867 time to fit residues: 231.2411 Evaluate side-chains 422 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 417 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3982 time to fit residues: 5.6837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.6980 chunk 146 optimal weight: 0.0470 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 163 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 GLN F 436 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.087148 restraints weight = 29842.018| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.55 r_work: 0.2979 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 16786 Z= 0.183 Angle : 0.585 9.422 22795 Z= 0.299 Chirality : 0.043 0.156 2577 Planarity : 0.004 0.046 2901 Dihedral : 4.719 23.875 2239 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % 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: 0.24 (0.19), residues: 1983 helix: 0.96 (0.26), residues: 418 sheet: 0.51 (0.22), residues: 535 loop : -0.30 (0.20), residues: 1030 =============================================================================== Job complete usr+sys time: 4676.84 seconds wall clock time: 84 minutes 42.79 seconds (5082.79 seconds total)