Starting phenix.real_space_refine (version: dev) on Mon Apr 4 23:41:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/04_2022/7shn_25131_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/04_2022/7shn_25131.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/04_2022/7shn_25131_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/04_2022/7shn_25131_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/04_2022/7shn_25131_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/04_2022/7shn_25131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/04_2022/7shn_25131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/04_2022/7shn_25131_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/04_2022/7shn_25131_updated.pdb" } resolution = 3.1 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= 0.008 sd= 0.071 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 74": "NH1" <-> "NH2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ARG 568": "NH1" <-> "NH2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A ASP 581": "OD1" <-> "OD2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 629": "OD1" <-> "OD2" Residue "A ASP 638": "OD1" <-> "OD2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ASP 469": "OD1" <-> "OD2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 518": "NH1" <-> "NH2" Residue "B TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B GLU 577": "OE1" <-> "OE2" Residue "B GLU 592": "OE1" <-> "OE2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 629": "OD1" <-> "OD2" Residue "B ASP 638": "OD1" <-> "OD2" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 649": "OD1" <-> "OD2" Residue "B PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 9677 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4771 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 4783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4783 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 20, 'TRANS': 586} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'3VV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'3VV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 5.95, per 1000 atoms: 0.61 Number of scatterers: 9677 At special positions: 0 Unit cell: (73.428, 141.792, 112.252, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 6 15.00 O 1729 8.00 N 1704 7.00 C 6192 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: 3.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 6 sheets defined 59.8% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.535A pdb=" N GLN A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 81 " --> pdb=" O TRP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 98 removed outlier: 4.162A pdb=" N LEU A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 123 removed outlier: 3.634A pdb=" N ARG A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 156 removed outlier: 3.581A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 3.774A pdb=" N ARG A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 174 removed outlier: 3.644A pdb=" N ARG A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 193 through 196 No H-bonds generated for 'chain 'A' and resid 193 through 196' Processing helix chain 'A' and resid 201 through 233 removed outlier: 3.889A pdb=" N HIS A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 3.849A pdb=" N SER A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.585A pdb=" N GLY A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 299 through 335 removed outlier: 3.603A pdb=" N LEU A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 352 removed outlier: 3.531A pdb=" N VAL A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 374 through 394 removed outlier: 3.523A pdb=" N SER A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 409 through 431 removed outlier: 4.190A pdb=" N ARG A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.573A pdb=" N ILE A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 538 No H-bonds generated for 'chain 'A' and resid 536 through 538' Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.588A pdb=" N GLN A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 601 through 604 No H-bonds generated for 'chain 'A' and resid 601 through 604' Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.557A pdb=" N PHE A 619 " --> pdb=" O MET A 615 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 removed outlier: 3.851A pdb=" N LYS A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 643 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN A 645 " --> pdb=" O GLY A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 691 through 695 Processing helix chain 'A' and resid 698 through 706 removed outlier: 3.616A pdb=" N UNK A 703 " --> pdb=" O UNK A 699 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N UNK A 704 " --> pdb=" O UNK A 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 82 removed outlier: 3.587A pdb=" N GLN B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 removed outlier: 4.488A pdb=" N LEU B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 123 removed outlier: 3.600A pdb=" N LEU B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 156 removed outlier: 3.599A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Proline residue: B 143 - end of helix removed outlier: 3.699A pdb=" N ARG B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 161 No H-bonds generated for 'chain 'B' and resid 158 through 161' Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.814A pdb=" N ARG B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 193 through 196 No H-bonds generated for 'chain 'B' and resid 193 through 196' Processing helix chain 'B' and resid 201 through 233 removed outlier: 3.562A pdb=" N ALA B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Proline residue: B 218 - end of helix removed outlier: 3.900A pdb=" N SER B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 256 removed outlier: 3.556A pdb=" N ILE B 246 " --> pdb=" O TRP B 242 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 288 removed outlier: 3.514A pdb=" N ARG B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 299 through 335 removed outlier: 3.600A pdb=" N LEU B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 352 removed outlier: 3.607A pdb=" N VAL B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 374 through 394 removed outlier: 3.536A pdb=" N SER B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.562A pdb=" N GLU B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 431 removed outlier: 3.848A pdb=" N GLU B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 removed outlier: 3.670A pdb=" N ILE B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 538 No H-bonds generated for 'chain 'B' and resid 536 through 538' Processing helix chain 'B' and resid 563 through 569 Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 588 through 590 No H-bonds generated for 'chain 'B' and resid 588 through 590' Processing helix chain 'B' and resid 601 through 604 No H-bonds generated for 'chain 'B' and resid 601 through 604' Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.689A pdb=" N MET B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 650 removed outlier: 3.807A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 643 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 645 " --> pdb=" O GLY B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 666 No H-bonds generated for 'chain 'B' and resid 664 through 666' Processing helix chain 'B' and resid 691 through 695 Processing helix chain 'B' and resid 698 through 706 removed outlier: 3.552A pdb=" N UNK B 703 " --> pdb=" O UNK B 699 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 467 through 469 removed outlier: 6.622A pdb=" N LEU A 531 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 679 through 681 removed outlier: 3.534A pdb=" N THR A 506 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 673 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 503 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 656 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALA A 626 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE A 657 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 628 " --> pdb=" O ILE A 657 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 481 through 483 removed outlier: 3.644A pdb=" N VAL A 490 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A 483 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL A 488 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 475 through 477 Processing sheet with id= E, first strand: chain 'B' and resid 503 through 505 removed outlier: 3.803A pdb=" N LEU B 503 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA B 626 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE B 657 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 628 " --> pdb=" O ILE B 657 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 481 through 483 removed outlier: 3.606A pdb=" N VAL B 490 " --> pdb=" O ILE B 481 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR B 483 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL B 488 " --> pdb=" O THR B 483 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1535 1.26 - 1.40: 2544 1.40 - 1.54: 5657 1.54 - 1.68: 69 1.68 - 1.82: 78 Bond restraints: 9883 Sorted by residual: bond pdb=" C49 3VV A 800 " pdb=" O48 3VV A 800 " ideal model delta sigma weight residual 1.619 1.271 0.348 2.00e-02 2.50e+03 3.02e+02 bond pdb=" C49 3VV B 801 " pdb=" O48 3VV B 801 " ideal model delta sigma weight residual 1.619 1.272 0.347 2.00e-02 2.50e+03 3.00e+02 bond pdb=" C47 3VV A 800 " pdb=" O48 3VV A 800 " ideal model delta sigma weight residual 1.287 1.606 -0.319 2.00e-02 2.50e+03 2.55e+02 bond pdb=" C47 3VV B 801 " pdb=" O48 3VV B 801 " ideal model delta sigma weight residual 1.287 1.605 -0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" C49 3VV B 801 " pdb=" C50 3VV B 801 " ideal model delta sigma weight residual 1.293 1.559 -0.266 2.00e-02 2.50e+03 1.77e+02 ... (remaining 9878 not shown) Histogram of bond angle deviations from ideal: 97.89 - 105.30: 189 105.30 - 112.71: 5040 112.71 - 120.12: 4161 120.12 - 127.53: 3895 127.53 - 134.94: 109 Bond angle restraints: 13394 Sorted by residual: angle pdb=" C09 3VV B 801 " pdb=" C10 3VV B 801 " pdb=" C11 3VV B 801 " ideal model delta sigma weight residual 152.65 120.93 31.72 3.00e+00 1.11e-01 1.12e+02 angle pdb=" C09 3VV A 800 " pdb=" C10 3VV A 800 " pdb=" C11 3VV A 800 " ideal model delta sigma weight residual 152.65 121.23 31.42 3.00e+00 1.11e-01 1.10e+02 angle pdb=" C ILE A 352 " pdb=" CA ILE A 352 " pdb=" CB ILE A 352 " ideal model delta sigma weight residual 112.02 123.25 -11.23 1.31e+00 5.83e-01 7.35e+01 angle pdb=" N THR B 353 " pdb=" CA THR B 353 " pdb=" C THR B 353 " ideal model delta sigma weight residual 112.93 121.49 -8.56 1.12e+00 7.97e-01 5.84e+01 angle pdb=" N ILE A 352 " pdb=" CA ILE A 352 " pdb=" C ILE A 352 " ideal model delta sigma weight residual 110.53 103.49 7.04 9.40e-01 1.13e+00 5.61e+01 ... (remaining 13389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.81: 5659 30.81 - 61.61: 195 61.61 - 92.42: 16 92.42 - 123.22: 0 123.22 - 154.03: 4 Dihedral angle restraints: 5874 sinusoidal: 2345 harmonic: 3529 Sorted by residual: dihedral pdb=" CA LEU A 190 " pdb=" C LEU A 190 " pdb=" N ARG A 191 " pdb=" CA ARG A 191 " ideal model delta harmonic sigma weight residual -180.00 -150.05 -29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA MET B 186 " pdb=" C MET B 186 " pdb=" N ASP B 187 " pdb=" CA ASP B 187 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" C THR B 353 " pdb=" N THR B 353 " pdb=" CA THR B 353 " pdb=" CB THR B 353 " ideal model delta harmonic sigma weight residual -122.00 -136.48 14.48 0 2.50e+00 1.60e-01 3.36e+01 ... (remaining 5871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 1431 0.140 - 0.279: 53 0.279 - 0.419: 7 0.419 - 0.559: 1 0.559 - 0.698: 4 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA ARG B 389 " pdb=" N ARG B 389 " pdb=" C ARG B 389 " pdb=" CB ARG B 389 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA THR B 353 " pdb=" N THR B 353 " pdb=" C THR B 353 " pdb=" CB THR B 353 " both_signs ideal model delta sigma weight residual False 2.53 1.86 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C52 3VV B 801 " pdb=" C47 3VV B 801 " pdb=" C50 3VV B 801 " pdb=" O53 3VV B 801 " both_signs ideal model delta sigma weight residual False 2.56 1.95 0.61 2.00e-01 2.50e+01 9.44e+00 ... (remaining 1493 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 389 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ARG A 389 " -0.055 2.00e-02 2.50e+03 pdb=" O ARG A 389 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN A 390 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP B 242 " -0.052 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO B 243 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 389 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.40e+00 pdb=" C ARG B 389 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG B 389 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN B 390 " -0.018 2.00e-02 2.50e+03 ... (remaining 1686 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3340 2.84 - 3.36: 8886 3.36 - 3.87: 15856 3.87 - 4.39: 19794 4.39 - 4.90: 32541 Nonbonded interactions: 80417 Sorted by model distance: nonbonded pdb=" OE1 GLU B 640 " pdb=" NH2 ARG B 660 " model vdw 2.330 2.520 nonbonded pdb=" O VAL A 250 " pdb=" OG1 THR A 254 " model vdw 2.338 2.440 nonbonded pdb=" O VAL A 123 " pdb=" NH1 ARG B 381 " model vdw 2.341 2.520 nonbonded pdb=" O TYR B 547 " pdb=" NH2 ARG B 617 " model vdw 2.369 2.520 nonbonded pdb=" NH1 ARG A 89 " pdb=" OG SER A 161 " model vdw 2.372 2.520 ... (remaining 80412 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 67 through 707 or (resid 800 and (name C07 or name C08 or \ name C09 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C21 or name C22 or name C24 or name \ C26 or name C27 or name C29 or name C31 or name C33 or name C34 or name C35 or \ name C36 or name C46 or name C47 or name C49 or name C50 or name C52 or name C59 \ or name C61 or name C62 or name C65 or name C67 or name N23 or name N28 or name \ N58 or name N60 or name N63 or name N64 or name N66 or name O19 or name O25 or \ name O30 or name O32 or name O37 or name O39 or name O40 or name O41 or name O43 \ or name O44 or name O45 or name O48 or name O51 or name O53 or name O55 or name \ O56 or name O57 or name P38 or name P42 or name P54 or name S20)))) selection = (chain 'B' and (resid 67 through 436 or resid 463 through 683 or (resid 684 and \ (name N or name CA or name C or name O or name CB )) or resid 685 through 707 or \ resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 46 5.16 5 C 6192 2.51 5 N 1704 2.21 5 O 1729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 5.230 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.070 Process input model: 28.490 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.017 0.348 9883 Z= 1.038 Angle : 1.336 31.721 13394 Z= 0.683 Chirality : 0.079 0.698 1496 Planarity : 0.008 0.078 1689 Dihedral : 16.247 154.027 3600 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 0.00 % 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: -6.40 (0.15), residues: 1159 helix: -4.51 (0.08), residues: 779 sheet: -2.53 (0.68), residues: 49 loop : -3.03 (0.26), residues: 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 166 average time/residue: 0.3588 time to fit residues: 73.8585 Evaluate side-chains 125 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3084 time to fit residues: 2.3555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.0040 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 133 GLN A 136 GLN A 169 HIS A 289 ASN A 307 GLN A 316 GLN A 420 HIS A 430 GLN A 478 ASN A 544 GLN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 136 GLN B 169 HIS B 185 ASN B 256 ASN B 307 GLN B 316 GLN B 420 HIS B 430 GLN ** B 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN B 556 GLN B 567 GLN ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 9883 Z= 0.193 Angle : 0.656 8.014 13394 Z= 0.335 Chirality : 0.040 0.231 1496 Planarity : 0.006 0.065 1689 Dihedral : 10.935 154.792 1390 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.17 (0.19), residues: 1159 helix: -2.65 (0.14), residues: 770 sheet: -2.49 (0.66), residues: 56 loop : -2.52 (0.29), residues: 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 135 average time/residue: 0.2932 time to fit residues: 51.6971 Evaluate side-chains 119 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1196 time to fit residues: 3.4740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 0.0050 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN B 433 HIS B 611 GLN B 659 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 9883 Z= 0.225 Angle : 0.620 8.707 13394 Z= 0.308 Chirality : 0.041 0.275 1496 Planarity : 0.004 0.045 1689 Dihedral : 10.414 156.009 1390 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.71 (0.22), residues: 1159 helix: -1.37 (0.17), residues: 772 sheet: -2.52 (0.63), residues: 61 loop : -2.27 (0.30), residues: 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 126 average time/residue: 0.2393 time to fit residues: 41.6935 Evaluate side-chains 110 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0915 time to fit residues: 3.0965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 109 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN A 669 HIS ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 9883 Z= 0.291 Angle : 0.623 12.102 13394 Z= 0.306 Chirality : 0.043 0.278 1496 Planarity : 0.004 0.048 1689 Dihedral : 10.110 154.542 1390 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.24), residues: 1159 helix: -0.83 (0.18), residues: 766 sheet: -2.30 (0.68), residues: 54 loop : -1.96 (0.31), residues: 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 122 average time/residue: 0.2395 time to fit residues: 40.6430 Evaluate side-chains 112 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0889 time to fit residues: 2.9789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.0050 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 40.0000 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN B 433 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.100 9883 Z= 0.177 Angle : 0.578 10.059 13394 Z= 0.284 Chirality : 0.040 0.255 1496 Planarity : 0.004 0.054 1689 Dihedral : 9.626 152.858 1390 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.34 (0.24), residues: 1159 helix: -0.28 (0.19), residues: 774 sheet: -2.06 (0.71), residues: 54 loop : -1.88 (0.31), residues: 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 122 average time/residue: 0.2587 time to fit residues: 42.3070 Evaluate side-chains 109 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0926 time to fit residues: 2.4172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 6.9990 chunk 104 optimal weight: 0.0170 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.110 9883 Z= 0.192 Angle : 0.578 9.391 13394 Z= 0.285 Chirality : 0.040 0.259 1496 Planarity : 0.004 0.063 1689 Dihedral : 9.328 149.260 1390 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.25), residues: 1159 helix: 0.08 (0.19), residues: 770 sheet: -1.90 (0.72), residues: 54 loop : -1.77 (0.31), residues: 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.104 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 116 average time/residue: 0.2492 time to fit residues: 39.5170 Evaluate side-chains 113 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0981 time to fit residues: 3.6364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN A 556 GLN B 157 GLN B 430 GLN B 544 GLN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.118 9883 Z= 0.185 Angle : 0.574 9.885 13394 Z= 0.280 Chirality : 0.040 0.252 1496 Planarity : 0.004 0.070 1689 Dihedral : 9.036 141.064 1390 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1159 helix: 0.37 (0.19), residues: 769 sheet: -1.25 (0.65), residues: 64 loop : -1.80 (0.32), residues: 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.115 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 109 average time/residue: 0.2649 time to fit residues: 39.0119 Evaluate side-chains 95 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0921 time to fit residues: 2.0344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.0470 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 556 GLN B 136 GLN B 556 GLN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.132 9883 Z= 0.191 Angle : 0.588 11.318 13394 Z= 0.293 Chirality : 0.040 0.248 1496 Planarity : 0.004 0.081 1689 Dihedral : 8.744 135.327 1390 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1159 helix: 0.60 (0.19), residues: 769 sheet: -1.72 (0.74), residues: 54 loop : -1.61 (0.32), residues: 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.216 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 108 average time/residue: 0.2550 time to fit residues: 37.6930 Evaluate side-chains 105 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0985 time to fit residues: 2.6054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 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 136 GLN B 136 GLN B 556 GLN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.169 9883 Z= 0.213 Angle : 0.588 13.964 13394 Z= 0.294 Chirality : 0.040 0.244 1496 Planarity : 0.004 0.094 1689 Dihedral : 8.410 131.696 1390 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.25), residues: 1159 helix: 0.73 (0.20), residues: 769 sheet: -1.74 (0.73), residues: 54 loop : -1.51 (0.33), residues: 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.996 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 0.2216 time to fit residues: 33.3535 Evaluate side-chains 103 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0917 time to fit residues: 1.7212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.0870 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 40.0000 chunk 110 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN B 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.179 9883 Z= 0.252 Angle : 0.611 19.176 13394 Z= 0.312 Chirality : 0.040 0.236 1496 Planarity : 0.005 0.116 1689 Dihedral : 8.116 127.545 1390 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1159 helix: 0.86 (0.20), residues: 761 sheet: -1.74 (0.73), residues: 54 loop : -1.40 (0.33), residues: 344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.163 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 105 average time/residue: 0.2482 time to fit residues: 36.2636 Evaluate side-chains 98 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN B 556 GLN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.195387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129764 restraints weight = 10410.678| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.32 r_work: 0.3486 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work: 0.3441 rms_B_bonded: 3.07 restraints_weight: 0.1250 r_work: 0.3416 rms_B_bonded: 3.15 restraints_weight: 0.0625 r_work: 0.3390 rms_B_bonded: 3.29 restraints_weight: 0.0312 r_work: 0.3360 rms_B_bonded: 3.49 restraints_weight: 0.0156 r_work: 0.3328 rms_B_bonded: 3.75 restraints_weight: 0.0078 r_work: 0.3291 rms_B_bonded: 4.09 restraints_weight: 0.0039 r_work: 0.3250 rms_B_bonded: 4.51 restraints_weight: 0.0020 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4232 r_free = 0.4232 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4232 r_free = 0.4232 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.255 9883 Z= 0.311 Angle : 0.629 20.055 13394 Z= 0.326 Chirality : 0.041 0.236 1496 Planarity : 0.005 0.115 1689 Dihedral : 8.079 124.764 1390 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.25), residues: 1159 helix: 0.82 (0.19), residues: 763 sheet: -1.73 (0.73), residues: 54 loop : -1.40 (0.33), residues: 342 =============================================================================== Job complete usr+sys time: 1902.49 seconds wall clock time: 35 minutes 26.77 seconds (2126.77 seconds total)