Starting phenix.real_space_refine on Fri Mar 15 09:09:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/03_2024/6idf_9648_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/03_2024/6idf_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_9648/03_2024/6idf_9648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/03_2024/6idf_9648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/03_2024/6idf_9648_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/03_2024/6idf_9648_updated.pdb" } resolution = 2.7 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= 0.000 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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 6 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: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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: 6.74, per 1000 atoms: 0.60 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: 5.00 Conformation dependent library (CDL) restraints added in 2.1 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: 2.19 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: 3.23 Time building geometry restraints manager: 5.41 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=" 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 angle pdb=" N PRO B 117 " pdb=" CA PRO B 117 " pdb=" CB PRO B 117 " ideal model delta sigma weight residual 103.25 110.99 -7.74 1.05e+00 9.07e-01 5.44e+01 ... (remaining 15610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.33: 6779 23.33 - 46.66: 269 46.66 - 69.98: 75 69.98 - 93.31: 33 93.31 - 116.64: 14 Dihedral angle restraints: 7170 sinusoidal: 3193 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 7167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1707 0.097 - 0.194: 146 0.194 - 0.291: 10 0.291 - 0.388: 3 0.388 - 0.485: 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 5.87e+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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.750 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.830 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.008 0.177 11462 Z= 0.494 Angle : 1.173 23.476 15615 Z= 0.557 Chirality : 0.059 0.485 1868 Planarity : 0.007 0.084 1877 Dihedral : 15.399 116.639 4589 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 % Allowed : 2.99 % Favored : 96.58 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP C 227 HIS 0.012 0.003 HIS C 197 PHE 0.041 0.003 PHE C 132 TYR 0.030 0.002 TYR A 565 ARG 0.013 0.001 ARG A 432 *********************** 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 : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 PHE cc_start: 0.8577 (m-80) cc_final: 0.8260 (m-80) REVERT: B 165 TRP cc_start: 0.7314 (t60) cc_final: 0.6977 (t60) REVERT: B 248 LEU cc_start: 0.8061 (mt) cc_final: 0.7522 (tm) REVERT: B 259 VAL cc_start: 0.7387 (p) cc_final: 0.7093 (m) REVERT: C 117 MET cc_start: 0.8093 (mtm) cc_final: 0.7874 (mtt) outliers start: 5 outliers final: 2 residues processed: 222 average time/residue: 1.1062 time to fit residues: 266.5315 Evaluate side-chains 128 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain C residue 134 VAL 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: 0.6980 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: 1.1184 ------------------------------------------------------------------------------- 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: 0.8066 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11462 Z= 0.258 Angle : 0.694 9.900 15615 Z= 0.335 Chirality : 0.045 0.243 1868 Planarity : 0.005 0.101 1877 Dihedral : 14.030 109.943 2264 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.51 % Favored : 93.41 % Rotamer: Outliers : 4.04 % Allowed : 9.31 % Favored : 86.65 % 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: -2.37 (0.21), residues: 1351 helix: -0.58 (0.19), residues: 697 sheet: -1.62 (0.41), residues: 131 loop : -2.90 (0.22), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 227 HIS 0.008 0.002 HIS A 449 PHE 0.037 0.002 PHE A 302 TYR 0.015 0.002 TYR A 565 ARG 0.005 0.001 ARG A 432 *********************** 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 176 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 130 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.6864 (tp30) cc_final: 0.6522 (tm-30) REVERT: A 231 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8381 (mmm) REVERT: A 583 ARG cc_start: 0.6882 (ttp80) cc_final: 0.6644 (ttt180) REVERT: A 601 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: A 657 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8413 (ptt-90) REVERT: B 248 LEU cc_start: 0.7919 (mt) cc_final: 0.7515 (tm) REVERT: B 259 VAL cc_start: 0.7476 (p) cc_final: 0.7136 (m) outliers start: 46 outliers final: 17 residues processed: 160 average time/residue: 1.2567 time to fit residues: 216.9137 Evaluate side-chains 137 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 76 THR 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: 2.9990 chunk 102 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 121 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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 222 HIS A 553 HIS A 587 GLN B 135 ASN B 222 GLN C 240 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11462 Z= 0.399 Angle : 0.758 11.815 15615 Z= 0.370 Chirality : 0.049 0.256 1868 Planarity : 0.006 0.099 1877 Dihedral : 12.932 114.779 2264 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.83 % Allowed : 12.12 % Favored : 83.06 % 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: -0.00 (0.20), residues: 700 sheet: -1.47 (0.41), residues: 134 loop : -2.66 (0.23), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 209 HIS 0.013 0.002 HIS A 449 PHE 0.038 0.003 PHE A 302 TYR 0.022 0.002 TYR B 225 ARG 0.007 0.001 ARG A 432 *********************** 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 170 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 115 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8382 (tpt) REVERT: A 474 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7630 (tp30) REVERT: A 583 ARG cc_start: 0.7114 (ttp80) cc_final: 0.6840 (ttt180) REVERT: A 601 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: A 657 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8426 (ptt-90) REVERT: B 248 LEU cc_start: 0.7927 (mt) cc_final: 0.7541 (tm) REVERT: B 259 VAL cc_start: 0.7509 (p) cc_final: 0.7217 (m) REVERT: C 180 ASP cc_start: 0.8215 (t70) cc_final: 0.7929 (t0) outliers start: 55 outliers final: 26 residues processed: 153 average time/residue: 1.2215 time to fit residues: 202.1090 Evaluate side-chains 143 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.1980 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11462 Z= 0.255 Angle : 0.645 11.824 15615 Z= 0.314 Chirality : 0.045 0.260 1868 Planarity : 0.005 0.085 1877 Dihedral : 12.213 117.637 2264 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.69 % Allowed : 14.40 % Favored : 81.91 % 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: -1.19 (0.22), residues: 1351 helix: 0.45 (0.20), residues: 700 sheet: -1.31 (0.41), residues: 134 loop : -2.41 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 165 HIS 0.007 0.001 HIS A 449 PHE 0.033 0.002 PHE A 302 TYR 0.014 0.002 TYR B 225 ARG 0.008 0.001 ARG C 237 *********************** 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 161 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 119 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7708 (t0) cc_final: 0.7422 (t0) REVERT: A 174 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8188 (mm-30) REVERT: A 237 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: A 343 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8313 (tpt) REVERT: A 364 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: A 408 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7865 (p) REVERT: A 531 ASN cc_start: 0.7932 (m110) cc_final: 0.7650 (m-40) REVERT: A 583 ARG cc_start: 0.7115 (ttp80) cc_final: 0.6853 (ttt180) REVERT: A 601 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7055 (tt0) REVERT: A 657 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8365 (ptt-90) REVERT: A 669 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: B 153 LEU cc_start: 0.5235 (OUTLIER) cc_final: 0.5012 (tt) REVERT: B 248 LEU cc_start: 0.7918 (mt) cc_final: 0.7545 (tm) REVERT: B 259 VAL cc_start: 0.7469 (p) cc_final: 0.7121 (m) REVERT: C 180 ASP cc_start: 0.8166 (t70) cc_final: 0.7865 (t0) REVERT: D 54 LYS cc_start: 0.7687 (ttmm) cc_final: 0.7349 (ttpt) outliers start: 42 outliers final: 22 residues processed: 149 average time/residue: 1.2765 time to fit residues: 205.5913 Evaluate side-chains 142 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 0.0670 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- 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 33 ASN ** 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: 0.8139 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11462 Z= 0.292 Angle : 0.666 12.852 15615 Z= 0.324 Chirality : 0.046 0.255 1868 Planarity : 0.005 0.089 1877 Dihedral : 11.975 115.213 2264 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.57 % Allowed : 14.75 % Favored : 80.68 % 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: -1.00 (0.23), residues: 1351 helix: 0.61 (0.20), residues: 703 sheet: -1.20 (0.41), residues: 134 loop : -2.33 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 165 HIS 0.009 0.001 HIS A 449 PHE 0.035 0.002 PHE A 302 TYR 0.019 0.002 TYR D 18 ARG 0.010 0.001 ARG C 237 *********************** 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 167 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 115 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.6745 (tp30) cc_final: 0.6453 (tm-30) REVERT: A 237 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: A 343 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8335 (tpt) REVERT: A 408 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7940 (p) REVERT: A 583 ARG cc_start: 0.7108 (ttp80) cc_final: 0.6859 (ttt180) REVERT: A 601 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: A 657 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8397 (ptt-90) REVERT: A 669 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: B 153 LEU cc_start: 0.5254 (OUTLIER) cc_final: 0.5036 (tt) REVERT: B 194 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8267 (p0) REVERT: B 248 LEU cc_start: 0.7936 (mt) cc_final: 0.7573 (tm) REVERT: B 259 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.7012 (m) REVERT: C 180 ASP cc_start: 0.8182 (t70) cc_final: 0.7896 (t0) outliers start: 52 outliers final: 26 residues processed: 156 average time/residue: 1.2842 time to fit residues: 218.2370 Evaluate side-chains 147 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 112 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 125 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 33 ASN ** 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: 0.8108 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11462 Z= 0.193 Angle : 0.603 12.308 15615 Z= 0.292 Chirality : 0.043 0.244 1868 Planarity : 0.004 0.079 1877 Dihedral : 11.512 112.912 2264 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.60 % Allowed : 16.33 % Favored : 80.07 % 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: -0.66 (0.23), residues: 1351 helix: 0.89 (0.20), residues: 700 sheet: -0.95 (0.42), residues: 130 loop : -2.19 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 165 HIS 0.005 0.001 HIS A 449 PHE 0.030 0.001 PHE A 302 TYR 0.016 0.001 TYR D 19 ARG 0.011 0.000 ARG C 237 *********************** 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: 41 poor density : 122 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7654 (t0) cc_final: 0.7405 (t0) REVERT: A 186 GLU cc_start: 0.6659 (tp30) cc_final: 0.6381 (tm-30) REVERT: A 237 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7247 (mp10) REVERT: A 343 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8329 (tpt) REVERT: A 408 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7829 (p) REVERT: A 583 ARG cc_start: 0.6966 (ttp80) cc_final: 0.6701 (ttt180) REVERT: A 601 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7038 (tt0) REVERT: A 657 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8381 (ptt-90) REVERT: B 248 LEU cc_start: 0.7898 (mt) cc_final: 0.7560 (tm) REVERT: B 259 VAL cc_start: 0.7417 (p) cc_final: 0.7085 (m) REVERT: C 237 ARG cc_start: 0.6941 (mmm160) cc_final: 0.6673 (mmm-85) REVERT: D 54 LYS cc_start: 0.7804 (ttmm) cc_final: 0.7391 (ttpt) outliers start: 41 outliers final: 23 residues processed: 153 average time/residue: 1.1788 time to fit residues: 195.5918 Evaluate side-chains 141 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 76 THR 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: 0.6980 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 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: 0.8148 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11462 Z= 0.310 Angle : 0.681 13.484 15615 Z= 0.327 Chirality : 0.046 0.254 1868 Planarity : 0.005 0.086 1877 Dihedral : 11.634 111.889 2264 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.39 % Allowed : 15.54 % Favored : 80.07 % 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: -0.71 (0.23), residues: 1351 helix: 0.82 (0.20), residues: 704 sheet: -1.04 (0.41), residues: 134 loop : -2.17 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 165 HIS 0.008 0.001 HIS A 449 PHE 0.035 0.002 PHE A 302 TYR 0.018 0.002 TYR D 19 ARG 0.007 0.001 ARG C 237 *********************** 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 163 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 113 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 343 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8336 (tpt) REVERT: A 583 ARG cc_start: 0.7018 (ttp80) cc_final: 0.6742 (ttt90) REVERT: A 601 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7122 (tt0) REVERT: A 644 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.7052 (pt0) REVERT: A 657 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8409 (ptt-90) REVERT: B 248 LEU cc_start: 0.7937 (mt) cc_final: 0.7591 (tm) REVERT: B 259 VAL cc_start: 0.7435 (OUTLIER) cc_final: 0.7115 (m) REVERT: C 180 ASP cc_start: 0.8129 (t70) cc_final: 0.7894 (t0) REVERT: D 54 LYS cc_start: 0.7811 (ttmm) cc_final: 0.7499 (ttmm) outliers start: 50 outliers final: 31 residues processed: 154 average time/residue: 1.1576 time to fit residues: 193.7461 Evaluate side-chains 148 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 76 THR 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: 0.6980 chunk 25 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.8159 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11462 Z= 0.334 Angle : 0.703 13.940 15615 Z= 0.340 Chirality : 0.047 0.255 1868 Planarity : 0.005 0.083 1877 Dihedral : 11.717 110.935 2264 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.48 % Allowed : 16.15 % Favored : 79.37 % 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: -0.75 (0.23), residues: 1351 helix: 0.79 (0.20), residues: 703 sheet: -1.04 (0.41), residues: 134 loop : -2.19 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 165 HIS 0.009 0.002 HIS A 449 PHE 0.036 0.002 PHE A 302 TYR 0.018 0.002 TYR D 19 ARG 0.011 0.001 ARG C 237 *********************** 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 166 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 115 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8345 (tpt) REVERT: A 583 ARG cc_start: 0.7136 (ttp80) cc_final: 0.6871 (ttt90) REVERT: A 601 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: A 644 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7142 (pt0) REVERT: A 657 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8402 (ptt-90) REVERT: A 669 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: B 93 MET cc_start: 0.8623 (mtt) cc_final: 0.8422 (mtt) REVERT: B 210 MET cc_start: 0.7757 (mmm) cc_final: 0.7502 (mmm) REVERT: B 248 LEU cc_start: 0.7952 (mt) cc_final: 0.7599 (tm) REVERT: B 259 VAL cc_start: 0.7443 (OUTLIER) cc_final: 0.7123 (m) REVERT: C 237 ARG cc_start: 0.7006 (mmm160) cc_final: 0.6790 (mmm160) outliers start: 51 outliers final: 35 residues processed: 157 average time/residue: 1.2437 time to fit residues: 210.7395 Evaluate side-chains 155 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 114 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 76 THR 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: 8.9990 chunk 124 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11462 Z= 0.232 Angle : 0.642 13.432 15615 Z= 0.310 Chirality : 0.044 0.259 1868 Planarity : 0.005 0.083 1877 Dihedral : 11.416 108.790 2264 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.78 % Allowed : 17.21 % Favored : 79.02 % 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: -0.52 (0.23), residues: 1351 helix: 0.99 (0.20), residues: 701 sheet: -0.87 (0.42), residues: 130 loop : -2.11 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 165 HIS 0.006 0.001 HIS A 222 PHE 0.032 0.001 PHE A 302 TYR 0.019 0.002 TYR D 19 ARG 0.010 0.001 ARG C 237 *********************** 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 159 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 116 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7728 (t0) cc_final: 0.7474 (t0) REVERT: A 186 GLU cc_start: 0.6662 (tp30) cc_final: 0.6377 (tm-30) REVERT: A 237 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7488 (tp40) REVERT: A 343 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8305 (tpt) REVERT: A 507 PHE cc_start: 0.8567 (m-80) cc_final: 0.8354 (m-80) REVERT: A 583 ARG cc_start: 0.6985 (ttp80) cc_final: 0.6721 (ttt90) REVERT: A 601 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7136 (tt0) REVERT: A 644 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.7024 (pt0) REVERT: A 657 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8380 (ptt-90) REVERT: B 248 LEU cc_start: 0.7940 (mt) cc_final: 0.7592 (tm) REVERT: B 259 VAL cc_start: 0.7404 (OUTLIER) cc_final: 0.7062 (m) REVERT: C 237 ARG cc_start: 0.7040 (mmm160) cc_final: 0.6833 (mmm160) REVERT: D 54 LYS cc_start: 0.7862 (ttmm) cc_final: 0.7446 (ttpt) outliers start: 43 outliers final: 31 residues processed: 150 average time/residue: 1.2264 time to fit residues: 200.2710 Evaluate side-chains 151 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 7 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 444 HIS A 587 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: 0.8185 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11462 Z= 0.444 Angle : 0.775 14.917 15615 Z= 0.377 Chirality : 0.050 0.253 1868 Planarity : 0.005 0.086 1877 Dihedral : 11.947 110.624 2264 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.13 % Allowed : 17.30 % Favored : 78.58 % 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: -0.89 (0.23), residues: 1351 helix: 0.69 (0.20), residues: 707 sheet: -1.11 (0.40), residues: 140 loop : -2.30 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 165 HIS 0.012 0.002 HIS A 449 PHE 0.038 0.002 PHE A 302 TYR 0.022 0.002 TYR B 466 ARG 0.009 0.001 ARG C 237 ********************** 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 163 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 116 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7615 (tp40) REVERT: A 583 ARG cc_start: 0.7153 (ttp80) cc_final: 0.6921 (ttt90) REVERT: A 601 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7143 (tt0) REVERT: A 657 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8404 (ptt-90) REVERT: A 669 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: B 210 MET cc_start: 0.7918 (mmm) cc_final: 0.7689 (mmm) REVERT: B 248 LEU cc_start: 0.7927 (mt) cc_final: 0.7566 (tm) REVERT: B 259 VAL cc_start: 0.7375 (OUTLIER) cc_final: 0.7037 (m) REVERT: C 237 ARG cc_start: 0.6971 (mmm160) cc_final: 0.6749 (mmm160) REVERT: D 54 LYS cc_start: 0.7821 (ttmm) cc_final: 0.7405 (ttpt) outliers start: 47 outliers final: 34 residues processed: 154 average time/residue: 1.1966 time to fit residues: 199.5863 Evaluate side-chains 153 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 114 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 7 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105410 restraints weight = 14224.046| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.28 r_work: 0.3044 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11462 Z= 0.197 Angle : 0.641 13.896 15615 Z= 0.309 Chirality : 0.044 0.261 1868 Planarity : 0.004 0.079 1877 Dihedral : 11.305 108.255 2264 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.07 % Allowed : 18.79 % Favored : 78.14 % 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: 1.03 (0.20), residues: 700 sheet: -0.89 (0.42), residues: 130 loop : -2.14 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 165 HIS 0.006 0.001 HIS A 222 PHE 0.031 0.001 PHE A 302 TYR 0.019 0.001 TYR D 19 ARG 0.011 0.000 ARG A 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4222.18 seconds wall clock time: 75 minutes 1.46 seconds (4501.46 seconds total)