Starting phenix.real_space_refine (version: dev) on Mon Feb 20 03:13:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/02_2023/6idf_9648_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/02_2023/6idf_9648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/02_2023/6idf_9648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/02_2023/6idf_9648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/02_2023/6idf_9648_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/02_2023/6idf_9648_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11188 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2414 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 850 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "E" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 263 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 37} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 85 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 134 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 6.65, per 1000 atoms: 0.59 Number of scatterers: 11188 At special positions: 0 Unit cell: (110.191, 94.917, 133.102, 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) S 44 16.00 P 4 15.00 O 2034 8.00 N 1762 7.00 C 7344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS E 9 " 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=1, symmetry=0 Links applied BETA1-3 " BMA G 3 " - " BMA G 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA G 3 " - " BMA G 5 " NAG-ASN " NAG A 810 " - " ASN A 387 " " NAG A 817 " - " ASN A 464 " " NAG A 818 " - " ASN A 506 " " NAG A 819 " - " ASN A 264 " " NAG A 820 " - " ASN A 187 " " NAG F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 55 " " NAG H 1 " - " ASN A 435 " " NAG I 1 " - " ASN A 573 " " NAG J 1 " - " ASN A 530 " " NAG K 1 " - " ASN A 562 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.01 Conformation dependent library (CDL) restraints added in 1.7 seconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2566 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 4 sheets defined 50.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.862A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 removed outlier: 4.170A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 227 through 236 removed outlier: 3.998A pdb=" N ARG A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 235 " --> pdb=" O MET A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.572A pdb=" N ARG A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 404 removed outlier: 3.561A pdb=" N ASP A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 removed outlier: 4.163A pdb=" N LEU A 431 " --> pdb=" O GLN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 502 removed outlier: 3.705A pdb=" N ALA A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 540 through 545 removed outlier: 3.743A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 545' Processing helix chain 'A' and resid 562 through 575 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 666 through 692 removed outlier: 3.560A pdb=" N LEU A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 697 No H-bonds generated for 'chain 'A' and resid 694 through 697' Processing helix chain 'B' and resid 75 through 102 removed outlier: 3.902A pdb=" N HIS B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 125 through 153 removed outlier: 3.881A pdb=" N HIS B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 168 through 174 removed outlier: 4.334A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 195 through 213 removed outlier: 3.764A pdb=" N TRP B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 239 Processing helix chain 'B' and resid 243 through 262 removed outlier: 3.552A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.765A pdb=" N LEU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 398 removed outlier: 3.871A pdb=" N ALA B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 428 Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 454 through 462 Processing helix chain 'C' and resid 4 through 13 removed outlier: 3.564A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 24 Processing helix chain 'C' and resid 29 through 60 removed outlier: 4.150A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 106 removed outlier: 3.712A pdb=" N GLU C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 141 removed outlier: 3.597A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 184 removed outlier: 3.785A pdb=" N ALA C 166 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 202 removed outlier: 3.929A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 215 through 231 Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'D' and resid 8 through 23 removed outlier: 4.134A pdb=" N LEU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 41 removed outlier: 3.560A pdb=" N PHE D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 60 through 80 removed outlier: 3.575A pdb=" N PHE D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing helix chain 'E' and resid 4 through 7 removed outlier: 3.657A pdb=" N VAL E 7 " --> pdb=" O SER E 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.972A pdb=" N ALA E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 27 No H-bonds generated for 'chain 'E' and resid 24 through 27' Processing sheet with id= A, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.497A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 13.679A pdb=" N VAL A 75 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 74 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 626 through 630 removed outlier: 7.237A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ARG A 414 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.299A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 603 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 287 through 289 472 hydrogen bonds defined for protein. 1383 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: 2.98 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1680 1.31 - 1.44: 3232 1.44 - 1.57: 6471 1.57 - 1.70: 13 1.70 - 1.83: 66 Bond restraints: 11462 Sorted by residual: bond pdb=" C29 PC1 C 301 " pdb=" C2A PC1 C 301 " ideal model delta sigma weight residual 1.524 1.347 0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" C29 PC1 B 501 " pdb=" C2A PC1 B 501 " ideal model delta sigma weight residual 1.524 1.348 0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" C29 PC1 B 502 " pdb=" C2A PC1 B 502 " ideal model delta sigma weight residual 1.524 1.349 0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C29 PC1 D 201 " pdb=" C2A PC1 D 201 " ideal model delta sigma weight residual 1.524 1.349 0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" C31 PC1 B 502 " pdb=" O31 PC1 B 502 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 11457 not shown) Histogram of bond angle deviations from ideal: 94.89 - 102.72: 43 102.72 - 110.54: 3438 110.54 - 118.37: 5493 118.37 - 126.19: 6427 126.19 - 134.01: 214 Bond angle restraints: 15615 Sorted by residual: angle pdb=" C2 NAG J 2 " pdb=" N2 NAG J 2 " pdb=" C7 NAG J 2 " ideal model delta sigma weight residual 123.12 133.57 -10.45 1.28e+00 6.08e-01 6.63e+01 angle pdb=" O12 PC1 C 301 " pdb=" P PC1 C 301 " pdb=" O14 PC1 C 301 " ideal model delta sigma weight residual 123.67 100.19 23.48 3.00e+00 1.11e-01 6.12e+01 angle pdb=" O12 PC1 B 501 " pdb=" P PC1 B 501 " pdb=" O14 PC1 B 501 " ideal model delta sigma weight residual 123.67 101.07 22.60 3.00e+00 1.11e-01 5.68e+01 angle pdb=" O12 PC1 D 201 " pdb=" P PC1 D 201 " pdb=" O14 PC1 D 201 " ideal model delta sigma weight residual 123.67 101.14 22.53 3.00e+00 1.11e-01 5.64e+01 angle pdb=" O12 PC1 B 502 " pdb=" P PC1 B 502 " pdb=" O14 PC1 B 502 " ideal model delta sigma weight residual 123.67 101.17 22.50 3.00e+00 1.11e-01 5.62e+01 ... (remaining 15610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 6266 17.21 - 34.42: 286 34.42 - 51.63: 81 51.63 - 68.84: 21 68.84 - 86.06: 12 Dihedral angle restraints: 6666 sinusoidal: 2689 harmonic: 3977 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -169.97 83.97 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -164.97 78.97 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N PRO A 211 " pdb=" CA PRO A 211 " ideal model delta harmonic sigma weight residual 180.00 137.02 42.98 0 5.00e+00 4.00e-02 7.39e+01 ... (remaining 6663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1715 0.097 - 0.194: 141 0.194 - 0.291: 7 0.291 - 0.387: 3 0.387 - 0.484: 2 Chirality restraints: 1868 Sorted by residual: chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.01 -0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1 NAG A 819 " pdb=" ND2 ASN A 264 " pdb=" C2 NAG A 819 " pdb=" O5 NAG A 819 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1865 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 210 " -0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO A 211 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.020 2.00e-02 2.50e+03 1.73e-02 7.45e+00 pdb=" CG TRP C 227 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO A 560 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.036 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2843 2.80 - 3.33: 9818 3.33 - 3.85: 18037 3.85 - 4.38: 20936 4.38 - 4.90: 36250 Nonbonded interactions: 87884 Sorted by model distance: nonbonded pdb=" O VAL A 383 " pdb=" O6 NAG H 1 " model vdw 2.279 2.440 nonbonded pdb=" OG SER A 286 " pdb=" O VAL A 291 " model vdw 2.285 2.440 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.318 2.440 nonbonded pdb=" O PHE C 162 " pdb=" OH TYR C 218 " model vdw 2.323 2.440 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.329 2.440 ... (remaining 87879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 44 5.16 5 C 7344 2.51 5 N 1762 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.270 Check model and map are aligned: 0.170 Process input model: 31.190 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:11.430 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.007 0.177 11462 Z= 0.494 Angle : 1.147 23.476 15615 Z= 0.565 Chirality : 0.057 0.484 1868 Planarity : 0.007 0.084 1877 Dihedral : 12.102 86.056 4085 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.81 % Favored : 93.04 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.17), residues: 1351 helix: -2.36 (0.14), residues: 697 sheet: -1.88 (0.43), residues: 125 loop : -3.14 (0.21), residues: 529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 222 average time/residue: 1.1871 time to fit residues: 285.9642 Evaluate side-chains 128 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.6327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 142 ASN A 158 HIS A 305 GLN A 331 GLN A 358 ASN A 454 GLN A 531 ASN A 587 GLN A 606 GLN B 81 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 11462 Z= 0.248 Angle : 0.653 10.160 15615 Z= 0.333 Chirality : 0.044 0.314 1868 Planarity : 0.005 0.100 1877 Dihedral : 10.564 98.242 1758 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.49 % Rotamer Outliers : 4.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.21), residues: 1351 helix: -0.58 (0.19), residues: 697 sheet: -1.61 (0.41), residues: 131 loop : -2.88 (0.22), residues: 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 134 time to evaluate : 1.296 Fit side-chains outliers start: 47 outliers final: 18 residues processed: 164 average time/residue: 1.3055 time to fit residues: 231.5437 Evaluate side-chains 131 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1378 time to fit residues: 2.6633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 102 HIS A 194 GLN A 553 HIS A 585 GLN A 587 GLN B 222 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 11462 Z= 0.396 Angle : 0.732 11.850 15615 Z= 0.374 Chirality : 0.048 0.309 1868 Planarity : 0.006 0.100 1877 Dihedral : 10.405 98.575 1758 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 4.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.72 (0.22), residues: 1351 helix: -0.05 (0.20), residues: 706 sheet: -1.29 (0.43), residues: 123 loop : -2.64 (0.23), residues: 522 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 118 time to evaluate : 1.187 Fit side-chains outliers start: 50 outliers final: 23 residues processed: 153 average time/residue: 1.3083 time to fit residues: 216.9242 Evaluate side-chains 138 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 6 average time/residue: 0.1637 time to fit residues: 3.2186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 587 GLN B 222 GLN C 240 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 11462 Z= 0.268 Angle : 0.630 12.379 15615 Z= 0.322 Chirality : 0.044 0.316 1868 Planarity : 0.005 0.088 1877 Dihedral : 9.930 99.234 1758 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 3.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.18 (0.22), residues: 1351 helix: 0.47 (0.20), residues: 694 sheet: -1.26 (0.41), residues: 134 loop : -2.39 (0.24), residues: 523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 117 time to evaluate : 1.367 Fit side-chains outliers start: 43 outliers final: 22 residues processed: 147 average time/residue: 1.2689 time to fit residues: 202.6440 Evaluate side-chains 135 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 4 average time/residue: 0.1778 time to fit residues: 2.8422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.9990 chunk 74 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 0.0170 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 531 ASN A 587 GLN B 135 ASN C 240 GLN D 33 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 11462 Z= 0.158 Angle : 0.558 12.153 15615 Z= 0.282 Chirality : 0.041 0.290 1868 Planarity : 0.004 0.082 1877 Dihedral : 9.439 99.808 1758 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.68 (0.23), residues: 1351 helix: 0.88 (0.20), residues: 699 sheet: -0.92 (0.42), residues: 130 loop : -2.20 (0.25), residues: 522 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.259 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 153 average time/residue: 1.2243 time to fit residues: 204.4417 Evaluate side-chains 133 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 1.6643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.1980 chunk 117 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 163 GLN A 169 ASN A 222 HIS A 587 GLN C 240 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11462 Z= 0.194 Angle : 0.582 12.242 15615 Z= 0.291 Chirality : 0.042 0.307 1868 Planarity : 0.004 0.080 1877 Dihedral : 9.364 100.082 1758 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.50 (0.23), residues: 1351 helix: 1.04 (0.20), residues: 700 sheet: -0.95 (0.42), residues: 134 loop : -2.13 (0.25), residues: 517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 119 time to evaluate : 1.107 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 26 residues processed: 150 average time/residue: 1.1904 time to fit residues: 194.8170 Evaluate side-chains 141 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 5 average time/residue: 0.2109 time to fit residues: 3.2107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 222 HIS A 587 GLN C 240 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 11462 Z= 0.322 Angle : 0.672 14.029 15615 Z= 0.337 Chirality : 0.046 0.324 1868 Planarity : 0.005 0.085 1877 Dihedral : 9.596 100.003 1758 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.62 (0.23), residues: 1351 helix: 0.90 (0.20), residues: 703 sheet: -0.93 (0.42), residues: 134 loop : -2.16 (0.25), residues: 514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 112 time to evaluate : 1.303 Fit side-chains outliers start: 44 outliers final: 28 residues processed: 149 average time/residue: 1.2049 time to fit residues: 195.3065 Evaluate side-chains 138 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 3 average time/residue: 0.6919 time to fit residues: 3.8122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 0.0370 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS B 222 GLN C 240 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11462 Z= 0.226 Angle : 0.610 13.647 15615 Z= 0.307 Chirality : 0.043 0.307 1868 Planarity : 0.004 0.080 1877 Dihedral : 9.446 100.167 1758 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.49 (0.23), residues: 1351 helix: 1.00 (0.20), residues: 702 sheet: -0.84 (0.42), residues: 134 loop : -2.10 (0.26), residues: 515 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 29 residues processed: 153 average time/residue: 1.1356 time to fit residues: 190.1347 Evaluate side-chains 141 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 0.2364 time to fit residues: 2.6939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 587 GLN C 240 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 11462 Z= 0.277 Angle : 0.649 13.923 15615 Z= 0.325 Chirality : 0.044 0.315 1868 Planarity : 0.005 0.084 1877 Dihedral : 9.481 100.223 1758 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.51 (0.23), residues: 1351 helix: 0.99 (0.20), residues: 703 sheet: -0.83 (0.42), residues: 134 loop : -2.12 (0.26), residues: 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 115 time to evaluate : 1.175 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 29 residues processed: 145 average time/residue: 1.2707 time to fit residues: 200.5671 Evaluate side-chains 138 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 2 average time/residue: 0.3569 time to fit residues: 2.6990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 11462 Z= 0.275 Angle : 0.656 14.088 15615 Z= 0.329 Chirality : 0.045 0.311 1868 Planarity : 0.005 0.081 1877 Dihedral : 9.478 100.354 1758 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.50 (0.23), residues: 1351 helix: 1.00 (0.20), residues: 701 sheet: -0.89 (0.42), residues: 136 loop : -2.09 (0.26), residues: 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 1.129 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 28 residues processed: 142 average time/residue: 1.1439 time to fit residues: 177.3888 Evaluate side-chains 137 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 26 residues processed: 2 average time/residue: 0.2197 time to fit residues: 2.3889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 222 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106480 restraints weight = 14234.685| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.23 r_work: 0.3053 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11462 Z= 0.207 Angle : 0.608 13.530 15615 Z= 0.305 Chirality : 0.043 0.301 1868 Planarity : 0.004 0.081 1877 Dihedral : 9.314 100.687 1758 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.34 (0.23), residues: 1351 helix: 1.14 (0.20), residues: 699 sheet: -0.68 (0.43), residues: 131 loop : -2.05 (0.26), residues: 521 =============================================================================== Job complete usr+sys time: 3943.56 seconds wall clock time: 71 minutes 22.96 seconds (4282.96 seconds total)