Starting phenix.real_space_refine on Fri Feb 16 20:30:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4s_25687/02_2024/7t4s_25687.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4s_25687/02_2024/7t4s_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_25687/02_2024/7t4s_25687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4s_25687/02_2024/7t4s_25687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4s_25687/02_2024/7t4s_25687.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4s_25687/02_2024/7t4s_25687.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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-dev-5238/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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.04, 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: 6.36 Conformation dependent library (CDL) restraints added in 2.9 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: 1.97 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: 5.82 Time building geometry restraints manager: 6.97 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: 9375 17.96 - 35.92: 627 35.92 - 53.89: 127 53.89 - 71.85: 33 71.85 - 89.81: 13 Dihedral angle restraints: 10175 sinusoidal: 4205 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 10172 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: 6.290 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: 0.000 Extract box with map and model: 5.900 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 45.440 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.620 ------------------------------------------------------------------------------- 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 : 13.121 89.808 6267 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 % Allowed : 0.17 % Favored : 99.83 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 100 HIS 0.008 0.001 HIS E 69 PHE 0.016 0.002 PHE F 165 TYR 0.018 0.002 TYR A 45 ARG 0.012 0.001 ARG C 74 *********************** 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 : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 THR cc_start: 0.8386 (p) cc_final: 0.8184 (p) REVERT: A 114 THR cc_start: 0.8334 (p) cc_final: 0.7471 (p) REVERT: A 193 GLN cc_start: 0.7433 (mp-120) cc_final: 0.7091 (mm-40) REVERT: A 633 THR cc_start: 0.7335 (p) cc_final: 0.7111 (m) REVERT: A 698 LEU cc_start: 0.8884 (mt) cc_final: 0.8608 (mt) REVERT: C 87 GLN cc_start: 0.7656 (tp-100) cc_final: 0.7408 (tp40) REVERT: C 120 TYR cc_start: 0.7513 (m-80) cc_final: 0.7275 (m-80) REVERT: C 121 LEU cc_start: 0.8343 (tp) cc_final: 0.8137 (tp) REVERT: D 117 ARG cc_start: 0.7443 (tpt170) cc_final: 0.6848 (tpt170) REVERT: D 142 GLU cc_start: 0.7351 (mp0) cc_final: 0.7108 (mp0) REVERT: D 169 TYR cc_start: 0.7635 (m-80) cc_final: 0.7334 (m-80) REVERT: F 217 ASP cc_start: 0.7232 (t0) cc_final: 0.7012 (t0) REVERT: F 246 SER cc_start: 0.8579 (t) cc_final: 0.8324 (p) REVERT: F 328 TYR cc_start: 0.7304 (p90) cc_final: 0.7039 (p90) REVERT: F 436 ASN cc_start: 0.8893 (m110) cc_final: 0.8684 (m-40) REVERT: F 487 TRP cc_start: 0.7667 (p-90) cc_final: 0.7411 (p-90) REVERT: F 494 THR cc_start: 0.7754 (p) cc_final: 0.7492 (m) REVERT: H 73 ASP cc_start: 0.5943 (t0) cc_final: 0.5730 (t0) REVERT: H 84 ASN cc_start: 0.8386 (m-40) cc_final: 0.7877 (m-40) REVERT: H 87 ARG cc_start: 0.7155 (mtt180) cc_final: 0.6775 (mtt90) REVERT: J 83 LEU cc_start: 0.7842 (tp) cc_final: 0.7613 (tp) REVERT: K 18 ARG cc_start: 0.8465 (ttt90) cc_final: 0.8228 (ttt180) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.3536 time to fit residues: 225.8232 Evaluate side-chains 395 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 1.940 ------------------------------------------------------------------------------- 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: 0.8980 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: 3.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 412 GLN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16786 Z= 0.188 Angle : 0.606 9.357 22795 Z= 0.314 Chirality : 0.044 0.173 2577 Planarity : 0.004 0.045 2901 Dihedral : 5.560 56.595 2428 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.00 % Allowed : 8.83 % Favored : 90.17 % 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: 0.26 (0.19), residues: 1983 helix: 0.85 (0.26), residues: 422 sheet: 0.43 (0.22), residues: 534 loop : -0.16 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 100 HIS 0.005 0.001 HIS E 69 PHE 0.022 0.002 PHE E 122 TYR 0.015 0.001 TYR J 33 ARG 0.006 0.001 ARG A 117 *********************** 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 444 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 426 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLN cc_start: 0.7075 (tm-30) cc_final: 0.6762 (tp40) REVERT: A 193 GLN cc_start: 0.7342 (mp-120) cc_final: 0.7003 (mm-40) REVERT: A 619 ASP cc_start: 0.7688 (t70) cc_final: 0.7394 (t70) REVERT: A 633 THR cc_start: 0.7292 (p) cc_final: 0.7062 (m) REVERT: A 637 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7865 (t) REVERT: A 698 LEU cc_start: 0.8886 (mt) cc_final: 0.8594 (mt) REVERT: C 44 TYR cc_start: 0.7087 (p90) cc_final: 0.6877 (p90) REVERT: C 87 GLN cc_start: 0.7580 (tp-100) cc_final: 0.7349 (tp40) REVERT: C 97 ASN cc_start: 0.7848 (m110) cc_final: 0.7581 (m-40) REVERT: C 110 ARG cc_start: 0.8407 (ppt170) cc_final: 0.7842 (ptt90) REVERT: C 121 LEU cc_start: 0.8352 (tp) cc_final: 0.8064 (tp) REVERT: D 117 ARG cc_start: 0.7362 (tpt170) cc_final: 0.7021 (tpt170) REVERT: D 159 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7906 (mp) REVERT: F 151 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7689 (mmmt) REVERT: F 217 ASP cc_start: 0.7311 (t0) cc_final: 0.7039 (t0) REVERT: F 246 SER cc_start: 0.8724 (t) cc_final: 0.8310 (p) REVERT: F 253 MET cc_start: 0.6411 (ttt) cc_final: 0.6179 (ttt) REVERT: F 338 MET cc_start: 0.7622 (mtm) cc_final: 0.7173 (mpp) REVERT: F 494 THR cc_start: 0.7797 (p) cc_final: 0.7501 (m) REVERT: H 6 GLU cc_start: 0.7424 (mp0) cc_final: 0.7134 (mp0) REVERT: H 84 ASN cc_start: 0.8413 (m-40) cc_final: 0.8022 (m-40) REVERT: J 87 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7114 (mtm110) REVERT: J 89 GLU cc_start: 0.7168 (pp20) cc_final: 0.6742 (pp20) REVERT: I 101 GLN cc_start: 0.8046 (mp10) cc_final: 0.7792 (mm-40) outliers start: 18 outliers final: 12 residues processed: 430 average time/residue: 0.3766 time to fit residues: 223.0905 Evaluate side-chains 413 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 399 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 0.0040 chunk 56 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 0.0870 chunk 181 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 overall best weight: 0.5972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN 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** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16786 Z= 0.218 Angle : 0.585 10.553 22795 Z= 0.302 Chirality : 0.044 0.151 2577 Planarity : 0.004 0.044 2901 Dihedral : 5.387 57.738 2428 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.28 % Allowed : 10.72 % Favored : 87.00 % 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: 0.29 (0.19), residues: 1983 helix: 0.89 (0.25), residues: 422 sheet: 0.50 (0.22), residues: 533 loop : -0.19 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 179 HIS 0.006 0.001 HIS E 69 PHE 0.018 0.002 PHE E 122 TYR 0.030 0.002 TYR E 52 ARG 0.006 0.001 ARG A 117 *********************** 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 465 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 424 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8191 (mm) cc_final: 0.7576 (mt) REVERT: A 193 GLN cc_start: 0.7292 (mp-120) cc_final: 0.6953 (mm-40) REVERT: A 466 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6815 (mm-30) REVERT: A 619 ASP cc_start: 0.7693 (t70) cc_final: 0.7384 (t70) REVERT: A 633 THR cc_start: 0.7305 (p) cc_final: 0.7044 (m) REVERT: A 637 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7872 (t) REVERT: A 698 LEU cc_start: 0.8876 (mt) cc_final: 0.8550 (mt) REVERT: B 197 ASN cc_start: 0.6894 (t0) cc_final: 0.6608 (t0) REVERT: C 44 TYR cc_start: 0.7028 (p90) cc_final: 0.6814 (p90) REVERT: C 87 GLN cc_start: 0.7590 (tp-100) cc_final: 0.7370 (tp40) REVERT: C 97 ASN cc_start: 0.8044 (m110) cc_final: 0.7762 (m-40) REVERT: C 110 ARG cc_start: 0.8439 (ppt170) cc_final: 0.7906 (ptt90) REVERT: C 121 LEU cc_start: 0.8375 (tp) cc_final: 0.8111 (tp) REVERT: D 159 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7894 (mp) REVERT: F 185 MET cc_start: 0.6479 (mmm) cc_final: 0.5992 (mmp) REVERT: F 217 ASP cc_start: 0.7294 (t0) cc_final: 0.7019 (t0) REVERT: F 246 SER cc_start: 0.8655 (t) cc_final: 0.8208 (p) REVERT: F 328 TYR cc_start: 0.7674 (p90) cc_final: 0.7368 (p90) REVERT: F 494 THR cc_start: 0.7825 (p) cc_final: 0.7501 (m) REVERT: H 84 ASN cc_start: 0.8362 (m-40) cc_final: 0.8036 (m-40) outliers start: 41 outliers final: 31 residues processed: 444 average time/residue: 0.3593 time to fit residues: 220.7548 Evaluate side-chains 441 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 408 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain I residue 21 LEU 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: 2.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 193 optimal weight: 0.0970 chunk 95 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN 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** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1738 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= 0.239 Angle : 0.589 9.500 22795 Z= 0.304 Chirality : 0.043 0.152 2577 Planarity : 0.004 0.045 2901 Dihedral : 5.362 58.114 2428 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.94 % Allowed : 11.78 % Favored : 85.28 % 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: 0.25 (0.19), residues: 1983 helix: 0.84 (0.25), residues: 423 sheet: 0.61 (0.23), residues: 527 loop : -0.29 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 179 HIS 0.006 0.001 HIS E 69 PHE 0.017 0.002 PHE E 122 TYR 0.045 0.002 TYR E 52 ARG 0.009 0.001 ARG A 117 *********************** 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 476 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 423 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8209 (mm) cc_final: 0.7601 (mt) REVERT: A 141 GLN cc_start: 0.7473 (tp-100) cc_final: 0.7270 (tp40) REVERT: A 193 GLN cc_start: 0.7105 (mp-120) cc_final: 0.6768 (mm-40) REVERT: A 458 PHE cc_start: 0.8473 (p90) cc_final: 0.8145 (p90) REVERT: A 466 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6786 (mm-30) REVERT: A 555 LEU cc_start: 0.8465 (mt) cc_final: 0.8209 (mt) REVERT: A 633 THR cc_start: 0.7301 (p) cc_final: 0.7043 (m) REVERT: A 637 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7858 (t) REVERT: A 696 MET cc_start: 0.7885 (tpp) cc_final: 0.7546 (ttm) REVERT: A 698 LEU cc_start: 0.8872 (mt) cc_final: 0.8568 (mt) REVERT: B 197 ASN cc_start: 0.7119 (t0) cc_final: 0.6882 (t0) REVERT: C 44 TYR cc_start: 0.7022 (p90) cc_final: 0.6780 (p90) REVERT: C 87 GLN cc_start: 0.7600 (tp-100) cc_final: 0.7369 (tp40) REVERT: C 97 ASN cc_start: 0.8087 (m110) cc_final: 0.7798 (m-40) REVERT: C 110 ARG cc_start: 0.8463 (ppt170) cc_final: 0.8020 (ptt90) REVERT: C 121 LEU cc_start: 0.8374 (tp) cc_final: 0.8102 (tp) REVERT: D 159 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7875 (mp) REVERT: F 190 GLN cc_start: 0.8567 (mt0) cc_final: 0.8134 (mt0) REVERT: F 217 ASP cc_start: 0.7266 (t0) cc_final: 0.7021 (t0) REVERT: F 246 SER cc_start: 0.8611 (t) cc_final: 0.8142 (p) REVERT: F 328 TYR cc_start: 0.7676 (p90) cc_final: 0.7425 (p90) REVERT: F 373 MET cc_start: 0.7681 (ttp) cc_final: 0.7435 (ttp) REVERT: H 76 LYS cc_start: 0.6767 (mtpp) cc_final: 0.6547 (ptpt) REVERT: K 48 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8290 (mp) outliers start: 53 outliers final: 41 residues processed: 452 average time/residue: 0.3598 time to fit residues: 225.4095 Evaluate side-chains 458 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 414 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 C 134 ASN ** 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 H 111 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN I 37 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16786 Z= 0.381 Angle : 0.669 9.273 22795 Z= 0.347 Chirality : 0.047 0.171 2577 Planarity : 0.005 0.044 2901 Dihedral : 5.703 59.637 2428 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.61 % Allowed : 13.11 % Favored : 83.28 % 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: 0.01 (0.19), residues: 1983 helix: 0.59 (0.25), residues: 422 sheet: 0.48 (0.23), residues: 528 loop : -0.43 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 94 HIS 0.008 0.001 HIS E 69 PHE 0.018 0.002 PHE E 122 TYR 0.067 0.002 TYR E 52 ARG 0.010 0.001 ARG A 117 *********************** 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 495 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 430 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8279 (mm) cc_final: 0.7547 (mt) REVERT: A 193 GLN cc_start: 0.7098 (mp-120) cc_final: 0.6758 (mm-40) REVERT: A 458 PHE cc_start: 0.8541 (p90) cc_final: 0.8215 (p90) REVERT: A 466 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6816 (mm-30) REVERT: A 555 LEU cc_start: 0.8553 (mt) cc_final: 0.8282 (mt) REVERT: A 633 THR cc_start: 0.7352 (p) cc_final: 0.7041 (m) REVERT: A 637 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7873 (t) REVERT: A 698 LEU cc_start: 0.8899 (mt) cc_final: 0.8574 (mt) REVERT: B 197 ASN cc_start: 0.7336 (t0) cc_final: 0.7044 (t0) REVERT: C 44 TYR cc_start: 0.7052 (p90) cc_final: 0.6805 (p90) REVERT: C 97 ASN cc_start: 0.8231 (m110) cc_final: 0.7891 (m-40) REVERT: C 110 ARG cc_start: 0.8459 (ppt170) cc_final: 0.8034 (ptt90) REVERT: C 121 LEU cc_start: 0.8370 (tp) cc_final: 0.8115 (tp) REVERT: E 78 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7541 (mmtt) REVERT: F 185 MET cc_start: 0.6405 (mmm) cc_final: 0.6118 (mmt) REVERT: F 246 SER cc_start: 0.8522 (t) cc_final: 0.8039 (p) REVERT: F 328 TYR cc_start: 0.7713 (p90) cc_final: 0.7452 (p90) REVERT: F 373 MET cc_start: 0.7679 (ttp) cc_final: 0.7435 (ttp) REVERT: K 48 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8324 (mp) REVERT: I 42 GLN cc_start: 0.7316 (mp10) cc_final: 0.7026 (mp10) outliers start: 65 outliers final: 52 residues processed: 467 average time/residue: 0.3537 time to fit residues: 230.3101 Evaluate side-chains 467 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 413 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 276 GLN Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 141 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 31 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN K 79 GLN I 37 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16786 Z= 0.235 Angle : 0.606 8.535 22795 Z= 0.314 Chirality : 0.043 0.166 2577 Planarity : 0.005 0.058 2901 Dihedral : 5.500 59.264 2428 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.56 % Allowed : 14.78 % Favored : 81.67 % 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: 0.11 (0.19), residues: 1983 helix: 0.80 (0.26), residues: 416 sheet: 0.47 (0.23), residues: 532 loop : -0.38 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 94 HIS 0.006 0.001 HIS E 69 PHE 0.020 0.002 PHE E 122 TYR 0.073 0.002 TYR E 52 ARG 0.012 0.001 ARG A 117 *********************** 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 485 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 421 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8150 (mm) cc_final: 0.7551 (mt) REVERT: A 141 GLN cc_start: 0.7393 (tp-100) cc_final: 0.7145 (tp40) REVERT: A 193 GLN cc_start: 0.7057 (mp-120) cc_final: 0.6722 (mm-40) REVERT: A 458 PHE cc_start: 0.8501 (p90) cc_final: 0.8213 (p90) REVERT: A 466 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6948 (mm-30) REVERT: A 555 LEU cc_start: 0.8478 (mt) cc_final: 0.8189 (mt) REVERT: A 637 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7859 (t) REVERT: A 698 LEU cc_start: 0.8895 (mt) cc_final: 0.8555 (mt) REVERT: B 113 TYR cc_start: 0.8049 (t80) cc_final: 0.7683 (t80) REVERT: B 197 ASN cc_start: 0.7231 (t0) cc_final: 0.6984 (t0) REVERT: C 43 CYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5649 (p) REVERT: C 97 ASN cc_start: 0.8213 (m110) cc_final: 0.7913 (m-40) REVERT: C 110 ARG cc_start: 0.8447 (ppt170) cc_final: 0.8065 (ptt90) REVERT: C 121 LEU cc_start: 0.8385 (tp) cc_final: 0.8130 (tp) REVERT: E 78 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7502 (mmtt) REVERT: F 185 MET cc_start: 0.6479 (mmm) cc_final: 0.5935 (mmt) REVERT: F 246 SER cc_start: 0.8427 (t) cc_final: 0.8027 (p) REVERT: F 328 TYR cc_start: 0.7669 (p90) cc_final: 0.7469 (p90) REVERT: F 373 MET cc_start: 0.7658 (ttp) cc_final: 0.7428 (ttp) REVERT: K 48 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8288 (mp) REVERT: I 42 GLN cc_start: 0.7286 (mp10) cc_final: 0.6997 (mp10) outliers start: 64 outliers final: 53 residues processed: 458 average time/residue: 0.3534 time to fit residues: 225.6094 Evaluate side-chains 468 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 412 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 276 GLN Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 3.9990 chunk 21 optimal weight: 0.0570 chunk 110 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 162 optimal weight: 0.0050 chunk 108 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 0.5112 ------------------------------------------------------------------------------- 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 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 H 82 GLN J 31 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.003 0.042 16786 Z= 0.202 Angle : 0.582 8.324 22795 Z= 0.301 Chirality : 0.043 0.152 2577 Planarity : 0.005 0.056 2901 Dihedral : 5.310 57.073 2428 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.22 % Allowed : 15.33 % Favored : 81.44 % 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: 0.18 (0.19), residues: 1983 helix: 0.91 (0.26), residues: 416 sheet: 0.50 (0.23), residues: 533 loop : -0.35 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 94 HIS 0.006 0.001 HIS E 69 PHE 0.020 0.002 PHE E 122 TYR 0.069 0.002 TYR E 52 ARG 0.013 0.001 ARG A 117 *********************** 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 480 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 422 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8167 (mm) cc_final: 0.7550 (mt) REVERT: A 193 GLN cc_start: 0.7021 (mp-120) cc_final: 0.6690 (mm-40) REVERT: A 466 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6950 (mm-30) REVERT: A 555 LEU cc_start: 0.8473 (mt) cc_final: 0.8198 (mt) REVERT: A 637 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7834 (t) REVERT: A 698 LEU cc_start: 0.8895 (mt) cc_final: 0.8558 (mt) REVERT: B 113 TYR cc_start: 0.8040 (t80) cc_final: 0.7701 (t80) REVERT: B 197 ASN cc_start: 0.7169 (t0) cc_final: 0.6907 (t0) REVERT: C 43 CYS cc_start: 0.6028 (OUTLIER) cc_final: 0.5616 (p) REVERT: C 97 ASN cc_start: 0.8199 (m110) cc_final: 0.7909 (m-40) REVERT: C 110 ARG cc_start: 0.8450 (ppt170) cc_final: 0.8111 (ptt90) REVERT: C 121 LEU cc_start: 0.8343 (tp) cc_final: 0.8060 (tp) REVERT: F 185 MET cc_start: 0.6409 (mmm) cc_final: 0.5878 (mmt) REVERT: F 246 SER cc_start: 0.8389 (t) cc_final: 0.7996 (p) REVERT: F 328 TYR cc_start: 0.7643 (p90) cc_final: 0.7400 (p90) REVERT: H 73 ASP cc_start: 0.5869 (t0) cc_final: 0.5625 (t70) REVERT: K 48 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8257 (mp) REVERT: I 42 GLN cc_start: 0.7295 (mp10) cc_final: 0.6993 (mp10) outliers start: 58 outliers final: 48 residues processed: 457 average time/residue: 0.3546 time to fit residues: 225.6955 Evaluate side-chains 466 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 415 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 276 GLN Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 17 optimal weight: 0.0970 chunk 151 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 141 GLN ** 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 J 31 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN K 79 GLN I 37 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16786 Z= 0.234 Angle : 0.596 9.468 22795 Z= 0.308 Chirality : 0.043 0.149 2577 Planarity : 0.005 0.049 2901 Dihedral : 5.319 57.541 2428 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.44 % Allowed : 15.56 % Favored : 81.00 % 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: 0.14 (0.19), residues: 1983 helix: 0.87 (0.26), residues: 416 sheet: 0.50 (0.22), residues: 533 loop : -0.39 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 94 HIS 0.006 0.001 HIS E 69 PHE 0.019 0.002 PHE E 122 TYR 0.060 0.002 TYR E 52 ARG 0.013 0.001 ARG A 117 *********************** 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 483 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 421 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8146 (mm) cc_final: 0.7530 (mt) REVERT: A 193 GLN cc_start: 0.7010 (mp-120) cc_final: 0.6678 (mm-40) REVERT: A 466 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6971 (mm-30) REVERT: A 555 LEU cc_start: 0.8489 (mt) cc_final: 0.8202 (mt) REVERT: A 637 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7835 (t) REVERT: A 698 LEU cc_start: 0.8896 (mt) cc_final: 0.8554 (mt) REVERT: B 197 ASN cc_start: 0.7143 (t0) cc_final: 0.6885 (t0) REVERT: C 43 CYS cc_start: 0.6047 (OUTLIER) cc_final: 0.5627 (p) REVERT: C 97 ASN cc_start: 0.8200 (m110) cc_final: 0.7817 (m-40) REVERT: C 110 ARG cc_start: 0.8447 (ppt170) cc_final: 0.8127 (ptt90) REVERT: C 121 LEU cc_start: 0.8329 (tp) cc_final: 0.8063 (tp) REVERT: F 185 MET cc_start: 0.6507 (mmm) cc_final: 0.5967 (mmt) REVERT: F 246 SER cc_start: 0.8359 (t) cc_final: 0.7946 (p) REVERT: F 577 ARG cc_start: 0.7032 (mtt-85) cc_final: 0.6777 (mtt90) REVERT: J 45 LEU cc_start: 0.8852 (mt) cc_final: 0.8468 (mt) REVERT: K 48 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8259 (mp) REVERT: I 42 GLN cc_start: 0.7300 (mp10) cc_final: 0.7001 (mp10) outliers start: 62 outliers final: 54 residues processed: 457 average time/residue: 0.3581 time to fit residues: 227.8281 Evaluate side-chains 471 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 414 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 276 GLN Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** 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 ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16786 Z= 0.284 Angle : 0.625 10.374 22795 Z= 0.322 Chirality : 0.044 0.162 2577 Planarity : 0.005 0.046 2901 Dihedral : 5.435 58.724 2428 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.61 % Allowed : 15.83 % Favored : 80.56 % 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: 0.06 (0.19), residues: 1983 helix: 0.77 (0.26), residues: 416 sheet: 0.43 (0.22), residues: 538 loop : -0.41 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 94 HIS 0.007 0.001 HIS E 69 PHE 0.020 0.002 PHE E 122 TYR 0.060 0.002 TYR E 52 ARG 0.016 0.001 ARG A 117 *********************** 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 487 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 422 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8154 (mm) cc_final: 0.7539 (mt) REVERT: A 193 GLN cc_start: 0.7006 (mp-120) cc_final: 0.6666 (mm-40) REVERT: A 466 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6796 (mm-30) REVERT: A 555 LEU cc_start: 0.8549 (mt) cc_final: 0.8271 (mt) REVERT: A 637 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7841 (t) REVERT: A 698 LEU cc_start: 0.8896 (mt) cc_final: 0.8564 (mt) REVERT: B 197 ASN cc_start: 0.7211 (t0) cc_final: 0.6956 (t0) REVERT: C 43 CYS cc_start: 0.6148 (OUTLIER) cc_final: 0.5742 (p) REVERT: C 97 ASN cc_start: 0.8229 (m110) cc_final: 0.7849 (m-40) REVERT: C 110 ARG cc_start: 0.8452 (ppt170) cc_final: 0.8134 (ptt90) REVERT: C 121 LEU cc_start: 0.8328 (tp) cc_final: 0.8078 (tp) REVERT: D 158 LEU cc_start: 0.8431 (mt) cc_final: 0.8166 (mp) REVERT: F 246 SER cc_start: 0.8358 (t) cc_final: 0.7954 (p) REVERT: F 577 ARG cc_start: 0.7043 (mtt-85) cc_final: 0.6789 (mtt90) REVERT: H 87 ARG cc_start: 0.7156 (mtt90) cc_final: 0.6844 (mtt180) REVERT: K 48 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8276 (mp) REVERT: I 42 GLN cc_start: 0.7279 (mp10) cc_final: 0.6987 (mp10) outliers start: 65 outliers final: 59 residues processed: 460 average time/residue: 0.3562 time to fit residues: 228.9171 Evaluate side-chains 480 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 418 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 276 GLN Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU 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: 4.9990 chunk 132 optimal weight: 0.0060 chunk 199 optimal weight: 0.9980 chunk 183 optimal weight: 0.3980 chunk 158 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 126 optimal weight: 0.0870 chunk 169 optimal weight: 0.0770 overall best weight: 0.1932 ------------------------------------------------------------------------------- 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 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 HIS ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS F 276 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN I 37 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 16786 Z= 0.148 Angle : 0.561 10.554 22795 Z= 0.288 Chirality : 0.042 0.146 2577 Planarity : 0.004 0.046 2901 Dihedral : 4.992 54.706 2428 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.28 % Allowed : 17.06 % Favored : 80.67 % 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: 0.27 (0.19), residues: 1983 helix: 0.99 (0.26), residues: 421 sheet: 0.57 (0.22), residues: 535 loop : -0.31 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 94 HIS 0.003 0.001 HIS E 69 PHE 0.018 0.001 PHE E 122 TYR 0.056 0.001 TYR E 52 ARG 0.019 0.001 ARG A 117 ********************** 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 479 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 438 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.7978 (mm) cc_final: 0.7493 (mt) REVERT: A 193 GLN cc_start: 0.6878 (mp-120) cc_final: 0.6535 (mm-40) REVERT: A 466 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 555 LEU cc_start: 0.8473 (mt) cc_final: 0.8188 (mt) REVERT: A 698 LEU cc_start: 0.8883 (mt) cc_final: 0.8541 (mt) REVERT: B 113 TYR cc_start: 0.8009 (t80) cc_final: 0.7667 (t80) REVERT: B 197 ASN cc_start: 0.7220 (t0) cc_final: 0.6933 (t0) REVERT: C 43 CYS cc_start: 0.6419 (OUTLIER) cc_final: 0.5872 (p) REVERT: C 110 ARG cc_start: 0.8416 (ppt170) cc_final: 0.8139 (ptt90) REVERT: F 185 MET cc_start: 0.6186 (mmm) cc_final: 0.5848 (mmp) REVERT: F 246 SER cc_start: 0.8326 (t) cc_final: 0.7925 (p) REVERT: F 330 GLN cc_start: 0.8097 (pt0) cc_final: 0.7810 (pt0) REVERT: F 577 ARG cc_start: 0.6943 (mtt-85) cc_final: 0.6697 (mtt90) REVERT: H 16 ARG cc_start: 0.7914 (mmt90) cc_final: 0.7620 (mmt-90) REVERT: H 87 ARG cc_start: 0.7064 (mtt90) cc_final: 0.6812 (mtt180) REVERT: J 32 TYR cc_start: 0.8675 (m-80) cc_final: 0.8459 (m-80) REVERT: J 45 LEU cc_start: 0.8815 (mt) cc_final: 0.8454 (mt) REVERT: I 42 GLN cc_start: 0.7359 (mp10) cc_final: 0.6985 (mp10) outliers start: 41 outliers final: 34 residues processed: 462 average time/residue: 0.3660 time to fit residues: 236.0236 Evaluate side-chains 456 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 421 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 276 GLN Chi-restraints excluded: chain F residue 309 SER Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.1980 chunk 146 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS F 276 GLN J 31 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.086738 restraints weight = 29664.491| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.52 r_work: 0.2964 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2374 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= 0.225 Angle : 0.593 9.681 22795 Z= 0.305 Chirality : 0.043 0.156 2577 Planarity : 0.004 0.047 2901 Dihedral : 5.154 56.719 2428 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.06 % Allowed : 17.89 % Favored : 80.06 % 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: 0.93 (0.26), residues: 418 sheet: 0.57 (0.23), residues: 526 loop : -0.33 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 179 HIS 0.006 0.001 HIS E 69 PHE 0.023 0.002 PHE E 122 TYR 0.069 0.002 TYR E 52 ARG 0.016 0.001 ARG A 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4790.10 seconds wall clock time: 86 minutes 57.25 seconds (5217.25 seconds total)