Starting phenix.real_space_refine on Sun Mar 17 18:55:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/03_2024/6okr_20102.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/03_2024/6okr_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_20102/03_2024/6okr_20102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/03_2024/6okr_20102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/03_2024/6okr_20102.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/03_2024/6okr_20102.pdb" } resolution = 4.2 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= 0.002 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.61, per 1000 atoms: 0.52 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: 6.58 Conformation dependent library (CDL) restraints added in 3.3 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: 1.89 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: 4.83 Time building geometry restraints manager: 7.15 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.380 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 45.530 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.110 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.650 ------------------------------------------------------------------------------- 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 % Allowed : 12.94 % Favored : 86.48 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP G 503 HIS 0.006 0.003 HIS A 314 PHE 0.032 0.006 PHE B 580 TYR 0.020 0.002 TYR F 261 ARG 0.003 0.000 ARG B 458 *********************** 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 : 2.005 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: A 552 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8748 (tm-30) REVERT: A 565 TYR cc_start: 0.6597 (m-80) cc_final: 0.6328 (m-10) REVERT: B 403 MET cc_start: 0.8547 (mtp) cc_final: 0.8283 (mtm) REVERT: B 432 ASN cc_start: 0.8095 (p0) cc_final: 0.7703 (p0) REVERT: B 509 GLN cc_start: 0.9305 (tt0) cc_final: 0.9103 (tt0) REVERT: B 533 LYS cc_start: 0.8969 (tttm) cc_final: 0.8403 (tttp) REVERT: B 583 ASN cc_start: 0.6175 (t0) cc_final: 0.5949 (t0) REVERT: B 607 ARG cc_start: 0.8615 (ttt180) cc_final: 0.7860 (ttt180) REVERT: C 520 ASP cc_start: 0.8931 (p0) cc_final: 0.8700 (p0) REVERT: C 533 LYS cc_start: 0.8778 (tttt) cc_final: 0.8169 (ttpt) REVERT: C 552 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8695 (tm-30) REVERT: C 565 TYR cc_start: 0.7027 (m-80) cc_final: 0.6638 (m-10) REVERT: D 235 TYR cc_start: 0.8938 (p90) cc_final: 0.8389 (p90) REVERT: D 286 LYS cc_start: 0.8621 (mmmm) cc_final: 0.8322 (mtpt) REVERT: D 432 ASN cc_start: 0.8134 (p0) cc_final: 0.7243 (p0) REVERT: D 533 LYS cc_start: 0.8934 (ttpt) cc_final: 0.8430 (ttpt) REVERT: D 544 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8207 (pm20) REVERT: D 549 GLU cc_start: 0.8781 (tt0) cc_final: 0.8198 (pt0) REVERT: E 431 ASN cc_start: 0.7971 (m-40) cc_final: 0.7006 (m-40) REVERT: E 552 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8851 (tm-30) REVERT: E 607 ARG cc_start: 0.8712 (ttt180) cc_final: 0.8401 (tpt-90) REVERT: F 235 TYR cc_start: 0.9000 (p90) cc_final: 0.8387 (p90) REVERT: F 237 ILE cc_start: 0.9278 (mm) cc_final: 0.9008 (mt) REVERT: F 311 THR cc_start: 0.8013 (p) cc_final: 0.7761 (p) REVERT: F 437 ASP cc_start: 0.8848 (m-30) cc_final: 0.8612 (m-30) REVERT: F 533 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8247 (tppp) REVERT: F 552 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8809 (tm-30) REVERT: G 283 LYS cc_start: 0.8752 (mmtp) cc_final: 0.8546 (mmtt) REVERT: G 533 LYS cc_start: 0.8842 (ttpp) cc_final: 0.8494 (ttmm) REVERT: G 552 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8733 (tm-30) REVERT: G 607 ARG cc_start: 0.8649 (ttt180) cc_final: 0.8352 (tpt-90) outliers start: 12 outliers final: 5 residues processed: 481 average time/residue: 0.2926 time to fit residues: 211.5509 Evaluate side-chains 376 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 371 time to evaluate : 2.130 ------------------------------------------------------------------------------- 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: 0.0170 chunk 100 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 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: 1.0024 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18893 Z= 0.162 Angle : 0.635 6.391 25585 Z= 0.343 Chirality : 0.046 0.164 2919 Planarity : 0.005 0.056 3339 Dihedral : 6.827 41.726 2555 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 0.19 % Allowed : 4.86 % Favored : 94.95 % 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: -3.42 (0.18), residues: 378 sheet: -1.97 (0.20), residues: 518 loop : -3.38 (0.13), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 245 HIS 0.002 0.001 HIS F 314 PHE 0.022 0.003 PHE B 566 TYR 0.013 0.001 TYR D 396 ARG 0.001 0.000 ARG G 232 *********************** 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 523 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 519 time to evaluate : 2.157 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 revert: symmetry clash REVERT: A 552 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8705 (tm-30) REVERT: A 609 MET cc_start: 0.8767 (ppp) cc_final: 0.8561 (ppp) REVERT: B 283 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8422 (mmpt) REVERT: B 389 ILE cc_start: 0.9273 (tt) cc_final: 0.9034 (mt) REVERT: B 403 MET cc_start: 0.8400 (mtp) cc_final: 0.8081 (mtm) REVERT: B 533 LYS cc_start: 0.9033 (tttm) cc_final: 0.8609 (tttm) REVERT: B 583 ASN cc_start: 0.5920 (t0) cc_final: 0.5632 (t0) REVERT: C 533 LYS cc_start: 0.8797 (tttt) cc_final: 0.8149 (ttpt) REVERT: C 549 GLU cc_start: 0.8680 (tt0) cc_final: 0.8204 (pt0) REVERT: C 614 LYS cc_start: 0.9372 (tptt) cc_final: 0.9102 (mmtp) REVERT: D 311 THR cc_start: 0.7456 (p) cc_final: 0.7243 (p) REVERT: D 482 GLN cc_start: 0.7096 (pt0) cc_final: 0.6822 (pt0) REVERT: D 533 LYS cc_start: 0.8972 (tttt) cc_final: 0.8278 (ttpt) REVERT: D 549 GLU cc_start: 0.8760 (tt0) cc_final: 0.8236 (pt0) REVERT: E 389 ILE cc_start: 0.9142 (tt) cc_final: 0.8937 (mt) REVERT: E 431 ASN cc_start: 0.7318 (m-40) cc_final: 0.6957 (m-40) REVERT: E 533 LYS cc_start: 0.8807 (ttpt) cc_final: 0.7865 (ttpt) REVERT: E 552 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8836 (tm-30) REVERT: F 235 TYR cc_start: 0.9015 (p90) cc_final: 0.8599 (p90) REVERT: F 533 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8105 (tppp) REVERT: F 552 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8722 (tm-30) REVERT: G 283 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8400 (mmtt) REVERT: G 311 THR cc_start: 0.7550 (p) cc_final: 0.7306 (p) REVERT: G 533 LYS cc_start: 0.8882 (ttpp) cc_final: 0.7987 (tppp) REVERT: G 552 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8773 (tm-30) outliers start: 4 outliers final: 0 residues processed: 519 average time/residue: 0.2980 time to fit residues: 233.3043 Evaluate side-chains 390 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 1.970 ------------------------------------------------------------------------------- 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: 0.0050 chunk 67 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 214 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 overall best weight: 5.4002 ------------------------------------------------------------------------------- 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** A 501 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 ASN G 454 GLN G 501 ASN G 509 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 18893 Z= 0.447 Angle : 0.811 8.833 25585 Z= 0.440 Chirality : 0.051 0.209 2919 Planarity : 0.005 0.047 3339 Dihedral : 7.400 38.465 2555 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % Rotamer: Outliers : 0.24 % Allowed : 7.12 % Favored : 92.64 % 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: -4.39 (0.14), residues: 2366 helix: -2.82 (0.22), residues: 378 sheet: -2.01 (0.21), residues: 469 loop : -3.46 (0.13), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 503 HIS 0.005 0.002 HIS A 314 PHE 0.030 0.005 PHE E 249 TYR 0.024 0.002 TYR G 526 ARG 0.007 0.001 ARG E 529 *********************** 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 439 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 434 time to evaluate : 2.252 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: A 311 THR cc_start: 0.7723 (p) cc_final: 0.7486 (p) REVERT: A 552 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8710 (tm-30) REVERT: B 283 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8583 (mmpt) REVERT: B 311 THR cc_start: 0.7730 (p) cc_final: 0.7494 (p) REVERT: B 509 GLN cc_start: 0.9474 (tt0) cc_final: 0.9234 (tt0) REVERT: B 533 LYS cc_start: 0.8866 (tttm) cc_final: 0.8504 (tttm) REVERT: B 583 ASN cc_start: 0.5683 (t0) cc_final: 0.5344 (t0) REVERT: B 607 ARG cc_start: 0.8516 (ttt180) cc_final: 0.8262 (tpt-90) REVERT: B 609 MET cc_start: 0.8749 (ppp) cc_final: 0.8338 (ppp) REVERT: B 612 LEU cc_start: 0.9127 (tp) cc_final: 0.8924 (tt) REVERT: C 288 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7777 (mm-30) REVERT: C 311 THR cc_start: 0.7906 (p) cc_final: 0.7690 (p) REVERT: C 499 GLU cc_start: 0.7462 (pp20) cc_final: 0.7082 (pp20) REVERT: C 533 LYS cc_start: 0.8759 (tttt) cc_final: 0.8032 (ttpt) REVERT: C 549 GLU cc_start: 0.8800 (tt0) cc_final: 0.8479 (pt0) REVERT: C 609 MET cc_start: 0.8675 (ppp) cc_final: 0.8318 (ppp) REVERT: C 614 LYS cc_start: 0.9418 (tptt) cc_final: 0.9165 (mmtp) REVERT: D 311 THR cc_start: 0.7891 (p) cc_final: 0.7636 (p) REVERT: D 432 ASN cc_start: 0.7864 (p0) cc_final: 0.7143 (p0) REVERT: D 533 LYS cc_start: 0.9005 (tttt) cc_final: 0.8751 (ttpp) REVERT: D 575 CYS cc_start: 0.8032 (t) cc_final: 0.7775 (t) REVERT: D 607 ARG cc_start: 0.8504 (ttt180) cc_final: 0.8287 (ttt180) REVERT: D 609 MET cc_start: 0.8742 (ppp) cc_final: 0.8360 (ppp) REVERT: E 609 MET cc_start: 0.8736 (ppp) cc_final: 0.8476 (ppp) REVERT: F 311 THR cc_start: 0.7901 (p) cc_final: 0.7593 (p) REVERT: F 533 LYS cc_start: 0.8649 (ttpp) cc_final: 0.7925 (tppp) REVERT: F 552 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8910 (tm-30) REVERT: F 609 MET cc_start: 0.8826 (ppp) cc_final: 0.8430 (ppp) REVERT: G 283 LYS cc_start: 0.8835 (mmtp) cc_final: 0.8628 (mmtt) REVERT: G 499 GLU cc_start: 0.7606 (pp20) cc_final: 0.7149 (pp20) REVERT: G 533 LYS cc_start: 0.8759 (ttpp) cc_final: 0.7920 (tppp) outliers start: 5 outliers final: 0 residues processed: 436 average time/residue: 0.3045 time to fit residues: 198.9380 Evaluate side-chains 335 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 2.355 ------------------------------------------------------------------------------- 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: 7.9990 chunk 162 optimal weight: 0.0670 chunk 112 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 chunk 230 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- 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 450 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 ASN G 509 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18893 Z= 0.248 Angle : 0.672 8.206 25585 Z= 0.365 Chirality : 0.047 0.184 2919 Planarity : 0.005 0.050 3339 Dihedral : 6.815 39.591 2555 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.48 % Favored : 86.52 % Rotamer: Outliers : 0.24 % Allowed : 3.22 % Favored : 96.54 % 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: -4.15 (0.15), residues: 2366 helix: -2.61 (0.23), residues: 378 sheet: -1.77 (0.21), residues: 476 loop : -3.33 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 503 HIS 0.003 0.001 HIS D 314 PHE 0.022 0.003 PHE F 566 TYR 0.018 0.001 TYR G 526 ARG 0.004 0.001 ARG G 529 *********************** 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 488 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 483 time to evaluate : 2.133 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: A 311 THR cc_start: 0.7712 (p) cc_final: 0.7467 (p) REVERT: A 499 GLU cc_start: 0.7401 (pp20) cc_final: 0.7037 (pp20) REVERT: A 533 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8126 (tppp) REVERT: A 552 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8901 (tm-30) REVERT: A 609 MET cc_start: 0.8854 (ppp) cc_final: 0.8517 (ppp) REVERT: B 283 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8453 (mmpt) REVERT: B 509 GLN cc_start: 0.9403 (tt0) cc_final: 0.9189 (tt0) REVERT: B 533 LYS cc_start: 0.8971 (tttm) cc_final: 0.8592 (tttm) REVERT: B 609 MET cc_start: 0.8616 (ppp) cc_final: 0.8358 (ppp) REVERT: B 612 LEU cc_start: 0.9177 (tp) cc_final: 0.8940 (tt) REVERT: C 499 GLU cc_start: 0.7395 (pp20) cc_final: 0.7093 (pp20) REVERT: C 533 LYS cc_start: 0.8801 (tttt) cc_final: 0.8079 (ttpt) REVERT: C 549 GLU cc_start: 0.8757 (tt0) cc_final: 0.8430 (pt0) REVERT: C 609 MET cc_start: 0.8575 (ppp) cc_final: 0.8363 (ppp) REVERT: D 311 THR cc_start: 0.7747 (p) cc_final: 0.7528 (p) REVERT: D 437 ASP cc_start: 0.8599 (m-30) cc_final: 0.8332 (m-30) REVERT: D 533 LYS cc_start: 0.9000 (tttt) cc_final: 0.8050 (ttpt) REVERT: D 575 CYS cc_start: 0.8012 (t) cc_final: 0.7807 (t) REVERT: D 609 MET cc_start: 0.8624 (ppp) cc_final: 0.8366 (ppp) REVERT: E 389 ILE cc_start: 0.9261 (tt) cc_final: 0.9026 (tt) REVERT: E 533 LYS cc_start: 0.8824 (ttpt) cc_final: 0.7843 (ttpt) REVERT: F 311 THR cc_start: 0.7881 (p) cc_final: 0.7646 (p) REVERT: F 533 LYS cc_start: 0.8726 (ttpp) cc_final: 0.7919 (tppp) REVERT: F 552 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8858 (tm-30) REVERT: F 609 MET cc_start: 0.8703 (ppp) cc_final: 0.8483 (ppp) REVERT: G 283 LYS cc_start: 0.8790 (mmtp) cc_final: 0.8549 (mmtt) REVERT: G 499 GLU cc_start: 0.7476 (pp20) cc_final: 0.7085 (pp20) REVERT: G 533 LYS cc_start: 0.8806 (ttpp) cc_final: 0.8277 (ttpp) outliers start: 5 outliers final: 2 residues processed: 483 average time/residue: 0.2927 time to fit residues: 214.0494 Evaluate side-chains 369 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 367 time to evaluate : 1.991 ------------------------------------------------------------------------------- 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: 6.9990 chunk 130 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** B 382 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 425 GLN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 18893 Z= 0.462 Angle : 0.816 9.145 25585 Z= 0.444 Chirality : 0.052 0.217 2919 Planarity : 0.005 0.050 3339 Dihedral : 7.378 38.219 2555 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.68 % Favored : 81.32 % Rotamer: Outliers : 0.05 % Allowed : 5.82 % Favored : 94.13 % 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: -4.28 (0.15), residues: 2366 helix: -2.43 (0.24), residues: 378 sheet: -1.82 (0.22), residues: 469 loop : -3.52 (0.13), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 503 HIS 0.005 0.002 HIS A 314 PHE 0.028 0.006 PHE C 580 TYR 0.028 0.002 TYR C 526 ARG 0.006 0.001 ARG E 529 *********************** 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 440 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 439 time to evaluate : 2.145 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: A 524 GLU cc_start: 0.8473 (tt0) cc_final: 0.7989 (tt0) REVERT: A 552 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8930 (tm-30) REVERT: A 565 TYR cc_start: 0.6174 (m-80) cc_final: 0.5830 (m-80) REVERT: B 311 THR cc_start: 0.7799 (p) cc_final: 0.7576 (p) REVERT: B 533 LYS cc_start: 0.8848 (tttm) cc_final: 0.8458 (tttm) REVERT: C 246 GLU cc_start: 0.7038 (pm20) cc_final: 0.6523 (pm20) REVERT: C 288 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7816 (mm-30) REVERT: C 311 THR cc_start: 0.7723 (p) cc_final: 0.7506 (p) REVERT: C 533 LYS cc_start: 0.8770 (tttt) cc_final: 0.8015 (ttpt) REVERT: C 549 GLU cc_start: 0.8807 (tt0) cc_final: 0.8355 (pt0) REVERT: D 246 GLU cc_start: 0.7066 (pm20) cc_final: 0.6718 (pm20) REVERT: D 426 GLU cc_start: 0.7755 (pt0) cc_final: 0.7530 (pt0) REVERT: D 432 ASN cc_start: 0.7875 (p0) cc_final: 0.7165 (p0) REVERT: D 533 LYS cc_start: 0.8983 (tttt) cc_final: 0.7999 (ttpt) REVERT: D 575 CYS cc_start: 0.8106 (t) cc_final: 0.7856 (t) REVERT: E 311 THR cc_start: 0.7583 (p) cc_final: 0.7371 (p) REVERT: E 529 ARG cc_start: 0.7464 (mpt-90) cc_final: 0.7137 (mtt90) REVERT: F 311 THR cc_start: 0.8115 (p) cc_final: 0.7811 (p) REVERT: F 533 LYS cc_start: 0.8666 (ttpp) cc_final: 0.7844 (tppp) REVERT: F 552 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8891 (tm-30) REVERT: G 283 LYS cc_start: 0.8851 (mmtp) cc_final: 0.8646 (mmtt) REVERT: G 437 ASP cc_start: 0.8681 (m-30) cc_final: 0.8433 (m-30) REVERT: G 533 LYS cc_start: 0.8757 (ttpp) cc_final: 0.7820 (tppp) outliers start: 1 outliers final: 0 residues processed: 439 average time/residue: 0.3004 time to fit residues: 198.5929 Evaluate side-chains 354 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 2.163 ------------------------------------------------------------------------------- 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: 0.9980 chunk 207 optimal weight: 0.3980 chunk 45 optimal weight: 7.9990 chunk 135 optimal weight: 0.5980 chunk 56 optimal weight: 0.0170 chunk 230 optimal weight: 0.4980 chunk 191 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 A 501 ASN B 382 ASN B 450 ASN B 463 ASN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 509 GLN C 382 ASN C 428 GLN D 425 GLN D 450 ASN D 463 ASN D 501 ASN E 432 ASN E 463 ASN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 ASN G 463 ASN G 501 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18893 Z= 0.159 Angle : 0.649 7.927 25585 Z= 0.345 Chirality : 0.046 0.179 2919 Planarity : 0.005 0.059 3339 Dihedral : 6.363 40.007 2555 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.34 % Allowed : 2.36 % Favored : 97.31 % 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: -3.81 (0.15), residues: 2366 helix: -2.43 (0.23), residues: 378 sheet: -1.45 (0.22), residues: 476 loop : -3.11 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 245 HIS 0.002 0.001 HIS F 314 PHE 0.023 0.002 PHE A 455 TYR 0.017 0.001 TYR C 235 ARG 0.007 0.001 ARG B 529 *********************** 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 551 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 544 time to evaluate : 2.453 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: A 499 GLU cc_start: 0.7201 (pp20) cc_final: 0.6962 (pp20) REVERT: A 533 LYS cc_start: 0.8676 (ttpp) cc_final: 0.8170 (tppp) REVERT: A 552 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8848 (tm-30) REVERT: A 565 TYR cc_start: 0.6312 (m-80) cc_final: 0.6069 (m-10) REVERT: A 609 MET cc_start: 0.8676 (ppp) cc_final: 0.8426 (ppp) REVERT: B 499 GLU cc_start: 0.7415 (pp20) cc_final: 0.7000 (pp20) REVERT: B 509 GLN cc_start: 0.9409 (OUTLIER) cc_final: 0.9170 (tt0) REVERT: B 524 GLU cc_start: 0.8120 (tt0) cc_final: 0.7768 (tt0) REVERT: B 609 MET cc_start: 0.8631 (ppp) cc_final: 0.8358 (ppp) REVERT: C 235 TYR cc_start: 0.8960 (p90) cc_final: 0.8564 (p90) REVERT: C 246 GLU cc_start: 0.6863 (pm20) cc_final: 0.6594 (pm20) REVERT: C 549 GLU cc_start: 0.8671 (tt0) cc_final: 0.8401 (pt0) REVERT: C 607 ARG cc_start: 0.8559 (ttt180) cc_final: 0.8059 (tpt-90) REVERT: D 389 ILE cc_start: 0.9214 (tt) cc_final: 0.8857 (mt) REVERT: D 426 GLU cc_start: 0.7936 (pt0) cc_final: 0.7627 (pt0) REVERT: D 437 ASP cc_start: 0.8669 (m-30) cc_final: 0.8455 (m-30) REVERT: D 499 GLU cc_start: 0.7154 (pp20) cc_final: 0.6786 (pp20) REVERT: D 533 LYS cc_start: 0.9016 (tttt) cc_final: 0.8090 (ttpt) REVERT: D 549 GLU cc_start: 0.8775 (tt0) cc_final: 0.8310 (pt0) REVERT: D 609 MET cc_start: 0.8778 (ppp) cc_final: 0.8362 (ppp) REVERT: D 614 LYS cc_start: 0.9266 (mmtm) cc_final: 0.8993 (mmtp) REVERT: E 389 ILE cc_start: 0.9059 (tt) cc_final: 0.8839 (mt) REVERT: E 499 GLU cc_start: 0.7121 (pp20) cc_final: 0.6724 (pp20) REVERT: E 529 ARG cc_start: 0.7253 (mpt-90) cc_final: 0.6933 (mtt90) REVERT: E 533 LYS cc_start: 0.8857 (ttpt) cc_final: 0.7858 (ttpp) REVERT: E 614 LYS cc_start: 0.9238 (mmtp) cc_final: 0.9012 (mmtp) REVERT: F 533 LYS cc_start: 0.8599 (ttpp) cc_final: 0.7858 (tppp) REVERT: F 552 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8870 (tm-30) REVERT: F 555 PHE cc_start: 0.7955 (m-10) cc_final: 0.7431 (m-10) REVERT: F 609 MET cc_start: 0.8706 (ppp) cc_final: 0.8456 (ppp) REVERT: G 283 LYS cc_start: 0.8680 (mmtp) cc_final: 0.8471 (mmtt) REVERT: G 311 THR cc_start: 0.7601 (p) cc_final: 0.7383 (p) REVERT: G 437 ASP cc_start: 0.8614 (m-30) cc_final: 0.8407 (m-30) REVERT: G 529 ARG cc_start: 0.7218 (mpt-90) cc_final: 0.6986 (mmt90) REVERT: G 533 LYS cc_start: 0.8826 (ttpp) cc_final: 0.8074 (tppp) REVERT: G 609 MET cc_start: 0.8758 (ppp) cc_final: 0.8446 (ppp) outliers start: 7 outliers final: 2 residues processed: 544 average time/residue: 0.2913 time to fit residues: 243.4135 Evaluate side-chains 404 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 401 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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: 8.9990 chunk 25 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 168 optimal weight: 0.0870 chunk 130 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 229 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 139 optimal weight: 0.2980 chunk 105 optimal weight: 4.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 463 ASN C 501 ASN C 509 GLN D 450 ASN D 463 ASN E 450 ASN E 463 ASN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 ASN ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 GLN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 ASN ** G 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18893 Z= 0.155 Angle : 0.615 8.176 25585 Z= 0.329 Chirality : 0.045 0.171 2919 Planarity : 0.004 0.067 3339 Dihedral : 6.105 38.910 2555 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 0.34 % Allowed : 2.16 % Favored : 97.50 % 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: -3.60 (0.16), residues: 2366 helix: -2.28 (0.24), residues: 378 sheet: -1.28 (0.22), residues: 483 loop : -2.98 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 245 HIS 0.001 0.001 HIS B 314 PHE 0.024 0.003 PHE A 455 TYR 0.016 0.001 TYR A 274 ARG 0.005 0.000 ARG B 607 *********************** 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 524 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 517 time to evaluate : 1.918 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: A 311 THR cc_start: 0.7497 (p) cc_final: 0.7259 (p) REVERT: A 499 GLU cc_start: 0.7221 (pp20) cc_final: 0.6993 (pp20) REVERT: A 533 LYS cc_start: 0.8636 (ttpp) cc_final: 0.8109 (tppp) REVERT: A 552 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8893 (tm-30) REVERT: A 555 PHE cc_start: 0.7522 (m-10) cc_final: 0.6741 (m-10) REVERT: A 565 TYR cc_start: 0.6519 (m-80) cc_final: 0.6119 (m-10) REVERT: B 499 GLU cc_start: 0.7430 (pp20) cc_final: 0.7027 (pp20) REVERT: B 524 GLU cc_start: 0.8114 (tt0) cc_final: 0.7787 (tt0) REVERT: B 533 LYS cc_start: 0.8854 (tttt) cc_final: 0.8114 (tttp) REVERT: C 235 TYR cc_start: 0.8948 (p90) cc_final: 0.8572 (p90) REVERT: C 246 GLU cc_start: 0.6781 (pm20) cc_final: 0.6555 (pm20) REVERT: C 533 LYS cc_start: 0.8805 (tttt) cc_final: 0.8283 (ttpt) REVERT: C 607 ARG cc_start: 0.8513 (ttt180) cc_final: 0.8046 (tpt-90) REVERT: D 389 ILE cc_start: 0.9345 (tt) cc_final: 0.8949 (mt) REVERT: D 426 GLU cc_start: 0.7731 (pt0) cc_final: 0.7447 (pt0) REVERT: D 437 ASP cc_start: 0.8626 (m-30) cc_final: 0.8378 (m-30) REVERT: D 499 GLU cc_start: 0.7140 (pp20) cc_final: 0.6793 (pp20) REVERT: D 533 LYS cc_start: 0.9003 (tttt) cc_final: 0.8693 (ttpt) REVERT: D 549 GLU cc_start: 0.8788 (tt0) cc_final: 0.8418 (pt0) REVERT: D 609 MET cc_start: 0.8561 (ppp) cc_final: 0.8245 (ppp) REVERT: E 389 ILE cc_start: 0.9265 (tt) cc_final: 0.9034 (mt) REVERT: E 499 GLU cc_start: 0.7246 (pp20) cc_final: 0.6867 (pp20) REVERT: E 533 LYS cc_start: 0.8815 (ttpt) cc_final: 0.7977 (ttpt) REVERT: F 269 ASP cc_start: 0.9131 (p0) cc_final: 0.8739 (p0) REVERT: F 533 LYS cc_start: 0.8504 (ttpp) cc_final: 0.7766 (tppp) REVERT: G 269 ASP cc_start: 0.9126 (p0) cc_final: 0.8902 (p0) REVERT: G 529 ARG cc_start: 0.7231 (mpt-90) cc_final: 0.6929 (mpt-90) REVERT: G 533 LYS cc_start: 0.8830 (ttpp) cc_final: 0.7928 (tppp) REVERT: G 609 MET cc_start: 0.8794 (ppp) cc_final: 0.8549 (ppp) outliers start: 7 outliers final: 4 residues processed: 518 average time/residue: 0.2776 time to fit residues: 220.7349 Evaluate side-chains 411 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 407 time to evaluate : 2.091 ------------------------------------------------------------------------------- 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: 2.9990 chunk 91 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 GLN C 450 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 GLN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18893 Z= 0.309 Angle : 0.715 8.837 25585 Z= 0.383 Chirality : 0.048 0.165 2919 Planarity : 0.005 0.062 3339 Dihedral : 6.568 38.170 2555 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.84 % Favored : 85.16 % Rotamer: Outliers : 0.10 % Allowed : 0.91 % Favored : 98.99 % 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: -3.80 (0.15), residues: 2366 helix: -2.18 (0.24), residues: 378 sheet: -1.59 (0.24), residues: 413 loop : -3.09 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 503 HIS 0.003 0.001 HIS D 314 PHE 0.023 0.004 PHE A 455 TYR 0.015 0.002 TYR C 235 ARG 0.007 0.001 ARG B 290 *********************** 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 472 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 470 time to evaluate : 2.081 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: A 311 THR cc_start: 0.7696 (p) cc_final: 0.7451 (p) REVERT: A 499 GLU cc_start: 0.7316 (pp20) cc_final: 0.7043 (pp20) REVERT: A 533 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8136 (tppp) REVERT: A 552 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8898 (tm-30) REVERT: A 565 TYR cc_start: 0.6481 (m-80) cc_final: 0.6209 (m-10) REVERT: A 609 MET cc_start: 0.8752 (ppp) cc_final: 0.8547 (ppp) REVERT: B 499 GLU cc_start: 0.7550 (pp20) cc_final: 0.7136 (pp20) REVERT: B 524 GLU cc_start: 0.8387 (tt0) cc_final: 0.7909 (tt0) REVERT: B 583 ASN cc_start: 0.6042 (t0) cc_final: 0.5832 (t0) REVERT: B 609 MET cc_start: 0.8635 (ppp) cc_final: 0.8416 (ppp) REVERT: C 246 GLU cc_start: 0.6872 (pm20) cc_final: 0.6656 (pm20) REVERT: C 533 LYS cc_start: 0.8838 (tttt) cc_final: 0.8096 (ttpt) REVERT: C 609 MET cc_start: 0.8535 (ppp) cc_final: 0.8296 (ppp) REVERT: D 311 THR cc_start: 0.7771 (p) cc_final: 0.7483 (p) REVERT: D 426 GLU cc_start: 0.7709 (pt0) cc_final: 0.7449 (pt0) REVERT: D 437 ASP cc_start: 0.8615 (m-30) cc_final: 0.8410 (m-30) REVERT: D 533 LYS cc_start: 0.9002 (tttt) cc_final: 0.8216 (ttpt) REVERT: D 544 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8264 (pm20) REVERT: D 549 GLU cc_start: 0.8763 (tt0) cc_final: 0.8301 (pt0) REVERT: D 609 MET cc_start: 0.8543 (ppp) cc_final: 0.8242 (ppp) REVERT: D 610 ASN cc_start: 0.8286 (p0) cc_final: 0.7938 (p0) REVERT: E 246 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6588 (mt-10) REVERT: E 255 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8485 (mmtp) REVERT: E 533 LYS cc_start: 0.8833 (ttpt) cc_final: 0.7932 (ttpt) REVERT: E 552 GLU cc_start: 0.9028 (pp20) cc_final: 0.8662 (pp20) REVERT: F 533 LYS cc_start: 0.8567 (ttpp) cc_final: 0.7769 (tppp) REVERT: G 311 THR cc_start: 0.7851 (p) cc_final: 0.7625 (p) REVERT: G 533 LYS cc_start: 0.8849 (ttpp) cc_final: 0.8088 (tppp) REVERT: G 609 MET cc_start: 0.8856 (ppp) cc_final: 0.8507 (ppp) outliers start: 2 outliers final: 0 residues processed: 470 average time/residue: 0.2856 time to fit residues: 204.8980 Evaluate side-chains 362 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 2.246 ------------------------------------------------------------------------------- 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: 4.9990 chunk 219 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 128 optimal weight: 0.0070 chunk 93 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 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 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN D 450 ASN D 454 GLN E 450 ASN E 463 ASN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN ** F 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8189 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 : 0.004 0.040 18893 Z= 0.243 Angle : 0.682 8.565 25585 Z= 0.365 Chirality : 0.047 0.166 2919 Planarity : 0.005 0.056 3339 Dihedral : 6.488 39.249 2555 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 0.29 % Allowed : 0.43 % Favored : 99.28 % 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: -3.63 (0.16), residues: 2366 helix: -2.01 (0.25), residues: 364 sheet: -1.23 (0.23), residues: 441 loop : -3.08 (0.14), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 503 HIS 0.003 0.001 HIS D 314 PHE 0.027 0.004 PHE A 566 TYR 0.014 0.001 TYR C 235 ARG 0.005 0.001 ARG E 529 *********************** 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 483 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 477 time to evaluate : 2.172 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: A 311 THR cc_start: 0.7650 (p) cc_final: 0.7377 (p) REVERT: A 417 ASP cc_start: 0.9041 (m-30) cc_final: 0.8241 (p0) REVERT: A 499 GLU cc_start: 0.7246 (pp20) cc_final: 0.6987 (pp20) REVERT: A 533 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8084 (tppp) REVERT: A 552 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8887 (tm-30) REVERT: A 565 TYR cc_start: 0.6493 (m-80) cc_final: 0.6078 (m-10) REVERT: B 285 ILE cc_start: 0.8941 (mt) cc_final: 0.8728 (mt) REVERT: B 403 MET cc_start: 0.8179 (mtp) cc_final: 0.7962 (ttm) REVERT: B 499 GLU cc_start: 0.7484 (pp20) cc_final: 0.7079 (pp20) REVERT: C 246 GLU cc_start: 0.6879 (pm20) cc_final: 0.6654 (pm20) REVERT: C 533 LYS cc_start: 0.8802 (tttt) cc_final: 0.8076 (ttpt) REVERT: C 609 MET cc_start: 0.8585 (ppp) cc_final: 0.8385 (ppp) REVERT: D 311 THR cc_start: 0.7722 (p) cc_final: 0.7458 (p) REVERT: D 426 GLU cc_start: 0.7800 (pt0) cc_final: 0.7468 (pt0) REVERT: D 437 ASP cc_start: 0.8637 (m-30) cc_final: 0.8432 (m-30) REVERT: D 533 LYS cc_start: 0.8992 (tttt) cc_final: 0.8219 (ttpt) REVERT: D 544 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8265 (pm20) REVERT: D 549 GLU cc_start: 0.8678 (tt0) cc_final: 0.8313 (pt0) REVERT: D 609 MET cc_start: 0.8590 (ppp) cc_final: 0.8277 (ppp) REVERT: D 610 ASN cc_start: 0.8215 (p0) cc_final: 0.7892 (p0) REVERT: F 533 LYS cc_start: 0.8596 (ttpp) cc_final: 0.7956 (ptpt) REVERT: G 311 THR cc_start: 0.7802 (p) cc_final: 0.7594 (p) REVERT: G 437 ASP cc_start: 0.8620 (m-30) cc_final: 0.8350 (m-30) REVERT: G 533 LYS cc_start: 0.8859 (ttpp) cc_final: 0.8111 (tppp) REVERT: G 609 MET cc_start: 0.8820 (ppp) cc_final: 0.8514 (ppp) outliers start: 6 outliers final: 0 residues processed: 478 average time/residue: 0.2851 time to fit residues: 209.1159 Evaluate side-chains 382 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 2.204 ------------------------------------------------------------------------------- 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: 0.8980 chunk 137 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 chunk 218 optimal weight: 0.0980 chunk 188 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 GLN C 450 ASN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN D 450 ASN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 ASN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN ** F 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 ASN ** 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: 0.8138 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18893 Z= 0.177 Angle : 0.639 7.836 25585 Z= 0.340 Chirality : 0.046 0.167 2919 Planarity : 0.004 0.054 3339 Dihedral : 6.186 39.350 2555 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 0.34 % Allowed : 0.29 % Favored : 99.37 % 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: -3.47 (0.16), residues: 2366 helix: -2.02 (0.25), residues: 371 sheet: -1.30 (0.22), residues: 483 loop : -2.89 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 245 HIS 0.002 0.001 HIS D 314 PHE 0.028 0.003 PHE C 566 TYR 0.015 0.001 TYR A 274 ARG 0.004 0.000 ARG E 529 ********************** 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 504 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 497 time to evaluate : 2.101 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: A 235 TYR cc_start: 0.9150 (p90) cc_final: 0.8739 (p90) REVERT: A 311 THR cc_start: 0.7453 (p) cc_final: 0.7183 (p) REVERT: A 529 ARG cc_start: 0.7457 (mpt-90) cc_final: 0.7202 (mmt90) REVERT: A 533 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8101 (tppp) REVERT: A 552 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8893 (tm-30) REVERT: A 565 TYR cc_start: 0.6530 (m-80) cc_final: 0.6164 (m-10) REVERT: B 499 GLU cc_start: 0.7469 (pp20) cc_final: 0.7093 (pp20) REVERT: C 290 ARG cc_start: 0.8630 (mtp85) cc_final: 0.8253 (mtp85) REVERT: C 533 LYS cc_start: 0.8785 (tttt) cc_final: 0.8112 (ttpt) REVERT: C 607 ARG cc_start: 0.8509 (tpt-90) cc_final: 0.7808 (tpt-90) REVERT: D 246 GLU cc_start: 0.6350 (pm20) cc_final: 0.5893 (pm20) REVERT: D 288 GLU cc_start: 0.7858 (tp30) cc_final: 0.7592 (tp30) REVERT: D 311 THR cc_start: 0.7766 (p) cc_final: 0.7552 (p) REVERT: D 403 MET cc_start: 0.7784 (mtp) cc_final: 0.7434 (ttm) REVERT: D 426 GLU cc_start: 0.7914 (pt0) cc_final: 0.7543 (pt0) REVERT: D 437 ASP cc_start: 0.8632 (m-30) cc_final: 0.8416 (m-30) REVERT: D 533 LYS cc_start: 0.8985 (tttt) cc_final: 0.8221 (ttpt) REVERT: D 544 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8245 (pm20) REVERT: D 549 GLU cc_start: 0.8665 (tt0) cc_final: 0.8377 (pt0) REVERT: D 609 MET cc_start: 0.8609 (ppp) cc_final: 0.8328 (ppp) REVERT: D 610 ASN cc_start: 0.8240 (p0) cc_final: 0.7936 (p0) REVERT: E 417 ASP cc_start: 0.8984 (m-30) cc_final: 0.8366 (p0) REVERT: E 426 GLU cc_start: 0.7843 (pt0) cc_final: 0.7533 (pt0) REVERT: E 533 LYS cc_start: 0.8805 (ttpt) cc_final: 0.7839 (ttpp) REVERT: F 426 GLU cc_start: 0.7578 (pt0) cc_final: 0.7234 (pt0) REVERT: F 533 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8002 (ptpt) REVERT: G 437 ASP cc_start: 0.8566 (m-30) cc_final: 0.8338 (m-30) REVERT: G 533 LYS cc_start: 0.8847 (ttpp) cc_final: 0.8038 (tppp) REVERT: G 609 MET cc_start: 0.8874 (ppp) cc_final: 0.8659 (ppp) outliers start: 7 outliers final: 2 residues processed: 497 average time/residue: 0.2802 time to fit residues: 213.8763 Evaluate side-chains 398 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 396 time to evaluate : 2.270 ------------------------------------------------------------------------------- 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: 5.9990 chunk 57 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 189 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 450 ASN B 463 ASN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 GLN C 450 ASN C 454 GLN ** C 463 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** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN ** F 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121328 restraints weight = 36681.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124341 restraints weight = 21168.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126430 restraints weight = 14585.453| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3070 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= 0.197 Angle : 0.644 8.290 25585 Z= 0.344 Chirality : 0.046 0.162 2919 Planarity : 0.004 0.051 3339 Dihedral : 6.158 38.447 2555 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.19 % Favored : 86.81 % Rotamer: Outliers : 0.34 % Allowed : 0.91 % Favored : 98.75 % 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: -3.42 (0.16), residues: 2366 helix: -1.98 (0.25), residues: 371 sheet: -1.27 (0.22), residues: 483 loop : -2.86 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 503 HIS 0.002 0.001 HIS D 314 PHE 0.027 0.003 PHE A 566 TYR 0.014 0.001 TYR A 274 ARG 0.004 0.000 ARG G 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4239.73 seconds wall clock time: 77 minutes 23.24 seconds (4643.24 seconds total)