Starting phenix.real_space_refine on Mon Apr 8 04:41:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7r_18230/04_2024/8q7r_18230_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7r_18230/04_2024/8q7r_18230.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7r_18230/04_2024/8q7r_18230_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7r_18230/04_2024/8q7r_18230_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7r_18230/04_2024/8q7r_18230_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7r_18230/04_2024/8q7r_18230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7r_18230/04_2024/8q7r_18230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7r_18230/04_2024/8q7r_18230_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7r_18230/04_2024/8q7r_18230_updated.pdb" } resolution = 3.71 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= 0.001 sd= 0.021 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 Zn 3 6.06 5 S 80 5.16 5 C 7996 2.51 5 N 2162 2.21 5 O 2295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12536 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4582 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 17, 'TRANS': 604} Chain breaks: 4 Unresolved non-hydrogen bonds: 535 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 34, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 349 Chain: "H" Number of atoms: 4328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4328 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 570} Chain breaks: 6 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 153 Chain: "U" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 40 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1053 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 162, 1047 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 13, 'TRANS': 148} Chain breaks: 4 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 162, 1047 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 13, 'TRANS': 148} Chain breaks: 4 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 1063 Chain: "D" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 671 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 729 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 91} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 548 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain breaks: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "U" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'U9O': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12134 SG CYS R 42 49.223 72.893 56.598 1.00 68.29 S ATOM 12150 SG CYS R 45 48.339 69.492 58.509 1.00 65.56 S ATOM 12360 SG CYS R 83 48.083 72.779 60.264 1.00 73.17 S ATOM 12289 SG CYS R 75 51.831 86.414 50.724 1.00 84.04 S ATOM 12445 SG CYS R 94 51.858 84.349 54.082 1.00 73.92 S ATOM 12200 SG CYS R 53 42.888 70.402 60.615 1.00 77.11 S ATOM 12219 SG CYS R 56 40.368 69.087 63.141 1.00 78.49 S ATOM 12245 SG CYS R 68 39.414 71.845 60.483 1.00 71.21 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER C 138 " occ=0.59 ... (10 atoms not shown) pdb=" OG BSER C 138 " occ=0.41 Time building chain proxies: 7.70, per 1000 atoms: 0.61 Number of scatterers: 12536 At special positions: 0 Unit cell: (132.787, 148.96, 171.091, 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) Zn 3 29.99 S 80 16.00 O 2295 8.00 N 2162 7.00 C 7996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY U 75 " - pdb=" N U9O U 701 " Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.54 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " Number of angles added : 6 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 7 sheets defined 49.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 11 through 26 removed outlier: 3.737A pdb=" N LYS A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.873A pdb=" N PHE A 39 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 77 Processing helix chain 'A' and resid 83 through 104 removed outlier: 3.542A pdb=" N ARG A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.969A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 229 Proline residue: A 210 - end of helix removed outlier: 3.960A pdb=" N GLU A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 250 removed outlier: 3.718A pdb=" N MET A 236 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.563A pdb=" N HIS A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 4.061A pdb=" N LEU A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 327 removed outlier: 3.512A pdb=" N GLN A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 357 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.670A pdb=" N SER A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 Processing helix chain 'A' and resid 411 through 424 removed outlier: 4.574A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 443 removed outlier: 3.858A pdb=" N GLN A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 465 Processing helix chain 'A' and resid 468 through 494 removed outlier: 3.717A pdb=" N SER A 471 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS A 472 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 473 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 487 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 494 " --> pdb=" O ASN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.919A pdb=" N LYS A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 590 removed outlier: 4.171A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.963A pdb=" N VAL A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 13 removed outlier: 3.642A pdb=" N ASN H 9 " --> pdb=" O THR H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 22 removed outlier: 3.557A pdb=" N LYS H 21 " --> pdb=" O ARG H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.637A pdb=" N ILE H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 31 through 35' Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 44 through 50 Processing helix chain 'H' and resid 54 through 63 Processing helix chain 'H' and resid 86 through 92 Processing helix chain 'H' and resid 96 through 104 Processing helix chain 'H' and resid 119 through 126 removed outlier: 4.147A pdb=" N ASP H 126 " --> pdb=" O ALA H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 137 Processing helix chain 'H' and resid 152 through 158 Processing helix chain 'H' and resid 162 through 170 Processing helix chain 'H' and resid 185 through 192 Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.608A pdb=" N TYR H 204 " --> pdb=" O MET H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 224 Processing helix chain 'H' and resid 227 through 235 removed outlier: 4.350A pdb=" N HIS H 235 " --> pdb=" O ASP H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 248 No H-bonds generated for 'chain 'H' and resid 246 through 248' Processing helix chain 'H' and resid 250 through 258 removed outlier: 3.534A pdb=" N VAL H 256 " --> pdb=" O GLY H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 267 Processing helix chain 'H' and resid 271 through 277 removed outlier: 4.185A pdb=" N MET H 275 " --> pdb=" O LYS H 271 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG H 276 " --> pdb=" O ALA H 272 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR H 277 " --> pdb=" O MET H 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 271 through 277' Processing helix chain 'H' and resid 315 through 330 Processing helix chain 'H' and resid 335 through 350 Processing helix chain 'H' and resid 354 through 371 removed outlier: 3.838A pdb=" N ASN H 359 " --> pdb=" O LYS H 355 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP H 361 " --> pdb=" O CYS H 357 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS H 362 " --> pdb=" O ILE H 358 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR H 363 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA H 364 " --> pdb=" O LEU H 360 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER H 370 " --> pdb=" O ASP H 366 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN H 371 " --> pdb=" O MET H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 394 Processing helix chain 'H' and resid 408 through 427 removed outlier: 3.670A pdb=" N GLU H 421 " --> pdb=" O LYS H 417 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE H 422 " --> pdb=" O SER H 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 454 removed outlier: 4.098A pdb=" N LYS H 454 " --> pdb=" O CYS H 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 475 removed outlier: 4.385A pdb=" N HIS H 463 " --> pdb=" O LEU H 459 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE H 464 " --> pdb=" O GLU H 460 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU H 475 " --> pdb=" O ARG H 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 489 Processing helix chain 'H' and resid 492 through 495 Processing helix chain 'H' and resid 508 through 517 removed outlier: 3.604A pdb=" N LEU H 514 " --> pdb=" O VAL H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 531 through 538 removed outlier: 3.725A pdb=" N ASN H 538 " --> pdb=" O ILE H 534 " (cutoff:3.500A) Processing helix chain 'H' and resid 541 through 550 Processing helix chain 'H' and resid 586 through 597 removed outlier: 4.329A pdb=" N ARG H 592 " --> pdb=" O CYS H 588 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL H 593 " --> pdb=" O LEU H 589 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE H 594 " --> pdb=" O ALA H 590 " (cutoff:3.500A) Processing helix chain 'H' and resid 607 through 615 removed outlier: 4.365A pdb=" N THR H 611 " --> pdb=" O GLU H 607 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE H 612 " --> pdb=" O LYS H 608 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 34 Processing helix chain 'U' and resid 38 through 40 No H-bonds generated for 'chain 'U' and resid 38 through 40' Processing helix chain 'U' and resid 56 through 59 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 121 through 132 removed outlier: 4.577A pdb=" N ASN C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 153 Processing helix chain 'C' and resid 160 through 178 Processing helix chain 'D' and resid 33 through 38 removed outlier: 4.138A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 46 Processing helix chain 'D' and resid 67 through 80 removed outlier: 4.086A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 75 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 78 " --> pdb=" O CYS D 74 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR D 79 " --> pdb=" O MET D 75 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS D 80 " --> pdb=" O TYR D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 110 removed outlier: 3.567A pdb=" N ASN D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 109 " --> pdb=" O MET D 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 34 removed outlier: 3.921A pdb=" N ARG G 29 " --> pdb=" O PHE G 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 57 No H-bonds generated for 'chain 'R' and resid 54 through 57' Processing helix chain 'R' and resid 82 through 88 Processing sheet with id= A, first strand: chain 'A' and resid 561 through 566 Processing sheet with id= B, first strand: chain 'A' and resid 593 through 595 Processing sheet with id= C, first strand: chain 'H' and resid 74 through 76 Processing sheet with id= D, first strand: chain 'U' and resid 12 through 16 Processing sheet with id= E, first strand: chain 'C' and resid 28 through 30 Processing sheet with id= F, first strand: chain 'D' and resid 28 through 32 removed outlier: 3.538A pdb=" N ILE D 22 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 2 through 9 removed outlier: 3.666A pdb=" N LEU G 5 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR G 16 " --> pdb=" O LEU G 5 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1440 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: 3.43 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4102 1.34 - 1.47: 2968 1.47 - 1.59: 5584 1.59 - 1.71: 0 1.71 - 1.84: 124 Bond restraints: 12778 Sorted by residual: bond pdb=" N ARG A 249 " pdb=" CA ARG A 249 " ideal model delta sigma weight residual 1.457 1.508 -0.051 1.32e-02 5.74e+03 1.48e+01 bond pdb=" N ILE C 94 " pdb=" CA ILE C 94 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.19e-02 7.06e+03 1.30e+01 bond pdb=" C PRO H 377 " pdb=" N MET H 378 " ideal model delta sigma weight residual 1.334 1.281 0.053 1.61e-02 3.86e+03 1.07e+01 bond pdb=" N VAL R 39 " pdb=" CA VAL R 39 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.47e+00 bond pdb=" N VAL R 38 " pdb=" CA VAL R 38 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.56e+00 ... (remaining 12773 not shown) Histogram of bond angle deviations from ideal: 97.50 - 104.85: 222 104.85 - 112.20: 6652 112.20 - 119.55: 4124 119.55 - 126.90: 6270 126.90 - 134.24: 163 Bond angle restraints: 17431 Sorted by residual: angle pdb=" CA ASN A 169 " pdb=" C ASN A 169 " pdb=" N ASP A 170 " ideal model delta sigma weight residual 118.44 108.40 10.04 1.41e+00 5.03e-01 5.07e+01 angle pdb=" CA PRO H 531 " pdb=" N PRO H 531 " pdb=" CD PRO H 531 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" N LEU U 73 " pdb=" CA LEU U 73 " pdb=" CB LEU U 73 " ideal model delta sigma weight residual 111.56 104.05 7.51 1.52e+00 4.33e-01 2.44e+01 angle pdb=" C ARG A 249 " pdb=" CA ARG A 249 " pdb=" CB ARG A 249 " ideal model delta sigma weight residual 110.11 101.91 8.20 1.90e+00 2.77e-01 1.86e+01 angle pdb=" O ASN A 169 " pdb=" C ASN A 169 " pdb=" N ASP A 170 " ideal model delta sigma weight residual 122.39 128.45 -6.06 1.48e+00 4.57e-01 1.67e+01 ... (remaining 17426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 6605 16.85 - 33.71: 717 33.71 - 50.56: 230 50.56 - 67.42: 44 67.42 - 84.27: 10 Dihedral angle restraints: 7606 sinusoidal: 2538 harmonic: 5068 Sorted by residual: dihedral pdb=" CA TYR H 500 " pdb=" C TYR H 500 " pdb=" N PRO H 501 " pdb=" CA PRO H 501 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA VAL H 502 " pdb=" C VAL H 502 " pdb=" N CYS H 503 " pdb=" CA CYS H 503 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLY C 90 " pdb=" C GLY C 90 " pdb=" N ASP C 91 " pdb=" CA ASP C 91 " ideal model delta harmonic sigma weight residual -180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 7603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1826 0.060 - 0.119: 237 0.119 - 0.179: 22 0.179 - 0.238: 5 0.238 - 0.298: 2 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CG LEU A 559 " pdb=" CB LEU A 559 " pdb=" CD1 LEU A 559 " pdb=" CD2 LEU A 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA GLU A 208 " pdb=" N GLU A 208 " pdb=" C GLU A 208 " pdb=" CB GLU A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA TRP R 35 " pdb=" N TRP R 35 " pdb=" C TRP R 35 " pdb=" CB TRP R 35 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2089 not shown) Planarity restraints: 2225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 530 " 0.077 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO H 531 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO H 531 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO H 531 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 93 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C CYS C 93 " 0.059 2.00e-02 2.50e+03 pdb=" O CYS C 93 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE C 94 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP H 434 " -0.055 5.00e-02 4.00e+02 8.46e-02 1.15e+01 pdb=" N PRO H 435 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO H 435 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO H 435 " -0.045 5.00e-02 4.00e+02 ... (remaining 2222 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 69 2.57 - 3.15: 10254 3.15 - 3.73: 18866 3.73 - 4.32: 23609 4.32 - 4.90: 39321 Nonbonded interactions: 92119 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.987 2.230 nonbonded pdb=" N GLN H 437 " pdb=" OE1 GLN H 437 " model vdw 2.260 2.520 nonbonded pdb=" OG SER A 591 " pdb=" O THR A 593 " model vdw 2.281 2.440 nonbonded pdb=" ND2 ASN C 115 " pdb=" O PRO R 95 " model vdw 2.296 2.520 nonbonded pdb=" NH2 ARG R 91 " pdb=" OD1 ASN R 98 " model vdw 2.304 2.520 ... (remaining 92114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 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: 11.510 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 39.890 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 12778 Z= 0.289 Angle : 0.740 12.867 17431 Z= 0.395 Chirality : 0.043 0.298 2092 Planarity : 0.006 0.123 2224 Dihedral : 16.368 84.272 4295 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.26 % Allowed : 24.94 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.20), residues: 1678 helix: 0.44 (0.18), residues: 871 sheet: -1.05 (0.66), residues: 72 loop : -2.18 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 35 HIS 0.008 0.001 HIS A 320 PHE 0.023 0.002 PHE A 202 TYR 0.023 0.002 TYR A 558 ARG 0.013 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 255 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6301 (mt-10) REVERT: A 470 THR cc_start: 0.5829 (t) cc_final: 0.4718 (m) REVERT: H 412 MET cc_start: 0.7356 (mmm) cc_final: 0.7122 (mmm) REVERT: D 108 ASN cc_start: 0.7969 (t0) cc_final: 0.7737 (t0) outliers start: 15 outliers final: 7 residues processed: 266 average time/residue: 0.2446 time to fit residues: 94.3646 Evaluate side-chains 249 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 241 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain C residue 95 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 0.0370 chunk 132 optimal weight: 0.5980 chunk 51 optimal weight: 0.0270 chunk 80 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 292 ASN A 320 HIS H 100 GLN H 368 GLN H 467 GLN ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12778 Z= 0.174 Angle : 0.564 12.731 17431 Z= 0.288 Chirality : 0.038 0.183 2092 Planarity : 0.005 0.063 2224 Dihedral : 5.373 54.971 1821 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.88 % Allowed : 24.85 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1678 helix: 0.63 (0.18), residues: 895 sheet: -1.07 (0.62), residues: 84 loop : -2.08 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 33 HIS 0.007 0.001 HIS A 320 PHE 0.019 0.001 PHE A 202 TYR 0.018 0.001 TYR H 601 ARG 0.004 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 247 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8153 (mmp) cc_final: 0.7921 (mmp) REVERT: A 582 MET cc_start: 0.6436 (mmm) cc_final: 0.6214 (mmm) REVERT: A 599 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7202 (mt) REVERT: A 622 MET cc_start: 0.5020 (ptp) cc_final: 0.4460 (ptp) REVERT: H 200 MET cc_start: 0.6005 (tpp) cc_final: 0.5622 (tpt) REVERT: H 412 MET cc_start: 0.7391 (mmm) cc_final: 0.7082 (mmm) REVERT: H 515 ILE cc_start: 0.8087 (mp) cc_final: 0.7868 (mp) REVERT: H 545 ASN cc_start: 0.8288 (m-40) cc_final: 0.8013 (m-40) REVERT: C 83 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7848 (p-80) REVERT: D 33 ARG cc_start: 0.7531 (ttm170) cc_final: 0.7328 (mmm160) REVERT: D 108 ASN cc_start: 0.8011 (t0) cc_final: 0.7807 (t0) REVERT: G 77 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8084 (pp) outliers start: 46 outliers final: 25 residues processed: 271 average time/residue: 0.2259 time to fit residues: 90.5600 Evaluate side-chains 266 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 238 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 391 SER Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain R residue 79 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 166 optimal weight: 0.3980 chunk 136 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 123 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS H 368 GLN H 467 GLN ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12778 Z= 0.211 Angle : 0.569 12.638 17431 Z= 0.290 Chirality : 0.039 0.181 2092 Planarity : 0.005 0.058 2224 Dihedral : 4.508 46.261 1808 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.80 % Allowed : 24.85 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1678 helix: 0.72 (0.18), residues: 888 sheet: -1.02 (0.62), residues: 84 loop : -2.03 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 33 HIS 0.008 0.001 HIS A 320 PHE 0.023 0.001 PHE A 202 TYR 0.016 0.001 TYR H 343 ARG 0.005 0.000 ARG H 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 240 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8194 (mmp) cc_final: 0.7895 (mmp) REVERT: A 582 MET cc_start: 0.6526 (mmm) cc_final: 0.6291 (mmm) REVERT: A 599 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7270 (mt) REVERT: A 622 MET cc_start: 0.4864 (ptp) cc_final: 0.4314 (ptp) REVERT: H 412 MET cc_start: 0.7523 (mmm) cc_final: 0.7280 (mmm) REVERT: H 434 ASP cc_start: 0.7425 (t0) cc_final: 0.7104 (t70) REVERT: H 515 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7948 (mp) REVERT: U 1 MET cc_start: 0.3690 (tmt) cc_final: 0.3284 (tpt) REVERT: C 83 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7789 (p-80) REVERT: D 108 ASN cc_start: 0.8040 (t0) cc_final: 0.7836 (t0) REVERT: G 77 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8069 (pp) outliers start: 57 outliers final: 38 residues processed: 269 average time/residue: 0.1721 time to fit residues: 67.5058 Evaluate side-chains 276 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 391 SER Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain R residue 79 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 103 optimal weight: 0.1980 chunk 154 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 320 HIS H 368 GLN H 467 GLN ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12778 Z= 0.198 Angle : 0.548 12.178 17431 Z= 0.281 Chirality : 0.039 0.185 2092 Planarity : 0.005 0.056 2224 Dihedral : 4.441 42.142 1808 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.99 % Favored : 92.96 % Rotamer: Outliers : 4.97 % Allowed : 24.77 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1678 helix: 0.72 (0.18), residues: 892 sheet: -0.96 (0.63), residues: 84 loop : -1.98 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 87 HIS 0.008 0.001 HIS A 320 PHE 0.020 0.001 PHE A 202 TYR 0.015 0.001 TYR H 158 ARG 0.005 0.000 ARG H 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 244 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8162 (mmp) cc_final: 0.7898 (mmp) REVERT: A 352 GLN cc_start: 0.8033 (tp40) cc_final: 0.7709 (tp-100) REVERT: A 359 ASN cc_start: 0.8327 (t0) cc_final: 0.8126 (t0) REVERT: A 599 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7227 (mt) REVERT: A 622 MET cc_start: 0.5104 (ptp) cc_final: 0.4758 (ptp) REVERT: H 412 MET cc_start: 0.7507 (mmm) cc_final: 0.7278 (mmm) REVERT: H 434 ASP cc_start: 0.7367 (t0) cc_final: 0.7095 (t70) REVERT: H 515 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7948 (mp) REVERT: H 595 VAL cc_start: 0.7813 (m) cc_final: 0.7497 (t) REVERT: U 1 MET cc_start: 0.3704 (tmt) cc_final: 0.3101 (tpt) REVERT: C 83 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7801 (p-80) REVERT: G 77 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8061 (pp) outliers start: 59 outliers final: 37 residues processed: 278 average time/residue: 0.2371 time to fit residues: 96.4816 Evaluate side-chains 279 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 238 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 391 SER Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 544 MET Chi-restraints excluded: chain H residue 588 CYS Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain R residue 79 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 146 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 320 HIS ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12778 Z= 0.174 Angle : 0.549 12.287 17431 Z= 0.274 Chirality : 0.038 0.184 2092 Planarity : 0.005 0.053 2224 Dihedral : 4.249 38.942 1807 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.75 % Favored : 93.19 % Rotamer: Outliers : 5.39 % Allowed : 24.77 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1678 helix: 0.85 (0.18), residues: 888 sheet: -0.60 (0.65), residues: 81 loop : -1.94 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 87 HIS 0.007 0.001 HIS A 320 PHE 0.020 0.001 PHE A 112 TYR 0.014 0.001 TYR H 601 ARG 0.004 0.000 ARG H 478 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 247 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8138 (mmp) cc_final: 0.7819 (mmp) REVERT: A 352 GLN cc_start: 0.7950 (tp40) cc_final: 0.7738 (tp-100) REVERT: A 359 ASN cc_start: 0.8341 (t0) cc_final: 0.8068 (t0) REVERT: A 599 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7190 (mp) REVERT: A 622 MET cc_start: 0.5286 (ptp) cc_final: 0.4953 (ptp) REVERT: H 209 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.6205 (mt-10) REVERT: H 412 MET cc_start: 0.7462 (mmm) cc_final: 0.7236 (mmm) REVERT: H 434 ASP cc_start: 0.7423 (t0) cc_final: 0.7132 (t70) REVERT: H 515 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7960 (mp) REVERT: U 1 MET cc_start: 0.3774 (tmt) cc_final: 0.3324 (tpt) REVERT: C 83 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7855 (p-80) REVERT: G 77 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8066 (pp) outliers start: 64 outliers final: 42 residues processed: 280 average time/residue: 0.2390 time to fit residues: 98.0048 Evaluate side-chains 292 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 245 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 235 HIS Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain H residue 336 ASP Chi-restraints excluded: chain H residue 391 SER Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain R residue 79 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 6.9990 chunk 147 optimal weight: 0.0470 chunk 32 optimal weight: 0.0000 chunk 95 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 135 optimal weight: 0.0770 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.2640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 320 HIS ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12778 Z= 0.142 Angle : 0.526 12.377 17431 Z= 0.263 Chirality : 0.037 0.184 2092 Planarity : 0.005 0.052 2224 Dihedral : 4.108 38.599 1807 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.51 % Favored : 93.43 % Rotamer: Outliers : 4.97 % Allowed : 25.61 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1678 helix: 1.00 (0.18), residues: 885 sheet: -0.54 (0.65), residues: 81 loop : -1.88 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 87 HIS 0.008 0.001 HIS A 320 PHE 0.021 0.001 PHE A 112 TYR 0.011 0.001 TYR H 601 ARG 0.004 0.000 ARG H 478 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 252 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8098 (mmp) cc_final: 0.7790 (mmp) REVERT: A 359 ASN cc_start: 0.8297 (t0) cc_final: 0.7979 (t0) REVERT: A 370 LYS cc_start: 0.8318 (mttm) cc_final: 0.8111 (mttm) REVERT: A 599 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7193 (mp) REVERT: H 209 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6234 (mt-10) REVERT: H 412 MET cc_start: 0.7432 (mmm) cc_final: 0.7178 (mmm) REVERT: H 434 ASP cc_start: 0.7384 (t0) cc_final: 0.7046 (t70) REVERT: H 515 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7915 (mp) REVERT: H 600 TYR cc_start: 0.7084 (t80) cc_final: 0.6791 (t80) REVERT: U 1 MET cc_start: 0.3726 (tmt) cc_final: 0.3404 (tpt) REVERT: C 83 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.7844 (p-80) REVERT: G 77 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8078 (pp) outliers start: 59 outliers final: 42 residues processed: 278 average time/residue: 0.2310 time to fit residues: 94.6362 Evaluate side-chains 291 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 244 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 235 HIS Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain H residue 336 ASP Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 544 MET Chi-restraints excluded: chain H residue 588 CYS Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain R residue 79 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 137 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 320 HIS A 445 HIS H 481 ASN ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12778 Z= 0.236 Angle : 0.583 12.188 17431 Z= 0.296 Chirality : 0.039 0.195 2092 Planarity : 0.005 0.053 2224 Dihedral : 4.340 36.691 1807 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.16 % Favored : 92.78 % Rotamer: Outliers : 6.07 % Allowed : 24.68 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1678 helix: 0.76 (0.18), residues: 893 sheet: -0.72 (0.63), residues: 81 loop : -1.92 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 87 HIS 0.008 0.001 HIS A 320 PHE 0.023 0.001 PHE A 202 TYR 0.019 0.002 TYR H 158 ARG 0.004 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 252 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8153 (mmp) cc_final: 0.7795 (mmp) REVERT: A 268 GLN cc_start: 0.7413 (tp40) cc_final: 0.6916 (tp40) REVERT: A 359 ASN cc_start: 0.8359 (t0) cc_final: 0.8020 (t0) REVERT: A 398 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 599 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7248 (mp) REVERT: H 434 ASP cc_start: 0.7419 (t0) cc_final: 0.7121 (t70) REVERT: H 515 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7971 (mp) REVERT: U 1 MET cc_start: 0.3745 (OUTLIER) cc_final: 0.3254 (tpt) REVERT: C 83 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7747 (p-80) REVERT: G 77 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8050 (pp) outliers start: 72 outliers final: 53 residues processed: 288 average time/residue: 0.2294 time to fit residues: 98.1086 Evaluate side-chains 307 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 248 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 235 HIS Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain H residue 336 ASP Chi-restraints excluded: chain H residue 391 SER Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 438 LEU Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 544 MET Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 588 CYS Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain R residue 79 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 49 optimal weight: 0.0050 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12778 Z= 0.196 Angle : 0.572 12.123 17431 Z= 0.285 Chirality : 0.039 0.273 2092 Planarity : 0.005 0.051 2224 Dihedral : 4.307 35.726 1807 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.75 % Favored : 93.19 % Rotamer: Outliers : 5.22 % Allowed : 26.28 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1678 helix: 0.83 (0.18), residues: 891 sheet: -0.70 (0.63), residues: 81 loop : -1.94 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.018 0.001 HIS A 445 PHE 0.017 0.001 PHE A 202 TYR 0.027 0.001 TYR D 18 ARG 0.004 0.000 ARG H 478 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 248 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8120 (mmp) cc_final: 0.7725 (mmp) REVERT: A 268 GLN cc_start: 0.7415 (tp40) cc_final: 0.6928 (tp40) REVERT: A 359 ASN cc_start: 0.8334 (t0) cc_final: 0.7979 (t0) REVERT: A 370 LYS cc_start: 0.8329 (mttm) cc_final: 0.8126 (mttm) REVERT: A 599 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7237 (mp) REVERT: H 394 LEU cc_start: 0.7944 (tt) cc_final: 0.7743 (tp) REVERT: H 412 MET cc_start: 0.7305 (mmm) cc_final: 0.7006 (mmm) REVERT: H 434 ASP cc_start: 0.7428 (t0) cc_final: 0.7120 (t70) REVERT: H 515 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7949 (mp) REVERT: H 600 TYR cc_start: 0.7187 (t80) cc_final: 0.6908 (t80) REVERT: U 1 MET cc_start: 0.3704 (OUTLIER) cc_final: 0.3259 (tpt) REVERT: C 83 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7830 (p-80) REVERT: G 77 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8038 (pp) outliers start: 62 outliers final: 50 residues processed: 281 average time/residue: 0.2167 time to fit residues: 91.5664 Evaluate side-chains 298 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 243 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 235 HIS Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain H residue 336 ASP Chi-restraints excluded: chain H residue 391 SER Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 544 MET Chi-restraints excluded: chain H residue 588 CYS Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain R residue 79 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 0.0000 chunk 142 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 160 optimal weight: 0.2980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS H 481 ASN ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12778 Z= 0.175 Angle : 0.563 12.131 17431 Z= 0.280 Chirality : 0.038 0.184 2092 Planarity : 0.005 0.051 2224 Dihedral : 4.229 35.151 1807 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.93 % Favored : 93.01 % Rotamer: Outliers : 4.97 % Allowed : 26.71 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1678 helix: 0.87 (0.18), residues: 893 sheet: -0.64 (0.64), residues: 81 loop : -1.92 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 14 HIS 0.005 0.001 HIS C 61 PHE 0.026 0.001 PHE A 112 TYR 0.017 0.001 TYR D 18 ARG 0.004 0.000 ARG H 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 249 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 225 ASN cc_start: 0.7944 (t0) cc_final: 0.7686 (t0) REVERT: A 236 MET cc_start: 0.8076 (mmp) cc_final: 0.7728 (mmp) REVERT: A 268 GLN cc_start: 0.7385 (tp40) cc_final: 0.6902 (tp40) REVERT: A 359 ASN cc_start: 0.8314 (t0) cc_final: 0.7970 (t0) REVERT: A 370 LYS cc_start: 0.8329 (mttm) cc_final: 0.8129 (mttm) REVERT: A 599 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7234 (mp) REVERT: H 434 ASP cc_start: 0.7403 (t0) cc_final: 0.7187 (t70) REVERT: H 515 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7931 (mp) REVERT: U 1 MET cc_start: 0.3796 (OUTLIER) cc_final: 0.3331 (tpt) REVERT: C 83 HIS cc_start: 0.8211 (OUTLIER) cc_final: 0.7834 (p-80) REVERT: G 77 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8063 (pp) outliers start: 59 outliers final: 47 residues processed: 277 average time/residue: 0.2235 time to fit residues: 93.6481 Evaluate side-chains 303 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 251 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 235 HIS Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain H residue 336 ASP Chi-restraints excluded: chain H residue 391 SER Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 588 CYS Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 88 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 0.0020 chunk 168 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 106 optimal weight: 0.1980 chunk 142 optimal weight: 0.7980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 150 HIS H 226 HIS ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12778 Z= 0.174 Angle : 0.572 12.274 17431 Z= 0.283 Chirality : 0.038 0.183 2092 Planarity : 0.005 0.051 2224 Dihedral : 4.217 34.249 1807 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 4.47 % Allowed : 27.13 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.21), residues: 1678 helix: 0.95 (0.18), residues: 887 sheet: -0.59 (0.59), residues: 91 loop : -1.89 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 14 HIS 0.005 0.001 HIS C 61 PHE 0.016 0.001 PHE H 408 TYR 0.016 0.001 TYR A 219 ARG 0.004 0.000 ARG H 478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 251 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: A 225 ASN cc_start: 0.7937 (t0) cc_final: 0.7691 (t0) REVERT: A 236 MET cc_start: 0.8072 (mmp) cc_final: 0.7718 (mmp) REVERT: A 268 GLN cc_start: 0.7403 (tp40) cc_final: 0.6924 (tp40) REVERT: A 359 ASN cc_start: 0.8311 (t0) cc_final: 0.7972 (t0) REVERT: A 370 LYS cc_start: 0.8329 (mttm) cc_final: 0.8129 (mttm) REVERT: A 517 TRP cc_start: 0.7609 (m100) cc_final: 0.7053 (m100) REVERT: A 599 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7251 (mp) REVERT: H 56 MET cc_start: 0.5071 (tpp) cc_final: 0.4481 (tmm) REVERT: H 203 MET cc_start: 0.4432 (tmm) cc_final: 0.4208 (tmm) REVERT: H 434 ASP cc_start: 0.7415 (t0) cc_final: 0.7160 (t70) REVERT: H 515 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7907 (mp) REVERT: H 600 TYR cc_start: 0.7188 (t80) cc_final: 0.6894 (t80) REVERT: U 1 MET cc_start: 0.3719 (OUTLIER) cc_final: 0.3287 (tpt) REVERT: C 83 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7832 (p-80) REVERT: G 77 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8061 (pp) outliers start: 53 outliers final: 45 residues processed: 276 average time/residue: 0.2160 time to fit residues: 90.0756 Evaluate side-chains 297 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 247 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain H residue 336 ASP Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 544 MET Chi-restraints excluded: chain H residue 588 CYS Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 88 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 19 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 481 ASN ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.162255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132557 restraints weight = 39786.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.130808 restraints weight = 24805.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.133206 restraints weight = 16916.269| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12778 Z= 0.205 Angle : 0.589 12.603 17431 Z= 0.293 Chirality : 0.039 0.185 2092 Planarity : 0.005 0.051 2224 Dihedral : 4.312 31.448 1807 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.16 % Favored : 92.78 % Rotamer: Outliers : 4.38 % Allowed : 27.46 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1678 helix: 0.84 (0.18), residues: 894 sheet: -0.64 (0.63), residues: 81 loop : -1.85 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 14 HIS 0.005 0.001 HIS A 347 PHE 0.028 0.002 PHE A 112 TYR 0.017 0.001 TYR A 219 ARG 0.005 0.000 ARG H 478 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2909.63 seconds wall clock time: 57 minutes 6.29 seconds (3426.29 seconds total)