Starting phenix.real_space_refine on Sun Mar 17 06:12:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stj_25430/03_2024/7stj_25430_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stj_25430/03_2024/7stj_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_25430/03_2024/7stj_25430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stj_25430/03_2024/7stj_25430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stj_25430/03_2024/7stj_25430_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stj_25430/03_2024/7stj_25430_neut.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.13, per 1000 atoms: 0.53 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: 4.84 Conformation dependent library (CDL) restraints added in 2.5 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: 1.44 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: 4.29 Time building geometry restraints manager: 5.39 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 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 6.340 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.810 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 : 36.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.00 % Favored : 89.88 % Rotamer: Outliers : 0.33 % Allowed : 0.59 % Favored : 99.08 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 414 HIS 0.006 0.002 HIS B 627 PHE 0.016 0.002 PHE B 565 TYR 0.021 0.002 TYR A 277 ARG 0.009 0.001 ARG B 65 *********************** 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 : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6391 (mp0) REVERT: B 38 MET cc_start: 0.7913 (mmp) cc_final: 0.7605 (mmp) REVERT: B 553 MET cc_start: 0.9239 (mmp) cc_final: 0.8927 (mmm) outliers start: 5 outliers final: 3 residues processed: 44 average time/residue: 0.2394 time to fit residues: 18.0028 Evaluate side-chains 38 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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 275 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0980 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= 0.399 Angle : 0.722 8.803 18756 Z= 0.378 Chirality : 0.045 0.160 2035 Planarity : 0.005 0.048 2416 Dihedral : 5.373 21.858 1824 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 37.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 0.07 % Allowed : 8.28 % Favored : 91.66 % 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: -1.74 (0.31), residues: 213 sheet: -1.50 (0.28), residues: 332 loop : -1.39 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 414 HIS 0.007 0.002 HIS B 263 PHE 0.014 0.002 PHE B 88 TYR 0.021 0.002 TYR A 430 ARG 0.010 0.001 ARG A 389 *********************** 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 : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7036 (tpt) cc_final: 0.6634 (mmm) REVERT: A 300 MET cc_start: 0.9794 (tpt) cc_final: 0.9562 (tpt) REVERT: A 831 MET cc_start: 0.8635 (tpt) cc_final: 0.8273 (tpt) REVERT: B 98 MET cc_start: 0.7562 (mmp) cc_final: 0.7306 (mmm) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.1870 time to fit residues: 13.6532 Evaluate side-chains 35 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 0.9990 chunk 124 optimal weight: 0.0570 chunk 102 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 40.0000 chunk 162 optimal weight: 0.2980 chunk 133 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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** A 829 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1598 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= 0.165 Angle : 0.598 6.862 18756 Z= 0.306 Chirality : 0.045 0.161 2035 Planarity : 0.004 0.046 2416 Dihedral : 4.893 18.855 1824 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: -1.89 (0.21), residues: 1630 helix: -1.28 (0.33), residues: 220 sheet: -1.20 (0.29), residues: 322 loop : -1.29 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 414 HIS 0.004 0.001 HIS B 820 PHE 0.025 0.001 PHE A 248 TYR 0.015 0.001 TYR B 845 ARG 0.010 0.000 ARG A 83 *********************** 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 46 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.9800 (tpt) cc_final: 0.9597 (tpt) REVERT: A 831 MET cc_start: 0.8760 (tpt) cc_final: 0.8420 (tpt) REVERT: B 442 MET cc_start: 0.9108 (mmp) cc_final: 0.8855 (mmp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2354 time to fit residues: 18.3935 Evaluate side-chains 39 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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: 0.9990 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 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 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 ** 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: 0.8425 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13844 Z= 0.244 Angle : 0.586 6.330 18756 Z= 0.305 Chirality : 0.043 0.141 2035 Planarity : 0.004 0.044 2416 Dihedral : 4.874 18.724 1824 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 26.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: -1.93 (0.21), residues: 1630 helix: -1.25 (0.34), residues: 213 sheet: -1.51 (0.28), residues: 328 loop : -1.22 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 414 HIS 0.004 0.001 HIS A 440 PHE 0.017 0.001 PHE A 565 TYR 0.013 0.001 TYR C 16 ARG 0.006 0.000 ARG A 389 *********************** 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 40 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.9815 (tpt) cc_final: 0.9595 (tpt) REVERT: A 831 MET cc_start: 0.8782 (tpt) cc_final: 0.8436 (tpt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2144 time to fit residues: 14.8684 Evaluate side-chains 33 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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: 7.9990 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** 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: 0.8407 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13844 Z= 0.192 Angle : 0.559 8.636 18756 Z= 0.287 Chirality : 0.043 0.154 2035 Planarity : 0.003 0.044 2416 Dihedral : 4.816 18.444 1824 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.91 % 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: -1.84 (0.21), residues: 1630 helix: -1.01 (0.35), residues: 213 sheet: -1.34 (0.29), residues: 316 loop : -1.25 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 414 HIS 0.004 0.001 HIS B 263 PHE 0.015 0.001 PHE A 248 TYR 0.014 0.001 TYR C 16 ARG 0.006 0.000 ARG A 331 *********************** 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 : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7033 (tpt) cc_final: 0.6574 (mmm) REVERT: A 831 MET cc_start: 0.8782 (tpt) cc_final: 0.8432 (tpt) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.2563 time to fit residues: 19.8624 Evaluate side-chains 33 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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: 6.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 13 optimal weight: 50.0000 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1858 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= 0.325 Angle : 0.647 7.361 18756 Z= 0.334 Chirality : 0.044 0.198 2035 Planarity : 0.004 0.045 2416 Dihedral : 5.058 20.016 1824 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 31.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: -1.94 (0.21), residues: 1630 helix: -1.21 (0.35), residues: 213 sheet: -1.46 (0.29), residues: 315 loop : -1.28 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 414 HIS 0.007 0.001 HIS B 21 PHE 0.013 0.002 PHE B 88 TYR 0.018 0.002 TYR A 430 ARG 0.007 0.001 ARG A 389 *********************** 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 : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7085 (tpt) cc_final: 0.6580 (mmm) REVERT: A 831 MET cc_start: 0.8663 (tpt) cc_final: 0.8296 (tpt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2159 time to fit residues: 15.3489 Evaluate side-chains 34 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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: 30.0000 chunk 90 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 470 ASN ** 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: 0.8415 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13844 Z= 0.187 Angle : 0.570 7.054 18756 Z= 0.292 Chirality : 0.044 0.165 2035 Planarity : 0.003 0.044 2416 Dihedral : 4.845 18.287 1824 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: -1.84 (0.21), residues: 1630 helix: -1.00 (0.35), residues: 213 sheet: -1.34 (0.29), residues: 311 loop : -1.26 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 414 HIS 0.004 0.001 HIS B 263 PHE 0.012 0.001 PHE A 248 TYR 0.014 0.001 TYR C 16 ARG 0.005 0.000 ARG B 47 *********************** 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 42 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.6897 (tpt) cc_final: 0.6498 (mmm) REVERT: A 831 MET cc_start: 0.8771 (tpt) cc_final: 0.8414 (tpt) REVERT: B 442 MET cc_start: 0.9053 (mmp) cc_final: 0.8829 (mmp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1926 time to fit residues: 14.7341 Evaluate side-chains 33 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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: 7.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 101 optimal weight: 0.2980 chunk 108 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 0.3980 chunk 125 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13844 Z= 0.270 Angle : 0.619 7.690 18756 Z= 0.317 Chirality : 0.043 0.159 2035 Planarity : 0.004 0.045 2416 Dihedral : 4.972 18.926 1824 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 28.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -1.18 (0.34), residues: 220 sheet: -1.46 (0.28), residues: 315 loop : -1.29 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 632 HIS 0.008 0.001 HIS B 829 PHE 0.012 0.001 PHE B 88 TYR 0.015 0.001 TYR C 16 ARG 0.011 0.001 ARG B 47 *********************** 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 : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7051 (tpt) cc_final: 0.6651 (mmm) REVERT: A 831 MET cc_start: 0.8726 (tpt) cc_final: 0.8361 (tpt) REVERT: B 98 MET cc_start: 0.7261 (mmm) cc_final: 0.6777 (mmm) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2141 time to fit residues: 15.9113 Evaluate side-chains 34 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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: 7.9990 chunk 139 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 140 optimal weight: 30.0000 chunk 147 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 overall best weight: 3.2784 ------------------------------------------------------------------------------- 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 187 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: 0.8442 moved from start: 0.2210 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= 0.233 Angle : 0.600 10.710 18756 Z= 0.306 Chirality : 0.044 0.157 2035 Planarity : 0.004 0.044 2416 Dihedral : 4.949 18.467 1824 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 27.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -1.11 (0.34), residues: 215 sheet: -1.39 (0.29), residues: 315 loop : -1.30 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 414 HIS 0.005 0.001 HIS B 627 PHE 0.011 0.001 PHE A 248 TYR 0.015 0.001 TYR C 16 ARG 0.007 0.000 ARG B 47 *********************** 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 41 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7113 (tpt) cc_final: 0.6743 (mmm) REVERT: A 831 MET cc_start: 0.8741 (tpt) cc_final: 0.8370 (tpt) REVERT: B 98 MET cc_start: 0.7594 (mmm) cc_final: 0.7127 (mmm) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.2144 time to fit residues: 15.6258 Evaluate side-chains 33 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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: 40.0000 chunk 95 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 164 optimal weight: 20.0000 chunk 151 optimal weight: 50.0000 chunk 130 optimal weight: 10.0000 chunk 13 optimal weight: 40.0000 chunk 101 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** 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 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 13844 Z= 0.390 Angle : 0.717 9.172 18756 Z= 0.367 Chirality : 0.045 0.159 2035 Planarity : 0.005 0.045 2416 Dihedral : 5.344 22.218 1824 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 37.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -2.16 (0.21), residues: 1630 helix: -1.56 (0.33), residues: 219 sheet: -1.58 (0.29), residues: 301 loop : -1.41 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 414 HIS 0.008 0.002 HIS B 627 PHE 0.017 0.002 PHE B 88 TYR 0.024 0.002 TYR A 430 ARG 0.013 0.001 ARG B 780 ********************** 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 40 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7337 (tpt) cc_final: 0.6911 (mmm) REVERT: B 98 MET cc_start: 0.7745 (mmm) cc_final: 0.7234 (mmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2372 time to fit residues: 17.1121 Evaluate side-chains 33 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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: 6.9990 chunk 120 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 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 = 0.3357 r_free = 0.3357 target = 0.035631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.024080 restraints weight = 217831.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.024791 restraints weight = 120024.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.025247 restraints weight = 82139.890| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13844 Z= 0.189 Angle : 0.604 10.699 18756 Z= 0.307 Chirality : 0.044 0.169 2035 Planarity : 0.003 0.044 2416 Dihedral : 5.021 18.532 1824 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 25.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -1.93 (0.21), residues: 1630 helix: -1.12 (0.35), residues: 215 sheet: -1.41 (0.29), residues: 315 loop : -1.30 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 414 HIS 0.004 0.001 HIS B 263 PHE 0.014 0.001 PHE A 248 TYR 0.013 0.001 TYR C 16 ARG 0.005 0.000 ARG B 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2154.34 seconds wall clock time: 40 minutes 46.24 seconds (2446.24 seconds total)