Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 22:00:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/04_2023/6okr_20102.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/04_2023/6okr_20102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/04_2023/6okr_20102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/04_2023/6okr_20102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/04_2023/6okr_20102.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/04_2023/6okr_20102.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 11620 2.51 5 N 3031 2.21 5 O 3927 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ASP 537": "OD1" <-> "OD2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A ASP 582": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B ASP 537": "OD1" <-> "OD2" Residue "B ASP 540": "OD1" <-> "OD2" Residue "B ASP 561": "OD1" <-> "OD2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "C GLU 385": "OE1" <-> "OE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "C ASP 520": "OD1" <-> "OD2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "C ASP 537": "OD1" <-> "OD2" Residue "C GLU 539": "OE1" <-> "OE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "D ASP 437": "OD1" <-> "OD2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E ARG 290": "NH1" <-> "NH2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 458": "NH1" <-> "NH2" Residue "E GLU 479": "OE1" <-> "OE2" Residue "E GLU 499": "OE1" <-> "OE2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E GLU 539": "OE1" <-> "OE2" Residue "E ASP 540": "OD1" <-> "OD2" Residue "F GLU 215": "OE1" <-> "OE2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 263": "OE1" <-> "OE2" Residue "F ASP 269": "OD1" <-> "OD2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F GLU 313": "OE1" <-> "OE2" Residue "F TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 437": "OD1" <-> "OD2" Residue "F ARG 458": "NH1" <-> "NH2" Residue "F GLU 499": "OE1" <-> "OE2" Residue "F ASP 520": "OD1" <-> "OD2" Residue "F GLU 539": "OE1" <-> "OE2" Residue "F ASP 540": "OD1" <-> "OD2" Residue "F GLU 549": "OE1" <-> "OE2" Residue "F ASP 561": "OD1" <-> "OD2" Residue "F ASP 582": "OD1" <-> "OD2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G GLU 217": "OE1" <-> "OE2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 263": "OE1" <-> "OE2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "G ARG 290": "NH1" <-> "NH2" Residue "G GLU 313": "OE1" <-> "OE2" Residue "G TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 458": "NH1" <-> "NH2" Residue "G GLU 527": "OE1" <-> "OE2" Residue "G GLU 539": "OE1" <-> "OE2" Residue "G ASP 540": "OD1" <-> "OD2" Residue "G ASP 582": "OD1" <-> "OD2" Residue "G ASP 590": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18613 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "B" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "C" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "D" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "E" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "F" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "G" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Time building chain proxies: 9.84, per 1000 atoms: 0.53 Number of scatterers: 18613 At special positions: 0 Unit cell: (143.51, 143.51, 105.09, 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 35 16.00 O 3927 8.00 N 3031 7.00 C 11620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.94 Conformation dependent library (CDL) restraints added in 3.2 seconds 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4480 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 42 sheets defined 19.3% alpha, 18.1% 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 246 through 251 removed outlier: 3.686A pdb=" N PHE A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 251' Processing helix chain 'A' and resid 272 through 279 removed outlier: 3.852A pdb=" N GLY A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.674A pdb=" N ARG A 290 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 291 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 removed outlier: 4.401A pdb=" N LYS A 468 " --> pdb=" O TYR A 464 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 512 removed outlier: 3.701A pdb=" N SER A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 removed outlier: 4.100A pdb=" N GLU A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.951A pdb=" N LYS A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.961A pdb=" N VAL A 603 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 3.701A pdb=" N PHE B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 251' Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.787A pdb=" N GLY B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 removed outlier: 3.613A pdb=" N ARG B 290 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP B 291 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 473 removed outlier: 4.369A pdb=" N LYS B 468 " --> pdb=" O TYR B 464 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 removed outlier: 4.269A pdb=" N ASP B 505 " --> pdb=" O SER B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.669A pdb=" N SER B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 removed outlier: 4.221A pdb=" N GLU B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 592 removed outlier: 3.830A pdb=" N LYS B 587 " --> pdb=" O ASN B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.947A pdb=" N VAL B 603 " --> pdb=" O ILE B 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 removed outlier: 3.680A pdb=" N PHE C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 246 through 251' Processing helix chain 'C' and resid 272 through 279 removed outlier: 3.904A pdb=" N GLY C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.645A pdb=" N ARG C 290 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 473 removed outlier: 4.389A pdb=" N LYS C 468 " --> pdb=" O TYR C 464 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 512 removed outlier: 3.651A pdb=" N SER C 512 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 555 removed outlier: 4.035A pdb=" N GLU C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 592 removed outlier: 3.765A pdb=" N LYS C 587 " --> pdb=" O ASN C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.999A pdb=" N VAL C 603 " --> pdb=" O ILE C 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 removed outlier: 3.799A pdb=" N ALA D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 251 " --> pdb=" O SER D 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 247 through 251' Processing helix chain 'D' and resid 272 through 279 removed outlier: 3.827A pdb=" N GLY D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.691A pdb=" N ARG D 290 " --> pdb=" O THR D 287 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP D 291 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 473 removed outlier: 4.388A pdb=" N LYS D 468 " --> pdb=" O TYR D 464 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA D 472 " --> pdb=" O LYS D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 512 removed outlier: 3.674A pdb=" N SER D 512 " --> pdb=" O SER D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 removed outlier: 4.089A pdb=" N GLU D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE D 555 " --> pdb=" O ILE D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 592 removed outlier: 3.968A pdb=" N LYS D 587 " --> pdb=" O ASN D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 removed outlier: 4.038A pdb=" N VAL D 603 " --> pdb=" O ILE D 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 251 removed outlier: 3.885A pdb=" N ALA E 250 " --> pdb=" O ASP E 247 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 247 through 251' Processing helix chain 'E' and resid 272 through 279 removed outlier: 3.921A pdb=" N GLY E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.613A pdb=" N ARG E 290 " --> pdb=" O THR E 287 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP E 291 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 473 removed outlier: 4.385A pdb=" N LYS E 468 " --> pdb=" O TYR E 464 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA E 472 " --> pdb=" O LYS E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 512 removed outlier: 3.719A pdb=" N SER E 512 " --> pdb=" O SER E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 555 removed outlier: 4.229A pdb=" N GLU E 552 " --> pdb=" O GLY E 548 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE E 555 " --> pdb=" O ILE E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 592 removed outlier: 3.805A pdb=" N LYS E 587 " --> pdb=" O ASN E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 removed outlier: 4.020A pdb=" N VAL E 603 " --> pdb=" O ILE E 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.765A pdb=" N ALA F 250 " --> pdb=" O ASP F 247 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU F 251 " --> pdb=" O SER F 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 247 through 251' Processing helix chain 'F' and resid 272 through 279 removed outlier: 3.833A pdb=" N GLY F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 291 removed outlier: 3.654A pdb=" N ARG F 290 " --> pdb=" O THR F 287 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP F 291 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 473 removed outlier: 4.408A pdb=" N LYS F 468 " --> pdb=" O TYR F 464 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA F 472 " --> pdb=" O LYS F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 512 removed outlier: 3.669A pdb=" N SER F 512 " --> pdb=" O SER F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 555 removed outlier: 4.256A pdb=" N GLU F 552 " --> pdb=" O GLY F 548 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE F 555 " --> pdb=" O ILE F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 592 removed outlier: 3.842A pdb=" N LYS F 587 " --> pdb=" O ASN F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 removed outlier: 4.020A pdb=" N VAL F 603 " --> pdb=" O ILE F 600 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 251 removed outlier: 3.692A pdb=" N PHE G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA G 250 " --> pdb=" O ASP G 247 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 246 through 251' Processing helix chain 'G' and resid 272 through 279 removed outlier: 3.869A pdb=" N GLY G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.633A pdb=" N ARG G 290 " --> pdb=" O THR G 287 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 473 removed outlier: 4.360A pdb=" N LYS G 468 " --> pdb=" O TYR G 464 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA G 472 " --> pdb=" O LYS G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 506 through 512 removed outlier: 3.646A pdb=" N SER G 512 " --> pdb=" O SER G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 555 removed outlier: 4.267A pdb=" N GLU G 552 " --> pdb=" O GLY G 548 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE G 555 " --> pdb=" O ILE G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 592 removed outlier: 3.897A pdb=" N LYS G 587 " --> pdb=" O ASN G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 removed outlier: 3.963A pdb=" N VAL G 603 " --> pdb=" O ILE G 600 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 238 removed outlier: 3.823A pdb=" N THR A 236 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 310 removed outlier: 4.557A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 421 through 423 removed outlier: 3.829A pdb=" N GLN A 482 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN A 411 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N THR A 480 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 413 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU A 478 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.733A pdb=" N THR A 489 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 497 " --> pdb=" O THR A 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 525 through 530 removed outlier: 6.762A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 238 removed outlier: 3.814A pdb=" N THR B 236 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 300 through 310 removed outlier: 4.539A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 421 through 423 removed outlier: 6.487A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 489 through 490 removed outlier: 3.771A pdb=" N THR B 489 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 497 " --> pdb=" O THR B 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 525 through 530 removed outlier: 6.755A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 612 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AB4, first strand: chain 'C' and resid 236 through 238 removed outlier: 3.781A pdb=" N THR C 236 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 300 through 310 removed outlier: 4.545A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 421 through 423 removed outlier: 3.807A pdb=" N GLN C 482 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN C 411 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR C 480 " --> pdb=" O ASN C 411 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL C 413 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU C 478 " --> pdb=" O VAL C 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 489 through 490 removed outlier: 3.795A pdb=" N THR C 489 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 497 " --> pdb=" O THR C 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 525 through 530 removed outlier: 6.734A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AC1, first strand: chain 'D' and resid 236 through 238 removed outlier: 3.782A pdb=" N THR D 236 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 299 through 310 removed outlier: 3.806A pdb=" N ILE D 299 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 421 through 423 removed outlier: 3.818A pdb=" N GLN D 482 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN D 411 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N THR D 480 " --> pdb=" O ASN D 411 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL D 413 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU D 478 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 489 through 490 removed outlier: 3.784A pdb=" N THR D 489 " --> pdb=" O VAL D 497 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 497 " --> pdb=" O THR D 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 525 through 530 removed outlier: 6.755A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AC7, first strand: chain 'E' and resid 236 through 238 removed outlier: 3.825A pdb=" N THR E 236 " --> pdb=" O VAL E 243 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 300 through 310 removed outlier: 4.547A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 421 through 423 removed outlier: 6.406A pdb=" N THR E 407 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL E 483 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 489 through 490 removed outlier: 3.779A pdb=" N THR E 489 " --> pdb=" O VAL E 497 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 497 " --> pdb=" O THR E 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 525 through 530 removed outlier: 6.708A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AD4, first strand: chain 'F' and resid 236 through 238 removed outlier: 3.772A pdb=" N THR F 236 " --> pdb=" O VAL F 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 299 through 310 removed outlier: 3.807A pdb=" N ILE F 299 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 421 through 423 removed outlier: 6.427A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 489 through 490 removed outlier: 3.783A pdb=" N THR F 489 " --> pdb=" O VAL F 497 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 497 " --> pdb=" O THR F 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'F' and resid 525 through 530 removed outlier: 6.839A pdb=" N SER F 516 " --> pdb=" O ILE F 611 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ILE F 613 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE F 518 " --> pdb=" O ILE F 613 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU F 612 " --> pdb=" O ILE F 579 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AE1, first strand: chain 'G' and resid 236 through 238 removed outlier: 3.825A pdb=" N THR G 236 " --> pdb=" O VAL G 243 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 300 through 310 removed outlier: 4.569A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 421 through 423 removed outlier: 6.433A pdb=" N THR G 407 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL G 483 " --> pdb=" O THR G 407 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR G 409 " --> pdb=" O THR G 481 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 489 through 490 removed outlier: 3.767A pdb=" N THR G 489 " --> pdb=" O VAL G 497 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL G 497 " --> pdb=" O THR G 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'G' and resid 525 through 530 removed outlier: 6.779A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 558 through 559 376 hydrogen bonds defined for protein. 972 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: 5.00 Time building geometry restraints manager: 8.53 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: 6091 1.34 - 1.46: 3500 1.46 - 1.58: 9239 1.58 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 18893 Sorted by residual: bond pdb=" C LEU B 433 " pdb=" N SER B 434 " ideal model delta sigma weight residual 1.330 1.299 0.032 1.37e-02 5.33e+03 5.32e+00 bond pdb=" C LEU C 433 " pdb=" N SER C 434 " ideal model delta sigma weight residual 1.330 1.301 0.029 1.37e-02 5.33e+03 4.51e+00 bond pdb=" C LEU F 433 " pdb=" N SER F 434 " ideal model delta sigma weight residual 1.331 1.300 0.031 1.48e-02 4.57e+03 4.43e+00 bond pdb=" N ASP C 415 " pdb=" CA ASP C 415 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 2.96e+00 bond pdb=" N ASP B 415 " pdb=" CA ASP B 415 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.86e+00 ... (remaining 18888 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.77: 456 106.77 - 113.61: 10436 113.61 - 120.45: 7323 120.45 - 127.30: 7227 127.30 - 134.14: 143 Bond angle restraints: 25585 Sorted by residual: angle pdb=" C LEU C 433 " pdb=" N SER C 434 " pdb=" CA SER C 434 " ideal model delta sigma weight residual 120.60 127.89 -7.29 1.53e+00 4.27e-01 2.27e+01 angle pdb=" C LEU B 433 " pdb=" N SER B 434 " pdb=" CA SER B 434 " ideal model delta sigma weight residual 120.60 127.66 -7.06 1.53e+00 4.27e-01 2.13e+01 angle pdb=" C ASP E 224 " pdb=" N ASN E 225 " pdb=" CA ASN E 225 " ideal model delta sigma weight residual 122.08 128.51 -6.43 1.47e+00 4.63e-01 1.91e+01 angle pdb=" C LEU F 433 " pdb=" N SER F 434 " pdb=" CA SER F 434 " ideal model delta sigma weight residual 121.03 127.94 -6.91 1.60e+00 3.91e-01 1.86e+01 angle pdb=" C ASP C 224 " pdb=" N ASN C 225 " pdb=" CA ASN C 225 " ideal model delta sigma weight residual 122.61 129.33 -6.72 1.56e+00 4.11e-01 1.85e+01 ... (remaining 25580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 10049 17.28 - 34.57: 1158 34.57 - 51.85: 288 51.85 - 69.14: 56 69.14 - 86.42: 13 Dihedral angle restraints: 11564 sinusoidal: 4578 harmonic: 6986 Sorted by residual: dihedral pdb=" CA ILE E 460 " pdb=" C ILE E 460 " pdb=" N ALA E 461 " pdb=" CA ALA E 461 " ideal model delta harmonic sigma weight residual 180.00 -136.42 -43.58 0 5.00e+00 4.00e-02 7.60e+01 dihedral pdb=" CA ILE C 460 " pdb=" C ILE C 460 " pdb=" N ALA C 461 " pdb=" CA ALA C 461 " ideal model delta harmonic sigma weight residual -180.00 -136.44 -43.56 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" CA ILE B 460 " pdb=" C ILE B 460 " pdb=" N ALA B 461 " pdb=" CA ALA B 461 " ideal model delta harmonic sigma weight residual -180.00 -136.47 -43.53 0 5.00e+00 4.00e-02 7.58e+01 ... (remaining 11561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2057 0.060 - 0.120: 679 0.120 - 0.180: 160 0.180 - 0.240: 18 0.240 - 0.300: 5 Chirality restraints: 2919 Sorted by residual: chirality pdb=" CB THR D 451 " pdb=" CA THR D 451 " pdb=" OG1 THR D 451 " pdb=" CG2 THR D 451 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB THR C 451 " pdb=" CA THR C 451 " pdb=" OG1 THR C 451 " pdb=" CG2 THR C 451 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB THR F 451 " pdb=" CA THR F 451 " pdb=" OG1 THR F 451 " pdb=" CG2 THR F 451 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2916 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 306 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C LYS B 306 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS B 306 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU B 307 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 306 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C LYS C 306 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS C 306 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU C 307 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 306 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C LYS F 306 " 0.052 2.00e-02 2.50e+03 pdb=" O LYS F 306 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU F 307 " -0.018 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4904 2.79 - 3.32: 17213 3.32 - 3.84: 29143 3.84 - 4.37: 32522 4.37 - 4.90: 55312 Nonbonded interactions: 139094 Sorted by model distance: nonbonded pdb=" OG SER A 386 " pdb=" OD1 ASN A 463 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR B 438 " pdb=" O PRO B 440 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR C 438 " pdb=" O PRO C 440 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR F 438 " pdb=" O PRO F 440 " model vdw 2.265 2.440 nonbonded pdb=" OG1 THR D 438 " pdb=" O PRO D 440 " model vdw 2.265 2.440 ... (remaining 139089 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.170 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 47.650 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.007 0.049 18893 Z= 0.470 Angle : 1.044 10.479 25585 Z= 0.582 Chirality : 0.062 0.300 2919 Planarity : 0.008 0.065 3339 Dihedral : 15.822 86.421 7084 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.34 % Favored : 84.66 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.16 (0.13), residues: 2366 helix: -4.30 (0.12), residues: 371 sheet: -2.20 (0.21), residues: 518 loop : -3.87 (0.12), residues: 1477 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 472 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 481 average time/residue: 0.3125 time to fit residues: 225.4832 Evaluate side-chains 368 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 363 time to evaluate : 2.434 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1628 time to fit residues: 4.8989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 397 ASN A 450 ASN A 475 GLN A 501 ASN B 225 ASN B 312 ASN B 314 HIS B 382 ASN B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN B 486 ASN B 501 ASN C 312 ASN C 382 ASN C 397 ASN C 475 GLN C 501 ASN C 509 GLN D 463 ASN D 475 GLN D 501 ASN E 312 ASN E 382 ASN E 397 ASN E 463 ASN E 475 GLN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN F 382 ASN F 450 ASN F 475 GLN ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN G 382 ASN G 397 ASN G 425 GLN G 450 ASN G 475 GLN G 486 ASN G 501 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 18893 Z= 0.175 Angle : 0.640 6.460 25585 Z= 0.348 Chirality : 0.046 0.164 2919 Planarity : 0.005 0.056 3339 Dihedral : 6.908 41.634 2555 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.14), residues: 2366 helix: -3.38 (0.19), residues: 378 sheet: -1.99 (0.20), residues: 518 loop : -3.38 (0.13), residues: 1470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 506 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 506 average time/residue: 0.3142 time to fit residues: 243.6350 Evaluate side-chains 371 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 2.797 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN C 425 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN D 501 ASN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN F 397 ASN F 450 ASN ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 GLN G 450 ASN G 454 GLN G 501 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 18893 Z= 0.361 Angle : 0.749 9.485 25585 Z= 0.407 Chirality : 0.049 0.188 2919 Planarity : 0.005 0.048 3339 Dihedral : 7.120 38.386 2555 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.48 % Favored : 83.52 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.15), residues: 2366 helix: -2.83 (0.22), residues: 378 sheet: -1.87 (0.20), residues: 518 loop : -3.37 (0.14), residues: 1470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 453 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 454 average time/residue: 0.3205 time to fit residues: 218.6688 Evaluate side-chains 341 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 217 optimal weight: 0.8980 chunk 230 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN C 450 ASN C 454 GLN ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 18893 Z= 0.349 Angle : 0.731 9.150 25585 Z= 0.398 Chirality : 0.049 0.181 2919 Planarity : 0.005 0.050 3339 Dihedral : 7.041 39.055 2555 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.17 % Favored : 84.83 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.15), residues: 2366 helix: -2.52 (0.24), residues: 378 sheet: -1.81 (0.21), residues: 476 loop : -3.42 (0.14), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 452 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 452 average time/residue: 0.3231 time to fit residues: 219.8810 Evaluate side-chains 347 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.333 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 159 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 GLN ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN G 425 GLN ** G 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 18893 Z= 0.276 Angle : 0.683 7.221 25585 Z= 0.372 Chirality : 0.048 0.181 2919 Planarity : 0.005 0.052 3339 Dihedral : 6.815 39.536 2555 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.72 % Favored : 84.28 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.15), residues: 2366 helix: -2.42 (0.24), residues: 378 sheet: -1.70 (0.24), residues: 413 loop : -3.31 (0.13), residues: 1575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 468 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 468 average time/residue: 0.2935 time to fit residues: 210.7714 Evaluate side-chains 365 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.459 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 0.0270 chunk 230 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 450 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 GLN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 ASN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN F 450 ASN ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 GLN ** G 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 501 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 18893 Z= 0.311 Angle : 0.713 8.471 25585 Z= 0.386 Chirality : 0.049 0.178 2919 Planarity : 0.005 0.049 3339 Dihedral : 6.859 38.700 2555 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.15), residues: 2366 helix: -2.28 (0.24), residues: 378 sheet: -1.56 (0.25), residues: 371 loop : -3.35 (0.13), residues: 1617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 445 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 445 average time/residue: 0.2905 time to fit residues: 198.5808 Evaluate side-chains 349 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 2.058 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 131 optimal weight: 0.0060 chunk 168 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 105 optimal weight: 0.1980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 450 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN C 428 GLN C 501 ASN D 463 ASN E 463 ASN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN G 425 GLN ** G 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 18893 Z= 0.154 Angle : 0.630 7.127 25585 Z= 0.338 Chirality : 0.046 0.176 2919 Planarity : 0.005 0.051 3339 Dihedral : 6.276 39.421 2555 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.16), residues: 2366 helix: -2.29 (0.24), residues: 378 sheet: -1.33 (0.22), residues: 483 loop : -3.04 (0.14), residues: 1505 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 520 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 520 average time/residue: 0.2918 time to fit residues: 237.4119 Evaluate side-chains 392 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 391 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1808 time to fit residues: 3.4079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 450 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 GLN C 450 ASN ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 GLN G 450 ASN ** G 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 18893 Z= 0.252 Angle : 0.668 6.158 25585 Z= 0.361 Chirality : 0.047 0.167 2919 Planarity : 0.005 0.052 3339 Dihedral : 6.437 37.656 2555 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.41 % Favored : 85.59 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.15), residues: 2366 helix: -2.15 (0.24), residues: 378 sheet: -1.56 (0.24), residues: 413 loop : -3.03 (0.14), residues: 1575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 463 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 463 average time/residue: 0.3247 time to fit residues: 231.4062 Evaluate side-chains 373 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 2.295 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1680 time to fit residues: 3.5051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 450 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 GLN ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN E 425 GLN E 463 ASN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 GLN G 450 ASN ** G 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 18893 Z= 0.246 Angle : 0.672 5.873 25585 Z= 0.363 Chirality : 0.047 0.169 2919 Planarity : 0.005 0.052 3339 Dihedral : 6.504 39.828 2555 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.19 % Favored : 86.81 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.16), residues: 2366 helix: -2.09 (0.25), residues: 378 sheet: -1.39 (0.22), residues: 483 loop : -3.05 (0.14), residues: 1505 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 470 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 470 average time/residue: 0.2939 time to fit residues: 212.8568 Evaluate side-chains 376 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 374 time to evaluate : 2.258 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1718 time to fit residues: 3.7781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 1.9990 chunk 137 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 237 optimal weight: 7.9990 chunk 218 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 463 ASN B 509 GLN C 450 ASN ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 ASN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 GLN ** G 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 18893 Z= 0.156 Angle : 0.628 7.536 25585 Z= 0.334 Chirality : 0.046 0.216 2919 Planarity : 0.005 0.049 3339 Dihedral : 6.103 39.594 2555 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.16), residues: 2366 helix: -2.09 (0.24), residues: 378 sheet: -1.27 (0.22), residues: 483 loop : -2.86 (0.15), residues: 1505 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 501 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 501 average time/residue: 0.2939 time to fit residues: 227.4757 Evaluate side-chains 393 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 391 time to evaluate : 2.260 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1716 time to fit residues: 3.7667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 189 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 450 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN C 450 ASN ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN E 463 ASN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 GLN ** F 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 252 GLN G 425 GLN G 450 ASN ** G 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 509 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.147827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121500 restraints weight = 36742.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124615 restraints weight = 21328.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126629 restraints weight = 14689.964| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 18893 Z= 0.196 Angle : 0.638 7.780 25585 Z= 0.342 Chirality : 0.046 0.171 2919 Planarity : 0.005 0.046 3339 Dihedral : 6.165 38.950 2555 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.16), residues: 2366 helix: -1.97 (0.25), residues: 371 sheet: -1.23 (0.22), residues: 483 loop : -2.81 (0.15), residues: 1512 =============================================================================== Job complete usr+sys time: 4117.53 seconds wall clock time: 75 minutes 46.76 seconds (4546.76 seconds total)