Starting phenix.real_space_refine (version: dev) on Tue Dec 13 19:33:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stj_25430/12_2022/7stj_25430_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stj_25430/12_2022/7stj_25430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stj_25430/12_2022/7stj_25430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stj_25430/12_2022/7stj_25430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stj_25430/12_2022/7stj_25430_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stj_25430/12_2022/7stj_25430_neut.pdb" } resolution = 4.4 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3406 atoms to isotropic. 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 PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 13515 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6378 Classifications: {'peptide': 786} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 743} Chain breaks: 9 Chain: "B" Number of atoms: 6441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6441 Classifications: {'peptide': 797} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 752} Chain breaks: 6 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 320 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain breaks: 1 Time building chain proxies: 8.20, per 1000 atoms: 0.61 Number of scatterers: 13515 At special positions: 0 Unit cell: (131.76, 132.84, 182.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2490 8.00 N 2320 7.00 C 8597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.02 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.02 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 860 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.04 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 860 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 66 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.04 Conformation dependent library (CDL) restraints added in 2.2 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 15.0% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 Processing helix chain 'A' and resid 42 through 48 removed outlier: 3.877A pdb=" N PHE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.742A pdb=" N ILE A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.537A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 714 removed outlier: 3.734A pdb=" N LEU A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 869 Processing helix chain 'B' and resid 17 through 25 removed outlier: 4.012A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN B 25 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.370A pdb=" N ASN B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.531A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 Processing helix chain 'B' and resid 323 through 329 removed outlier: 4.238A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.168A pdb=" N PHE B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 removed outlier: 4.156A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.767A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 705 through 714 Processing helix chain 'B' and resid 808 through 813 removed outlier: 3.657A pdb=" N ASP B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 870 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.665A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 67 through 73 removed outlier: 3.872A pdb=" N GLU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 17 removed outlier: 3.568A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 67 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 4.023A pdb=" N LEU A 33 " --> pdb=" O TYR A 60 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N MET A 98 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ARG A 118 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 94 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLU A 120 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 96 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASN A 122 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET A 98 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 232 Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 311 removed outlier: 6.199A pdb=" N LYS A 310 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE A 336 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 363 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 321 removed outlier: 3.740A pdb=" N LYS A 319 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 341 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS A 425 " --> pdb=" O TYR A 398 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 473 Processing sheet with id=AA9, first strand: chain 'A' and resid 475 through 479 Processing sheet with id=AB1, first strand: chain 'A' and resid 531 through 534 removed outlier: 3.638A pdb=" N MET A 504 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 567 " --> pdb=" O MET A 504 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 598 through 604 removed outlier: 5.314A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 759 through 762 removed outlier: 3.860A pdb=" N GLY A 778 " --> pdb=" O GLN A 635 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AB5, first strand: chain 'A' and resid 857 through 862 removed outlier: 3.620A pdb=" N LEU A 844 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL A 886 " --> pdb=" O TRP A 897 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP A 897 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA A 888 " --> pdb=" O GLY A 895 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 880 through 881 Processing sheet with id=AB7, first strand: chain 'B' and resid 9 through 13 removed outlier: 8.832A pdb=" N GLN B 34 " --> pdb=" O PRO B 9 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET B 11 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU B 36 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 13 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET B 38 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET B 98 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ARG B 65 " --> pdb=" O MET B 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC1, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC2, first strand: chain 'B' and resid 278 through 279 Processing sheet with id=AC3, first strand: chain 'B' and resid 292 through 294 removed outlier: 3.501A pdb=" N THR B 293 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 321 removed outlier: 6.160A pdb=" N VAL B 335 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLN B 313 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN B 337 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 315 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER B 339 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY B 317 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 341 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS B 319 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 364 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 321 removed outlier: 6.160A pdb=" N VAL B 335 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLN B 313 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN B 337 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 315 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER B 339 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY B 317 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 341 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS B 319 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N HIS B 429 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 477 through 479 Processing sheet with id=AC7, first strand: chain 'B' and resid 531 through 534 removed outlier: 3.906A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 599 through 605 removed outlier: 4.567A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 762 Processing sheet with id=AD1, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.583A pdb=" N ALA B 803 " --> pdb=" O TYR B 779 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 818 through 822 removed outlier: 3.563A pdb=" N CYS B 872 " --> pdb=" O LEU B 830 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 856 through 862 334 hydrogen bonds defined for protein. 849 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: 5.19 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4409 1.34 - 1.46: 3296 1.46 - 1.58: 6007 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 13844 Sorted by residual: bond pdb=" CA ASN B 122 " pdb=" CB ASN B 122 " ideal model delta sigma weight residual 1.539 1.455 0.084 4.88e-02 4.20e+02 2.98e+00 bond pdb=" C LYS B 197 " pdb=" N SER B 198 " ideal model delta sigma weight residual 1.332 1.310 0.023 1.40e-02 5.10e+03 2.66e+00 bond pdb=" CA CYS A 468 " pdb=" C CYS A 468 " ideal model delta sigma weight residual 1.528 1.513 0.016 1.04e-02 9.25e+03 2.30e+00 bond pdb=" CA GLU A 469 " pdb=" C GLU A 469 " ideal model delta sigma weight residual 1.519 1.501 0.018 1.22e-02 6.72e+03 2.18e+00 bond pdb=" CA CYS A 308 " pdb=" C CYS A 308 " ideal model delta sigma weight residual 1.531 1.521 0.011 7.40e-03 1.83e+04 2.02e+00 ... (remaining 13839 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.11: 345 106.11 - 113.09: 7521 113.09 - 120.06: 4614 120.06 - 127.04: 6082 127.04 - 134.01: 194 Bond angle restraints: 18756 Sorted by residual: angle pdb=" N GLU A 469 " pdb=" CA GLU A 469 " pdb=" C GLU A 469 " ideal model delta sigma weight residual 113.55 101.76 11.79 1.26e+00 6.30e-01 8.75e+01 angle pdb=" N LEU A 305 " pdb=" CA LEU A 305 " pdb=" C LEU A 305 " ideal model delta sigma weight residual 113.20 108.47 4.73 1.21e+00 6.83e-01 1.53e+01 angle pdb=" CB MET A 442 " pdb=" CG MET A 442 " pdb=" SD MET A 442 " ideal model delta sigma weight residual 112.70 123.84 -11.14 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA TRP B 414 " pdb=" CB TRP B 414 " pdb=" CG TRP B 414 " ideal model delta sigma weight residual 113.60 107.46 6.14 1.90e+00 2.77e-01 1.04e+01 angle pdb=" N ASN A 470 " pdb=" CA ASN A 470 " pdb=" C ASN A 470 " ideal model delta sigma weight residual 110.80 117.39 -6.59 2.13e+00 2.20e-01 9.58e+00 ... (remaining 18751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7507 17.94 - 35.89: 738 35.89 - 53.83: 106 53.83 - 71.78: 19 71.78 - 89.72: 11 Dihedral angle restraints: 8381 sinusoidal: 3498 harmonic: 4883 Sorted by residual: dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 -177.28 -89.72 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 -167.36 81.36 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS B 196 " pdb=" SG CYS B 196 " pdb=" SG CYS B 207 " pdb=" CB CYS B 207 " ideal model delta sinusoidal sigma weight residual -86.00 -166.25 80.25 1 1.00e+01 1.00e-02 7.97e+01 ... (remaining 8378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1301 0.034 - 0.069: 466 0.069 - 0.103: 193 0.103 - 0.138: 64 0.138 - 0.172: 11 Chirality restraints: 2035 Sorted by residual: chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA MET A 442 " pdb=" N MET A 442 " pdb=" C MET A 442 " pdb=" CB MET A 442 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB VAL A 566 " pdb=" CA VAL A 566 " pdb=" CG1 VAL A 566 " pdb=" CG2 VAL A 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 2032 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 469 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C GLU B 469 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU B 469 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 470 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 834 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO B 835 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 835 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 835 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 414 " -0.013 2.00e-02 2.50e+03 9.67e-03 2.34e+00 pdb=" CG TRP B 414 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 414 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B 414 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 414 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 414 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B 414 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 414 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 414 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 414 " 0.003 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 357 2.62 - 3.19: 13749 3.19 - 3.76: 24225 3.76 - 4.33: 33478 4.33 - 4.90: 50161 Nonbonded interactions: 121970 Sorted by model distance: nonbonded pdb=" O LEU B 552 " pdb=" NH1 ARG B 554 " model vdw 2.047 2.520 nonbonded pdb=" O SER B 878 " pdb=" OH TYR B 882 " model vdw 2.060 2.440 nonbonded pdb=" OD1 ASP B 812 " pdb=" OG SER B 890 " model vdw 2.081 2.440 nonbonded pdb=" O HIS A 263 " pdb=" NE2 GLN A 276 " model vdw 2.105 2.520 nonbonded pdb=" O GLU C 59 " pdb=" OG1 THR C 63 " model vdw 2.117 2.440 ... (remaining 121965 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 3 through 526 or resid 529 through 656 or resid 704 throug \ h 905)) selection = (chain 'B' and (resid 3 through 150 or resid 168 through 172 or resid 178 throug \ h 314 or resid 317 through 346 or resid 351 through 539 or resid 547 through 905 \ )) } ncs_group { reference = (chain 'C' and (resid 7 through 26 or resid 56 through 76)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 8597 2.51 5 N 2320 2.21 5 O 2490 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 7.300 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.120 Process input model: 39.630 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 : 0.005 0.084 13844 Z= 0.345 Angle : 0.716 11.787 18756 Z= 0.383 Chirality : 0.045 0.172 2035 Planarity : 0.005 0.048 2416 Dihedral : 13.424 86.749 5114 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 36.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.00 % Favored : 89.88 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.96 (0.21), residues: 1630 helix: -1.37 (0.36), residues: 187 sheet: -1.39 (0.27), residues: 354 loop : -1.28 (0.19), residues: 1089 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 44 average time/residue: 0.2402 time to fit residues: 18.0187 Evaluate side-chains 37 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 1.827 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2421 time to fit residues: 3.4642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 149 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 21 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.096 13844 Z= 0.401 Angle : 0.722 8.678 18756 Z= 0.379 Chirality : 0.045 0.159 2035 Planarity : 0.005 0.048 2416 Dihedral : 5.375 21.865 1824 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 37.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.17 (0.20), residues: 1630 helix: -1.72 (0.32), residues: 213 sheet: -1.50 (0.28), residues: 332 loop : -1.39 (0.19), residues: 1085 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.2188 time to fit residues: 15.5539 Evaluate side-chains 35 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.747 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 150 optimal weight: 7.9990 chunk 162 optimal weight: 0.0370 chunk 133 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN D 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 13844 Z= 0.171 Angle : 0.591 6.411 18756 Z= 0.306 Chirality : 0.045 0.160 2035 Planarity : 0.004 0.047 2416 Dihedral : 4.928 19.255 1824 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.92 (0.21), residues: 1630 helix: -1.31 (0.33), residues: 219 sheet: -1.32 (0.29), residues: 328 loop : -1.27 (0.19), residues: 1083 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.2445 time to fit residues: 18.5621 Evaluate side-chains 34 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.0970 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 150 optimal weight: 30.0000 chunk 159 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 GLN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 13844 Z= 0.256 Angle : 0.596 6.546 18756 Z= 0.310 Chirality : 0.043 0.143 2035 Planarity : 0.004 0.045 2416 Dihedral : 4.938 18.385 1824 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 27.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.88 (0.21), residues: 1630 helix: -1.13 (0.35), residues: 207 sheet: -1.48 (0.28), residues: 318 loop : -1.22 (0.19), residues: 1105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2324 time to fit residues: 16.1176 Evaluate side-chains 33 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.865 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 0.0970 chunk 65 optimal weight: 7.9990 chunk 136 optimal weight: 20.0000 chunk 110 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 143 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 HIS ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 13844 Z= 0.155 Angle : 0.558 8.457 18756 Z= 0.284 Chirality : 0.044 0.166 2035 Planarity : 0.003 0.044 2416 Dihedral : 4.731 18.668 1824 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.82 (0.21), residues: 1630 helix: -1.04 (0.34), residues: 219 sheet: -1.22 (0.29), residues: 314 loop : -1.27 (0.19), residues: 1097 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.2277 time to fit residues: 17.6807 Evaluate side-chains 35 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 13 optimal weight: 50.0000 chunk 52 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 13844 Z= 0.329 Angle : 0.653 7.424 18756 Z= 0.337 Chirality : 0.044 0.205 2035 Planarity : 0.004 0.045 2416 Dihedral : 5.000 20.209 1824 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 31.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.21), residues: 1630 helix: -1.31 (0.34), residues: 220 sheet: -1.32 (0.29), residues: 311 loop : -1.32 (0.19), residues: 1099 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2208 time to fit residues: 15.8080 Evaluate side-chains 35 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 5.9990 chunk 17 optimal weight: 40.0000 chunk 90 optimal weight: 0.9990 chunk 116 optimal weight: 0.0470 chunk 134 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 159 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 overall best weight: 2.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 13844 Z= 0.222 Angle : 0.589 9.422 18756 Z= 0.301 Chirality : 0.044 0.165 2035 Planarity : 0.004 0.045 2416 Dihedral : 4.935 18.404 1824 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 26.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.88 (0.21), residues: 1630 helix: -1.07 (0.35), residues: 213 sheet: -1.33 (0.29), residues: 311 loop : -1.29 (0.19), residues: 1106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2321 time to fit residues: 17.1019 Evaluate side-chains 34 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 8.9990 chunk 94 optimal weight: 0.0050 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 overall best weight: 3.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 187 HIS ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 13844 Z= 0.229 Angle : 0.597 8.753 18756 Z= 0.306 Chirality : 0.044 0.163 2035 Planarity : 0.004 0.046 2416 Dihedral : 4.901 18.334 1824 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 27.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.92 (0.21), residues: 1630 helix: -1.18 (0.34), residues: 220 sheet: -1.40 (0.28), residues: 315 loop : -1.28 (0.19), residues: 1095 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2246 time to fit residues: 16.8111 Evaluate side-chains 35 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 148 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 140 optimal weight: 40.0000 chunk 147 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 13844 Z= 0.294 Angle : 0.644 12.941 18756 Z= 0.328 Chirality : 0.044 0.172 2035 Planarity : 0.004 0.044 2416 Dihedral : 5.112 21.112 1824 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 30.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.00 (0.21), residues: 1630 helix: -1.23 (0.34), residues: 212 sheet: -1.44 (0.29), residues: 315 loop : -1.35 (0.19), residues: 1103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2091 time to fit residues: 15.6289 Evaluate side-chains 35 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 30.0000 chunk 95 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 164 optimal weight: 30.0000 chunk 151 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 HIS B 187 HIS ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 13844 Z= 0.181 Angle : 0.589 7.945 18756 Z= 0.300 Chirality : 0.044 0.168 2035 Planarity : 0.003 0.045 2416 Dihedral : 4.875 17.530 1824 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 24.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.87 (0.21), residues: 1630 helix: -1.05 (0.35), residues: 214 sheet: -1.33 (0.29), residues: 311 loop : -1.29 (0.19), residues: 1105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2252 time to fit residues: 17.1786 Evaluate side-chains 34 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.035484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.023998 restraints weight = 219745.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.024715 restraints weight = 123840.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.025152 restraints weight = 84773.177| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 13844 Z= 0.239 Angle : 0.600 7.986 18756 Z= 0.307 Chirality : 0.044 0.156 2035 Planarity : 0.004 0.045 2416 Dihedral : 4.917 19.073 1824 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.91 (0.21), residues: 1630 helix: -1.10 (0.35), residues: 214 sheet: -1.35 (0.29), residues: 315 loop : -1.31 (0.19), residues: 1101 =============================================================================== Job complete usr+sys time: 2078.39 seconds wall clock time: 39 minutes 42.43 seconds (2382.43 seconds total)