Starting phenix.real_space_refine (version: dev) on Wed Feb 22 01:30:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qru_14124/02_2023/7qru_14124_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qru_14124/02_2023/7qru_14124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qru_14124/02_2023/7qru_14124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qru_14124/02_2023/7qru_14124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qru_14124/02_2023/7qru_14124_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qru_14124/02_2023/7qru_14124_updated.pdb" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 100": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16100 Number of models: 1 Model: "" Number of chains: 18 Chain: "D" Number of atoms: 3906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 474} Conformer: "B" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 474} bond proxies already assigned to first conformer: 3877 Chain: "A" Number of atoms: 6440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 805, 6306 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 776} Conformer: "B" Number of residues, atoms: 805, 6306 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 776} bond proxies already assigned to first conformer: 6327 Chain: "B" Number of atoms: 1089 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 140, 1078 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Conformer: "B" Number of residues, atoms: 140, 1078 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} bond proxies already assigned to first conformer: 1090 Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "E" Number of atoms: 1305 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 158, 1297 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Conformer: "B" Number of residues, atoms: 158, 1297 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} bond proxies already assigned to first conformer: 1317 Chain: "F" Number of atoms: 723 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 701 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 89} Conformer: "B" Number of residues, atoms: 91, 701 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 89} bond proxies already assigned to first conformer: 685 Chain: "G" Number of atoms: 888 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 113, 877 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Conformer: "B" Number of residues, atoms: 113, 877 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} bond proxies already assigned to first conformer: 883 Chain: "e" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 395 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 29 residue: pdb=" N AMET D 139 " occ=0.47 ... (14 atoms not shown) pdb=" CE BMET D 139 " occ=0.53 residue: pdb=" N ALEU D 172 " occ=0.43 ... (14 atoms not shown) pdb=" CD2BLEU D 172 " occ=0.57 residue: pdb=" N AMET D 218 " occ=0.45 ... (14 atoms not shown) pdb=" CE BMET D 218 " occ=0.55 residue: pdb=" N ALYS D 219 " occ=0.45 ... (16 atoms not shown) pdb=" NZ BLYS D 219 " occ=0.55 residue: pdb=" N AGLN D 307 " occ=0.69 ... (16 atoms not shown) pdb=" NE2BGLN D 307 " occ=0.31 residue: pdb=" N ATYR D 328 " occ=0.54 ... (22 atoms not shown) pdb=" OH BTYR D 328 " occ=0.46 residue: pdb=" N AMET D 423 " occ=0.54 ... (14 atoms not shown) pdb=" CE BMET D 423 " occ=0.46 residue: pdb=" N AMET A 118 " occ=0.45 ... (14 atoms not shown) pdb=" CE BMET A 118 " occ=0.55 residue: pdb=" N APHE A 119 " occ=0.45 ... (20 atoms not shown) pdb=" CZ BPHE A 119 " occ=0.55 residue: pdb=" N AMET A 167 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 167 " occ=0.50 residue: pdb=" N ATYR A 246 " occ=0.43 ... (22 atoms not shown) pdb=" OH BTYR A 246 " occ=0.57 residue: pdb=" N ALEU A 247 " occ=0.43 ... (14 atoms not shown) pdb=" CD2BLEU A 247 " occ=0.57 ... (remaining 17 not shown) Time building chain proxies: 15.77, per 1000 atoms: 0.98 Number of scatterers: 16100 At special positions: 0 Unit cell: (175.703, 92.137, 96.4224, 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 92 16.00 P 3 15.00 O 3017 8.00 N 2388 7.00 C 10600 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: 7.03 Conformation dependent library (CDL) restraints added in 4.3 seconds 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3678 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 85 helices and 4 sheets defined 75.1% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'D' and resid 3 through 20 Proline residue: D 8 - end of helix removed outlier: 4.643A pdb=" N ILE D 11 " --> pdb=" O PRO D 8 " (cutoff:3.500A) Proline residue: D 12 - end of helix removed outlier: 3.554A pdb=" N GLY D 16 " --> pdb=" O PHE D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 54 Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 76 through 98 removed outlier: 3.699A pdb=" N GLN D 98 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.873A pdb=" N TYR D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 125 Processing helix chain 'D' and resid 129 through 148 removed outlier: 3.687A pdb=" N VAL D 148 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 184 Processing helix chain 'D' and resid 189 through 198 Processing helix chain 'D' and resid 203 through 220 Processing helix chain 'D' and resid 227 through 230 No H-bonds generated for 'chain 'D' and resid 227 through 230' Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 238 through 262 removed outlier: 5.540A pdb=" N THR D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS D 250 " --> pdb=" O GLY D 246 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 291 removed outlier: 4.250A pdb=" N MET D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 317 removed outlier: 3.954A pdb=" N ILE D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 311 " --> pdb=" O AGLN D 307 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 315 " --> pdb=" O MET D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 351 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 367 through 380 Processing helix chain 'D' and resid 387 through 401 Processing helix chain 'D' and resid 405 through 429 Processing helix chain 'D' and resid 438 through 442 Processing helix chain 'D' and resid 446 through 464 Proline residue: D 451 - end of helix Proline residue: D 454 - end of helix Processing helix chain 'D' and resid 466 through 480 Processing helix chain 'D' and resid 483 through 490 Processing helix chain 'A' and resid 3 through 23 Proline residue: A 11 - end of helix Proline residue: A 19 - end of helix Processing helix chain 'A' and resid 30 through 54 removed outlier: 3.962A pdb=" N ALA A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU A 37 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Proline residue: A 38 - end of helix removed outlier: 4.209A pdb=" N TYR A 48 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 78 through 101 removed outlier: 3.814A pdb=" N PHE A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 128 Processing helix chain 'A' and resid 132 through 150 Processing helix chain 'A' and resid 157 through 188 Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.581A pdb=" N THR A 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 229 through 238 removed outlier: 3.824A pdb=" N TRP A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Proline residue: A 234 - end of helix removed outlier: 3.686A pdb=" N MET A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 238 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.577A pdb=" N BHIS A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N BSER A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 267 removed outlier: 4.345A pdb=" N GLY A 256 " --> pdb=" O AMET A 252 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 271 through 293 Processing helix chain 'A' and resid 298 through 329 removed outlier: 4.220A pdb=" N ALA A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER A 329 " --> pdb=" O TYR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 367 removed outlier: 5.003A pdb=" N ALA A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 426 through 456 removed outlier: 5.985A pdb=" N ILE A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 474 through 492 removed outlier: 4.526A pdb=" N SER A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Proline residue: A 480 - end of helix removed outlier: 3.547A pdb=" N ILE A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 532 through 549 Processing helix chain 'A' and resid 551 through 556 removed outlier: 4.646A pdb=" N LYS A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 561 No H-bonds generated for 'chain 'A' and resid 558 through 561' Processing helix chain 'A' and resid 566 through 589 removed outlier: 3.639A pdb=" N TRP A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 575 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 577 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 578 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 581 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 582 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'A' and resid 631 through 649 removed outlier: 3.743A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Proline residue: A 648 - end of helix Processing helix chain 'A' and resid 653 through 673 Processing helix chain 'A' and resid 677 through 699 removed outlier: 3.527A pdb=" N TYR A 699 " --> pdb=" O MET A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 742 Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.644A pdb=" N ASN A 754 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 770 Processing helix chain 'A' and resid 774 through 796 Processing helix chain 'B' and resid 9 through 32 removed outlier: 3.908A pdb=" N PHE B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 57 Processing helix chain 'B' and resid 60 through 66 Processing helix chain 'B' and resid 71 through 91 removed outlier: 3.551A pdb=" N GLY B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLY B 89 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 140 Processing helix chain 'C' and resid 2 through 21 Processing helix chain 'C' and resid 25 through 46 Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 67 through 98 Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'E' and resid 2 through 18 removed outlier: 3.654A pdb=" N ASN E 17 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.756A pdb=" N LEU E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 79 Processing helix chain 'E' and resid 100 through 112 Processing helix chain 'E' and resid 136 through 147 removed outlier: 4.624A pdb=" N GLU E 139 " --> pdb=" O PRO E 136 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP E 147 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 157 removed outlier: 3.724A pdb=" N VAL E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 26 removed outlier: 3.925A pdb=" N ARG F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 24 " --> pdb=" O CYS F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 54 removed outlier: 3.538A pdb=" N ILE F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY F 46 " --> pdb=" O ILE F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 84 removed outlier: 3.634A pdb=" N LEU F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 28 Processing helix chain 'G' and resid 32 through 62 removed outlier: 3.570A pdb=" N ALA G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR G 44 " --> pdb=" O THR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 94 Proline residue: G 81 - end of helix Processing helix chain 'G' and resid 106 through 112 removed outlier: 3.783A pdb=" N MET G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 19 removed outlier: 4.001A pdb=" N ASN e 17 " --> pdb=" O VAL e 13 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE e 18 " --> pdb=" O ILE e 14 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN e 19 " --> pdb=" O TRP e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 24 through 40 Processing sheet with id= A, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= B, first strand: chain 'A' and resid 58 through 65 removed outlier: 7.188A pdb=" N ILE A 70 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 101 through 105 Processing sheet with id= D, first strand: chain 'E' and resid 89 through 94 removed outlier: 3.652A pdb=" N ASP E 120 " --> pdb=" O TYR E 129 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N HIS E 131 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER E 118 " --> pdb=" O HIS E 131 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3129 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: 5.16 Time building geometry restraints manager: 7.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 2498 1.31 - 1.46: 5800 1.46 - 1.61: 7651 1.61 - 1.76: 20 1.76 - 1.91: 168 Bond restraints: 16137 Sorted by residual: bond pdb=" CE1 HIS D 266 " pdb=" NE2 HIS D 266 " ideal model delta sigma weight residual 1.321 1.451 -0.130 1.00e-02 1.00e+04 1.70e+02 bond pdb=" C29 3PE A 901 " pdb=" C2A 3PE A 901 " ideal model delta sigma weight residual 1.524 1.292 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" CE1 HIS D 303 " pdb=" NE2 HIS D 303 " ideal model delta sigma weight residual 1.321 1.428 -0.107 1.00e-02 1.00e+04 1.15e+02 bond pdb=" C29 3PE E 201 " pdb=" C2A 3PE E 201 " ideal model delta sigma weight residual 1.524 1.331 0.193 2.00e-02 2.50e+03 9.30e+01 bond pdb=" C29 3PE E 202 " pdb=" C2A 3PE E 202 " ideal model delta sigma weight residual 1.524 1.337 0.187 2.00e-02 2.50e+03 8.76e+01 ... (remaining 16132 not shown) Histogram of bond angle deviations from ideal: 90.17 - 99.13: 47 99.13 - 108.10: 1723 108.10 - 117.07: 9561 117.07 - 126.04: 10412 126.04 - 135.01: 196 Bond angle restraints: 21939 Sorted by residual: angle pdb=" O VAL D 453 " pdb=" C VAL D 453 " pdb=" N PRO D 454 " ideal model delta sigma weight residual 120.42 114.51 5.91 6.40e-01 2.44e+00 8.54e+01 angle pdb=" O PRO C 54 " pdb=" C PRO C 54 " pdb=" N PRO C 55 " ideal model delta sigma weight residual 121.31 117.11 4.20 4.60e-01 4.73e+00 8.32e+01 angle pdb=" N PRO B 68 " pdb=" CA PRO B 68 " pdb=" CB PRO B 68 " ideal model delta sigma weight residual 102.81 96.80 6.01 6.70e-01 2.23e+00 8.04e+01 angle pdb=" CA ASP A 297 " pdb=" CB ASP A 297 " pdb=" CG ASP A 297 " ideal model delta sigma weight residual 112.60 121.15 -8.55 1.00e+00 1.00e+00 7.30e+01 angle pdb=" C PRO A 473 " pdb=" CA PRO A 473 " pdb=" CB PRO A 473 " ideal model delta sigma weight residual 111.56 100.82 10.74 1.27e+00 6.20e-01 7.16e+01 ... (remaining 21934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8460 17.96 - 35.91: 698 35.91 - 53.86: 155 53.86 - 71.81: 26 71.81 - 89.77: 10 Dihedral angle restraints: 9349 sinusoidal: 3595 harmonic: 5754 Sorted by residual: dihedral pdb=" CA ARG F 90 " pdb=" C ARG F 90 " pdb=" N GLY F 91 " pdb=" CA GLY F 91 " ideal model delta harmonic sigma weight residual -180.00 -150.61 -29.39 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ALA A 333 " pdb=" C ALA A 333 " pdb=" N PHE A 334 " pdb=" CA PHE A 334 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ASP C 111 " pdb=" C ASP C 111 " pdb=" N GLU C 112 " pdb=" CA GLU C 112 " ideal model delta harmonic sigma weight residual 180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 9346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1723 0.093 - 0.186: 725 0.186 - 0.278: 159 0.278 - 0.371: 25 0.371 - 0.464: 1 Chirality restraints: 2633 Sorted by residual: chirality pdb=" CA PRO A 265 " pdb=" N PRO A 265 " pdb=" C PRO A 265 " pdb=" CB PRO A 265 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA ARG F 90 " pdb=" N ARG F 90 " pdb=" C ARG F 90 " pdb=" CB ARG F 90 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA TYR A 113 " pdb=" N TYR A 113 " pdb=" C TYR A 113 " pdb=" CB TYR A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 2630 not shown) Planarity restraints: 2637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE e 18 " 0.099 2.00e-02 2.50e+03 6.98e-02 8.54e+01 pdb=" CG PHE e 18 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE e 18 " -0.102 2.00e-02 2.50e+03 pdb=" CD2 PHE e 18 " -0.090 2.00e-02 2.50e+03 pdb=" CE1 PHE e 18 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 PHE e 18 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE e 18 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 28 " -0.122 2.00e-02 2.50e+03 6.32e-02 7.98e+01 pdb=" CG TYR B 28 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 28 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR B 28 " 0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR B 28 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR B 28 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 28 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR B 28 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 431 " -0.078 2.00e-02 2.50e+03 5.32e-02 7.07e+01 pdb=" CG TRP D 431 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP D 431 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 431 " 0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP D 431 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP D 431 " -0.050 2.00e-02 2.50e+03 pdb=" CE3 TRP D 431 " -0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 431 " -0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 431 " 0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP D 431 " -0.008 2.00e-02 2.50e+03 ... (remaining 2634 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 410 2.63 - 3.20: 15982 3.20 - 3.76: 28312 3.76 - 4.33: 41114 4.33 - 4.90: 64094 Nonbonded interactions: 149912 Sorted by model distance: nonbonded pdb=" OD1 ASP A 678 " pdb=" O HOH A1001 " model vdw 2.058 2.440 nonbonded pdb=" CE2APHE B 41 " pdb=" CD1 LEU B 45 " model vdw 2.083 3.760 nonbonded pdb=" NH1 ARG D 231 " pdb=" O HOH D 501 " model vdw 2.106 2.520 nonbonded pdb=" O HOH A1002 " pdb=" O HOH A1008 " model vdw 2.117 2.440 nonbonded pdb=" OG1 THR E 113 " pdb=" O HOH E 301 " model vdw 2.181 2.440 ... (remaining 149907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 92 5.16 5 C 10600 2.51 5 N 2388 2.21 5 O 3017 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=0.24 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 13.730 Check model and map are aligned: 0.240 Process input model: 52.790 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 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 : 0.020 0.232 16137 Z= 1.301 Angle : 2.179 13.447 21939 Z= 1.477 Chirality : 0.102 0.464 2633 Planarity : 0.022 0.249 2637 Dihedral : 14.535 89.768 5671 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 9.68 % 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: -1.62 (0.16), residues: 2010 helix: -0.87 (0.11), residues: 1509 sheet: -0.81 (0.71), residues: 48 loop : -1.15 (0.29), residues: 453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 256 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 14 residues processed: 285 average time/residue: 1.3911 time to fit residues: 437.0962 Evaluate side-chains 229 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 215 time to evaluate : 1.797 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1416 time to fit residues: 2.8636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN E 8 ASN E 137 ASN F 43 ASN e 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 16137 Z= 0.245 Angle : 0.636 8.308 21939 Z= 0.346 Chirality : 0.043 0.185 2633 Planarity : 0.005 0.040 2637 Dihedral : 7.592 84.316 2225 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 1.38 (0.18), residues: 2010 helix: 1.45 (0.13), residues: 1511 sheet: -0.46 (0.67), residues: 58 loop : -0.60 (0.29), residues: 441 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 232 time to evaluate : 1.808 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 10 residues processed: 250 average time/residue: 1.3877 time to fit residues: 383.8366 Evaluate side-chains 220 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 210 time to evaluate : 1.865 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.5066 time to fit residues: 4.3731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 189 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 140 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN E 8 ASN E 137 ASN E 146 HIS e 8 ASN e 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 16137 Z= 0.237 Angle : 0.588 7.154 21939 Z= 0.317 Chirality : 0.043 0.197 2633 Planarity : 0.005 0.042 2637 Dihedral : 7.126 79.409 2225 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 1.95 (0.18), residues: 2010 helix: 1.81 (0.13), residues: 1518 sheet: 0.21 (0.74), residues: 48 loop : -0.30 (0.30), residues: 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 212 time to evaluate : 2.252 Fit side-chains outliers start: 28 outliers final: 11 residues processed: 228 average time/residue: 1.5138 time to fit residues: 379.8050 Evaluate side-chains 219 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 1.755 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 5 average time/residue: 0.4029 time to fit residues: 5.1151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 0.3980 chunk 132 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 117 optimal weight: 0.2980 chunk 176 optimal weight: 0.5980 chunk 186 optimal weight: 0.0970 chunk 92 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN C 50 GLN E 8 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN e 8 ASN e 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16137 Z= 0.183 Angle : 0.533 7.496 21939 Z= 0.286 Chirality : 0.040 0.185 2633 Planarity : 0.004 0.043 2637 Dihedral : 6.561 75.159 2225 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.29 (0.18), residues: 2010 helix: 2.07 (0.13), residues: 1510 sheet: 0.20 (0.74), residues: 48 loop : -0.15 (0.30), residues: 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 215 time to evaluate : 1.841 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 229 average time/residue: 1.4860 time to fit residues: 374.2567 Evaluate side-chains 224 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 212 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.5118 time to fit residues: 6.0448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 chunk 159 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN e 8 ASN e 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 16137 Z= 0.246 Angle : 0.567 7.905 21939 Z= 0.306 Chirality : 0.042 0.191 2633 Planarity : 0.004 0.044 2637 Dihedral : 6.523 72.010 2225 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.18 (0.18), residues: 2010 helix: 1.94 (0.13), residues: 1514 sheet: 0.23 (0.75), residues: 48 loop : -0.05 (0.30), residues: 448 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 212 time to evaluate : 1.835 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 228 average time/residue: 1.5237 time to fit residues: 382.2248 Evaluate side-chains 226 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 213 time to evaluate : 1.753 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.1751 time to fit residues: 3.8820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 186 optimal weight: 0.0980 chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN e 8 ASN e 17 ASN e 20 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 16137 Z= 0.230 Angle : 0.553 8.440 21939 Z= 0.299 Chirality : 0.042 0.256 2633 Planarity : 0.004 0.044 2637 Dihedral : 6.433 71.659 2225 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.16 (0.18), residues: 2010 helix: 1.94 (0.13), residues: 1513 sheet: 0.16 (0.73), residues: 48 loop : -0.07 (0.30), residues: 449 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 1.857 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 229 average time/residue: 1.4876 time to fit residues: 374.9743 Evaluate side-chains 225 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 1.821 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.2265 time to fit residues: 4.2558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 136 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 186 optimal weight: 0.0970 chunk 116 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 85 optimal weight: 0.0170 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN e 8 ASN e 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 16137 Z= 0.181 Angle : 0.516 8.438 21939 Z= 0.279 Chirality : 0.040 0.202 2633 Planarity : 0.004 0.043 2637 Dihedral : 6.194 70.297 2225 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 0.98 % Favored : 98.97 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.34 (0.18), residues: 2010 helix: 2.07 (0.13), residues: 1515 sheet: 0.18 (0.74), residues: 48 loop : -0.04 (0.30), residues: 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 213 time to evaluate : 1.922 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 227 average time/residue: 1.5001 time to fit residues: 376.1126 Evaluate side-chains 224 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.2803 time to fit residues: 3.7063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 146 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN e 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 16137 Z= 0.211 Angle : 0.536 8.841 21939 Z= 0.291 Chirality : 0.041 0.202 2633 Planarity : 0.004 0.044 2637 Dihedral : 6.224 69.886 2225 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.28 (0.18), residues: 2010 helix: 2.02 (0.13), residues: 1517 sheet: 0.19 (0.73), residues: 48 loop : -0.01 (0.31), residues: 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 211 time to evaluate : 1.911 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 224 average time/residue: 1.5030 time to fit residues: 370.3030 Evaluate side-chains 226 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 210 time to evaluate : 1.796 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.2223 time to fit residues: 3.8278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 0.0670 chunk 136 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 113 optimal weight: 0.4980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN e 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 16137 Z= 0.230 Angle : 0.551 8.683 21939 Z= 0.298 Chirality : 0.042 0.204 2633 Planarity : 0.004 0.044 2637 Dihedral : 6.256 69.450 2225 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.24 (0.18), residues: 2010 helix: 1.98 (0.13), residues: 1518 sheet: 0.20 (0.72), residues: 48 loop : -0.00 (0.31), residues: 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 208 time to evaluate : 1.896 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 222 average time/residue: 1.4780 time to fit residues: 361.0552 Evaluate side-chains 222 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 1.836 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1718 time to fit residues: 3.0095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.0570 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN e 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 16137 Z= 0.225 Angle : 0.549 8.719 21939 Z= 0.297 Chirality : 0.042 0.201 2633 Planarity : 0.004 0.044 2637 Dihedral : 6.246 69.199 2225 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.24 (0.18), residues: 2010 helix: 1.98 (0.13), residues: 1517 sheet: 0.21 (0.72), residues: 48 loop : -0.02 (0.31), residues: 445 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 206 time to evaluate : 1.825 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 219 average time/residue: 1.6000 time to fit residues: 386.6421 Evaluate side-chains 220 residues out of total 1626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 1.851 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.1998 time to fit residues: 3.1279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 0.0270 chunk 46 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN e 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.103851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.076149 restraints weight = 98540.975| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.73 r_work: 0.2657 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 16137 Z= 0.225 Angle : 0.552 10.873 21939 Z= 0.297 Chirality : 0.042 0.203 2633 Planarity : 0.004 0.044 2637 Dihedral : 6.231 69.040 2225 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.24 (0.18), residues: 2010 helix: 1.98 (0.13), residues: 1517 sheet: 0.24 (0.72), residues: 48 loop : -0.02 (0.31), residues: 445 =============================================================================== Job complete usr+sys time: 6558.56 seconds wall clock time: 117 minutes 0.85 seconds (7020.85 seconds total)