Starting phenix.real_space_refine (version: dev) on Fri Mar 17 17:10:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4f_22667/03_2023/7k4f_22667_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4f_22667/03_2023/7k4f_22667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4f_22667/03_2023/7k4f_22667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4f_22667/03_2023/7k4f_22667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4f_22667/03_2023/7k4f_22667_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4f_22667/03_2023/7k4f_22667_neut_updated.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "C ARG 26": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 636": "NH1" <-> "NH2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 636": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19875 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4931 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "B" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4931 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "C" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4931 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "D" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4931 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' CA': 1, '5GK': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'5GK': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'5GK': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'5GK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.32, per 1000 atoms: 0.57 Number of scatterers: 19875 At special positions: 0 Unit cell: (146.012, 146.012, 124.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 160 16.00 F 15 9.00 O 3485 8.00 N 3359 7.00 C 12855 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 custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.99 Conformation dependent library (CDL) restraints added in 3.0 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 4 sheets defined 54.1% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 28 through 43 removed outlier: 4.283A pdb=" N GLU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 58 through 65 removed outlier: 3.540A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.533A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.671A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 4.169A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.862A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.694A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.511A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 removed outlier: 3.599A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.703A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.688A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.879A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 removed outlier: 3.534A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 4.102A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.990A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.528A pdb=" N PHE A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 419 through 422 No H-bonds generated for 'chain 'A' and resid 419 through 422' Processing helix chain 'A' and resid 425 through 444 removed outlier: 4.436A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 removed outlier: 3.563A pdb=" N ASN A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 477 through 486 removed outlier: 3.636A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 509 removed outlier: 4.046A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 removed outlier: 5.090A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 566 removed outlier: 3.561A pdb=" N THR A 558 " --> pdb=" O MET A 554 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 583 removed outlier: 3.813A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 3.845A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 4.283A pdb=" N GLU B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 58 through 65 removed outlier: 3.540A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 removed outlier: 3.534A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.671A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 removed outlier: 4.170A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.862A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.694A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.511A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.598A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.703A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.688A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.880A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 removed outlier: 3.535A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 342 removed outlier: 4.102A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.990A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.527A pdb=" N PHE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 409' Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 419 through 422 No H-bonds generated for 'chain 'B' and resid 419 through 422' Processing helix chain 'B' and resid 425 through 444 removed outlier: 4.435A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 464 removed outlier: 3.562A pdb=" N ASN B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 477 through 486 removed outlier: 3.636A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 509 removed outlier: 4.046A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 removed outlier: 5.089A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 566 removed outlier: 3.561A pdb=" N THR B 558 " --> pdb=" O MET B 554 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 583 removed outlier: 3.814A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 3.844A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 43 removed outlier: 4.282A pdb=" N GLU C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 58 through 65 removed outlier: 3.540A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 removed outlier: 3.533A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 101 removed outlier: 3.671A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 removed outlier: 4.169A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.862A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 138 Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.694A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.511A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.598A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.703A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.689A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.880A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 323 removed outlier: 3.535A pdb=" N ARG C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.101A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.990A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.527A pdb=" N PHE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 409' Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 419 through 422 No H-bonds generated for 'chain 'C' and resid 419 through 422' Processing helix chain 'C' and resid 425 through 444 removed outlier: 4.436A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 464 removed outlier: 3.562A pdb=" N ASN C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 468 No H-bonds generated for 'chain 'C' and resid 466 through 468' Processing helix chain 'C' and resid 477 through 486 removed outlier: 3.635A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 509 removed outlier: 4.046A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 removed outlier: 5.091A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 566 removed outlier: 3.561A pdb=" N THR C 558 " --> pdb=" O MET C 554 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 583 removed outlier: 3.813A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 3.845A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 43 removed outlier: 4.283A pdb=" N GLU D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.540A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.533A pdb=" N ALA D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.672A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 removed outlier: 4.169A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.861A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 138 Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.695A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.511A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 223 removed outlier: 3.598A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.702A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 removed outlier: 3.688A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.879A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 323 removed outlier: 3.535A pdb=" N ARG D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 342 removed outlier: 4.101A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.991A pdb=" N ILE D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.527A pdb=" N PHE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 409' Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 419 through 422 No H-bonds generated for 'chain 'D' and resid 419 through 422' Processing helix chain 'D' and resid 425 through 444 removed outlier: 4.436A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 464 removed outlier: 3.563A pdb=" N ASN D 464 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 468 No H-bonds generated for 'chain 'D' and resid 466 through 468' Processing helix chain 'D' and resid 477 through 486 removed outlier: 3.635A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 509 removed outlier: 4.046A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 505 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 removed outlier: 5.091A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 566 removed outlier: 3.561A pdb=" N THR D 558 " --> pdb=" O MET D 554 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 583 removed outlier: 3.813A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 3.844A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.658A pdb=" N LEU A 631 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.658A pdb=" N LEU B 631 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.658A pdb=" N LEU C 631 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.658A pdb=" N LEU D 631 " --> pdb=" O TYR D 278 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 8.54 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: 6162 1.34 - 1.45: 3606 1.45 - 1.57: 10291 1.57 - 1.69: 10 1.69 - 1.81: 272 Bond restraints: 20341 Sorted by residual: bond pdb=" C01 5GK A 702 " pdb=" O01 5GK A 702 " ideal model delta sigma weight residual 1.230 1.403 -0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C01 5GK D 701 " pdb=" O01 5GK D 701 " ideal model delta sigma weight residual 1.230 1.393 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" C01 5GK C 701 " pdb=" O01 5GK C 701 " ideal model delta sigma weight residual 1.230 1.393 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" C01 5GK A 701 " pdb=" O01 5GK A 701 " ideal model delta sigma weight residual 1.230 1.392 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" C01 5GK B 701 " pdb=" O01 5GK B 701 " ideal model delta sigma weight residual 1.230 1.392 -0.162 2.00e-02 2.50e+03 6.55e+01 ... (remaining 20336 not shown) Histogram of bond angle deviations from ideal: 95.87 - 103.66: 323 103.66 - 111.45: 8289 111.45 - 119.24: 8450 119.24 - 127.03: 10258 127.03 - 134.82: 287 Bond angle restraints: 27607 Sorted by residual: angle pdb=" C ARG C 224 " pdb=" N HIS C 225 " pdb=" CA HIS C 225 " ideal model delta sigma weight residual 121.54 132.34 -10.80 1.91e+00 2.74e-01 3.20e+01 angle pdb=" C ARG B 224 " pdb=" N HIS B 225 " pdb=" CA HIS B 225 " ideal model delta sigma weight residual 121.54 132.29 -10.75 1.91e+00 2.74e-01 3.17e+01 angle pdb=" C ARG A 224 " pdb=" N HIS A 225 " pdb=" CA HIS A 225 " ideal model delta sigma weight residual 121.54 132.28 -10.74 1.91e+00 2.74e-01 3.16e+01 angle pdb=" C ARG D 224 " pdb=" N HIS D 225 " pdb=" CA HIS D 225 " ideal model delta sigma weight residual 121.54 132.28 -10.74 1.91e+00 2.74e-01 3.16e+01 angle pdb=" C TYR B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 ... (remaining 27602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 10940 14.55 - 29.09: 835 29.09 - 43.64: 317 43.64 - 58.19: 32 58.19 - 72.73: 15 Dihedral angle restraints: 12139 sinusoidal: 4955 harmonic: 7184 Sorted by residual: dihedral pdb=" CA SER D 361 " pdb=" C SER D 361 " pdb=" N PRO D 362 " pdb=" CA PRO D 362 " ideal model delta harmonic sigma weight residual -180.00 -121.57 -58.43 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA SER A 361 " pdb=" C SER A 361 " pdb=" N PRO A 362 " pdb=" CA PRO A 362 " ideal model delta harmonic sigma weight residual -180.00 -121.61 -58.39 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA SER C 361 " pdb=" C SER C 361 " pdb=" N PRO C 362 " pdb=" CA PRO C 362 " ideal model delta harmonic sigma weight residual -180.00 -121.65 -58.35 0 5.00e+00 4.00e-02 1.36e+02 ... (remaining 12136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2587 0.081 - 0.162: 460 0.162 - 0.243: 57 0.243 - 0.324: 13 0.324 - 0.405: 1 Chirality restraints: 3118 Sorted by residual: chirality pdb=" C14 5GK A 702 " pdb=" C13 5GK A 702 " pdb=" C15 5GK A 702 " pdb=" C22 5GK A 702 " both_signs ideal model delta sigma weight residual False -2.50 -2.90 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" C14 5GK A 701 " pdb=" C13 5GK A 701 " pdb=" C15 5GK A 701 " pdb=" C22 5GK A 701 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CG LEU C 574 " pdb=" CB LEU C 574 " pdb=" CD1 LEU C 574 " pdb=" CD2 LEU C 574 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 3115 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 526 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO B 527 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 526 " 0.053 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO D 527 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 527 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 527 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 526 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.97e+00 pdb=" N PRO A 527 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.045 5.00e-02 4.00e+02 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4266 2.76 - 3.30: 18642 3.30 - 3.83: 31330 3.83 - 4.37: 35817 4.37 - 4.90: 58331 Nonbonded interactions: 148386 Sorted by model distance: nonbonded pdb=" OG SER D 506 " pdb=" OH TYR D 526 " model vdw 2.231 2.440 nonbonded pdb=" OG SER A 506 " pdb=" OH TYR A 526 " model vdw 2.231 2.440 nonbonded pdb=" OG SER B 506 " pdb=" OH TYR B 526 " model vdw 2.232 2.440 nonbonded pdb=" OG SER C 506 " pdb=" OH TYR C 526 " model vdw 2.232 2.440 nonbonded pdb=" O ASP B 590 " pdb=" NH1 ARG B 594 " model vdw 2.305 2.520 ... (remaining 148381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 639 or resid 701)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 160 5.16 5 C 12855 2.51 5 N 3359 2.21 5 O 3485 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.620 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: 5.480 Check model and map are aligned: 0.300 Process input model: 49.450 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 : 0.012 0.173 20341 Z= 0.773 Angle : 1.381 17.439 27607 Z= 0.683 Chirality : 0.065 0.405 3118 Planarity : 0.008 0.079 3474 Dihedral : 12.352 72.735 7499 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -5.98 (0.12), residues: 2448 helix: -4.20 (0.07), residues: 1324 sheet: -3.72 (0.52), residues: 40 loop : -3.55 (0.17), residues: 1084 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 788 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 6 residues processed: 805 average time/residue: 0.3248 time to fit residues: 393.3928 Evaluate side-chains 436 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 430 time to evaluate : 2.133 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1872 time to fit residues: 5.2966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 0.3980 chunk 142 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 252 ASN ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN A 464 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 252 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN B 464 ASN B 546 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 252 ASN ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 365 ASN C 546 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 252 ASN ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 365 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 20341 Z= 0.232 Angle : 0.834 10.867 27607 Z= 0.404 Chirality : 0.044 0.200 3118 Planarity : 0.006 0.068 3474 Dihedral : 7.356 84.535 2751 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.37 % Favored : 91.26 % Rotamer Outliers : 5.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -4.12 (0.14), residues: 2448 helix: -2.24 (0.11), residues: 1320 sheet: -0.56 (0.62), residues: 48 loop : -3.48 (0.17), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 521 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 45 residues processed: 599 average time/residue: 0.2955 time to fit residues: 277.1250 Evaluate side-chains 488 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 443 time to evaluate : 2.648 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.1762 time to fit residues: 17.9509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 150 optimal weight: 0.0980 chunk 61 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 239 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN B 118 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN D 74 GLN D 118 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS D 546 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 20341 Z= 0.172 Angle : 0.805 12.486 27607 Z= 0.373 Chirality : 0.043 0.194 3118 Planarity : 0.005 0.051 3474 Dihedral : 6.893 96.463 2751 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.62 % Favored : 91.14 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -3.21 (0.15), residues: 2448 helix: -1.32 (0.13), residues: 1372 sheet: -1.24 (0.61), residues: 56 loop : -3.33 (0.18), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 507 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 29 residues processed: 545 average time/residue: 0.2966 time to fit residues: 252.7199 Evaluate side-chains 460 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 431 time to evaluate : 2.378 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1990 time to fit residues: 13.5606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 222 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 20341 Z= 0.245 Angle : 0.793 12.587 27607 Z= 0.373 Chirality : 0.043 0.199 3118 Planarity : 0.005 0.046 3474 Dihedral : 6.648 96.439 2751 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.91 % Favored : 90.77 % Rotamer Outliers : 4.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.16), residues: 2448 helix: -0.63 (0.14), residues: 1336 sheet: -2.31 (0.53), residues: 76 loop : -3.22 (0.18), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 445 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 49 residues processed: 488 average time/residue: 0.2807 time to fit residues: 218.6315 Evaluate side-chains 463 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 414 time to evaluate : 2.340 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.1761 time to fit residues: 19.5555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 211 optimal weight: 0.0020 chunk 59 optimal weight: 8.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 20341 Z= 0.196 Angle : 0.771 14.371 27607 Z= 0.359 Chirality : 0.042 0.320 3118 Planarity : 0.004 0.044 3474 Dihedral : 6.465 97.158 2751 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.58 % Favored : 91.14 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.17), residues: 2448 helix: -0.26 (0.14), residues: 1340 sheet: -2.34 (0.53), residues: 76 loop : -3.11 (0.18), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 452 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 16 residues processed: 487 average time/residue: 0.2848 time to fit residues: 219.1060 Evaluate side-chains 432 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 416 time to evaluate : 2.120 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1756 time to fit residues: 8.1632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.8980 chunk 212 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 20341 Z= 0.228 Angle : 0.779 14.474 27607 Z= 0.364 Chirality : 0.043 0.306 3118 Planarity : 0.004 0.042 3474 Dihedral : 6.407 98.284 2751 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.03 % Favored : 90.73 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -1.89 (0.17), residues: 2448 helix: 0.05 (0.14), residues: 1340 sheet: -2.36 (0.54), residues: 76 loop : -3.02 (0.18), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 433 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 30 residues processed: 471 average time/residue: 0.3080 time to fit residues: 226.8713 Evaluate side-chains 440 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 410 time to evaluate : 2.313 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2051 time to fit residues: 14.1277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 198 optimal weight: 0.0470 chunk 131 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 overall best weight: 2.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 20341 Z= 0.231 Angle : 0.794 15.306 27607 Z= 0.369 Chirality : 0.043 0.213 3118 Planarity : 0.004 0.040 3474 Dihedral : 6.369 99.253 2751 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.56 % Favored : 90.28 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -1.69 (0.17), residues: 2448 helix: 0.15 (0.14), residues: 1364 sheet: -1.52 (0.64), residues: 56 loop : -2.95 (0.19), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 424 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 19 residues processed: 456 average time/residue: 0.2997 time to fit residues: 214.7572 Evaluate side-chains 426 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 407 time to evaluate : 2.346 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1918 time to fit residues: 9.9020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 20341 Z= 0.176 Angle : 0.800 15.644 27607 Z= 0.369 Chirality : 0.042 0.211 3118 Planarity : 0.004 0.044 3474 Dihedral : 6.213 100.478 2751 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.78 % Favored : 91.09 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -1.56 (0.17), residues: 2448 helix: 0.28 (0.14), residues: 1372 sheet: -1.39 (0.66), residues: 56 loop : -2.96 (0.19), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 454 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 461 average time/residue: 0.2990 time to fit residues: 217.5889 Evaluate side-chains 433 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 421 time to evaluate : 2.394 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2329 time to fit residues: 8.0061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.8980 chunk 225 optimal weight: 0.3980 chunk 205 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 218 optimal weight: 6.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 20341 Z= 0.201 Angle : 0.818 16.242 27607 Z= 0.376 Chirality : 0.043 0.224 3118 Planarity : 0.004 0.042 3474 Dihedral : 6.191 101.536 2751 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -1.43 (0.17), residues: 2448 helix: 0.41 (0.14), residues: 1364 sheet: -1.44 (0.66), residues: 56 loop : -2.92 (0.19), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 439 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 449 average time/residue: 0.3129 time to fit residues: 220.2520 Evaluate side-chains 428 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 422 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1916 time to fit residues: 5.2226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.0870 chunk 231 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 243 optimal weight: 10.0000 chunk 223 optimal weight: 0.7980 chunk 193 optimal weight: 0.0670 chunk 20 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 20341 Z= 0.183 Angle : 0.832 16.852 27607 Z= 0.379 Chirality : 0.043 0.220 3118 Planarity : 0.004 0.044 3474 Dihedral : 6.128 102.369 2751 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -1.43 (0.17), residues: 2448 helix: 0.41 (0.14), residues: 1360 sheet: -1.39 (0.68), residues: 56 loop : -2.89 (0.19), residues: 1032 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 447 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 450 average time/residue: 0.2929 time to fit residues: 209.8344 Evaluate side-chains 431 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 427 time to evaluate : 2.362 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2010 time to fit residues: 4.6810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 59 optimal weight: 0.0020 chunk 178 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107434 restraints weight = 36751.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110823 restraints weight = 18119.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113101 restraints weight = 11207.555| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 20341 Z= 0.182 Angle : 0.824 17.078 27607 Z= 0.377 Chirality : 0.043 0.222 3118 Planarity : 0.004 0.044 3474 Dihedral : 6.089 102.465 2751 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -1.31 (0.17), residues: 2448 helix: 0.51 (0.14), residues: 1340 sheet: -1.39 (0.68), residues: 56 loop : -2.79 (0.18), residues: 1052 Sorry: There was an error with writing 7k4f_22667_neut_updated_real_space_refined_001.pdb. [Errno 28] No space left on device