Starting phenix.real_space_refine (version: dev) on Fri Mar 17 17:14:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/03_2023/5li4_4052.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/03_2023/5li4_4052.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/5li4_4052/03_2023/5li4_4052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/03_2023/5li4_4052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/03_2023/5li4_4052.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/03_2023/5li4_4052.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.774 sd= 3.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ASP 70": "OD1" <-> "OD2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 401": "OD1" <-> "OD2" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 445": "OE1" <-> "OE2" Residue "D PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 360": "OE1" <-> "OE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "E PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 401": "OD1" <-> "OD2" Residue "E TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 445": "OE1" <-> "OE2" Residue "E PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 322": "OD1" <-> "OD2" Residue "F PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 360": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 401": "OD1" <-> "OD2" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 445": "OE1" <-> "OE2" Residue "F PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 20070 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3345 Classifications: {'peptide': 427} Link IDs: {'CIS': 7, 'PTRANS': 10, 'TRANS': 409} Chain breaks: 9 Chain: "B" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3345 Classifications: {'peptide': 427} Link IDs: {'CIS': 7, 'PTRANS': 10, 'TRANS': 409} Chain breaks: 9 Chain: "C" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3345 Classifications: {'peptide': 427} Link IDs: {'CIS': 7, 'PTRANS': 10, 'TRANS': 409} Chain breaks: 9 Chain: "D" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3345 Classifications: {'peptide': 427} Link IDs: {'CIS': 7, 'PTRANS': 10, 'TRANS': 409} Chain breaks: 9 Chain: "E" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3345 Classifications: {'peptide': 427} Link IDs: {'CIS': 7, 'PTRANS': 10, 'TRANS': 409} Chain breaks: 9 Chain: "F" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3345 Classifications: {'peptide': 427} Link IDs: {'CIS': 7, 'PTRANS': 10, 'TRANS': 409} Chain breaks: 9 Time building chain proxies: 11.35, per 1000 atoms: 0.57 Number of scatterers: 20070 At special positions: 0 Unit cell: (287.24, 276.92, 79.12, 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 42 16.00 O 3966 8.00 N 3402 7.00 C 12660 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: 9.37 Conformation dependent library (CDL) restraints added in 2.9 seconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB SER A 340 " pdb=" CB SER B 340 " pdb=" CB SER C 340 " pdb=" CB SER D 340 " pdb=" CB SER E 340 " pdb=" CB SER F 340 " Number of C-beta restraints generated: 4716 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 42 sheets defined 31.1% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.596A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 320 through 327 removed outlier: 4.217A pdb=" N LEU A 324 " --> pdb=" O TRP A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 removed outlier: 4.033A pdb=" N SER A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 382 removed outlier: 3.786A pdb=" N GLU A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA A 382 " --> pdb=" O PHE A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 Processing helix chain 'A' and resid 446 through 452 Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 508 through 515 removed outlier: 3.740A pdb=" N ILE A 513 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 514 " --> pdb=" O GLU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 removed outlier: 3.739A pdb=" N ILE A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.595A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 82 Proline residue: B 80 - end of helix Processing helix chain 'B' and resid 150 through 169 Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 320 through 327 removed outlier: 4.217A pdb=" N LEU B 324 " --> pdb=" O TRP B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 removed outlier: 4.032A pdb=" N SER B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 382 removed outlier: 3.786A pdb=" N GLU B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 382 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 420 Processing helix chain 'B' and resid 446 through 452 Processing helix chain 'B' and resid 493 through 507 Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.740A pdb=" N ILE B 513 " --> pdb=" O LEU B 508 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 514 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 540 removed outlier: 3.739A pdb=" N ILE B 524 " --> pdb=" O THR B 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP B 527 " --> pdb=" O SER B 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.596A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 Proline residue: C 80 - end of helix Processing helix chain 'C' and resid 150 through 169 Processing helix chain 'C' and resid 278 through 285 Processing helix chain 'C' and resid 320 through 327 removed outlier: 4.217A pdb=" N LEU C 324 " --> pdb=" O TRP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 353 removed outlier: 4.032A pdb=" N SER C 350 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 382 removed outlier: 3.786A pdb=" N GLU C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 382 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 420 Processing helix chain 'C' and resid 446 through 452 Processing helix chain 'C' and resid 493 through 507 Processing helix chain 'C' and resid 508 through 515 removed outlier: 3.740A pdb=" N ILE C 513 " --> pdb=" O LEU C 508 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY C 514 " --> pdb=" O GLU C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 540 removed outlier: 3.739A pdb=" N ILE C 524 " --> pdb=" O THR C 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP C 527 " --> pdb=" O SER C 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 63 removed outlier: 3.596A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 Proline residue: D 80 - end of helix Processing helix chain 'D' and resid 150 through 169 Processing helix chain 'D' and resid 278 through 285 Processing helix chain 'D' and resid 320 through 327 removed outlier: 4.218A pdb=" N LEU D 324 " --> pdb=" O TRP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 353 removed outlier: 4.033A pdb=" N SER D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE D 351 " --> pdb=" O GLU D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 382 removed outlier: 3.786A pdb=" N GLU D 375 " --> pdb=" O ASN D 371 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA D 382 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 420 Processing helix chain 'D' and resid 446 through 452 Processing helix chain 'D' and resid 493 through 507 Processing helix chain 'D' and resid 508 through 515 removed outlier: 3.740A pdb=" N ILE D 513 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY D 514 " --> pdb=" O GLU D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 540 removed outlier: 3.739A pdb=" N ILE D 524 " --> pdb=" O THR D 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP D 527 " --> pdb=" O SER D 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 63 removed outlier: 3.595A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 Proline residue: E 80 - end of helix Processing helix chain 'E' and resid 150 through 169 Processing helix chain 'E' and resid 278 through 285 Processing helix chain 'E' and resid 320 through 327 removed outlier: 4.218A pdb=" N LEU E 324 " --> pdb=" O TRP E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 353 removed outlier: 4.032A pdb=" N SER E 350 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE E 351 " --> pdb=" O GLU E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 382 removed outlier: 3.786A pdb=" N GLU E 375 " --> pdb=" O ASN E 371 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA E 382 " --> pdb=" O PHE E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 420 Processing helix chain 'E' and resid 446 through 452 Processing helix chain 'E' and resid 493 through 507 Processing helix chain 'E' and resid 508 through 515 removed outlier: 3.740A pdb=" N ILE E 513 " --> pdb=" O LEU E 508 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY E 514 " --> pdb=" O GLU E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 540 removed outlier: 3.739A pdb=" N ILE E 524 " --> pdb=" O THR E 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP E 527 " --> pdb=" O SER E 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 63 removed outlier: 3.596A pdb=" N LEU F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 82 Proline residue: F 80 - end of helix Processing helix chain 'F' and resid 150 through 169 Processing helix chain 'F' and resid 278 through 285 Processing helix chain 'F' and resid 320 through 327 removed outlier: 4.217A pdb=" N LEU F 324 " --> pdb=" O TRP F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 353 removed outlier: 4.032A pdb=" N SER F 350 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE F 351 " --> pdb=" O GLU F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 382 removed outlier: 3.786A pdb=" N GLU F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 382 " --> pdb=" O PHE F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 420 Processing helix chain 'F' and resid 446 through 452 Processing helix chain 'F' and resid 493 through 507 Processing helix chain 'F' and resid 508 through 515 removed outlier: 3.740A pdb=" N ILE F 513 " --> pdb=" O LEU F 508 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY F 514 " --> pdb=" O GLU F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 540 removed outlier: 3.739A pdb=" N ILE F 524 " --> pdb=" O THR F 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP F 527 " --> pdb=" O SER F 523 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 6.488A pdb=" N PHE A 36 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 7.116A pdb=" N GLY A 40 " --> pdb=" O ILE A 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 108 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 147 removed outlier: 6.856A pdb=" N PHE A 143 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 137 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU A 145 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU A 123 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 131 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE A 119 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 253 removed outlier: 6.375A pdb=" N GLY A 253 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 460 through 462 Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 565 Processing sheet with id=AA8, first strand: chain 'B' and resid 52 through 53 removed outlier: 6.489A pdb=" N PHE B 36 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 40 through 41 removed outlier: 7.116A pdb=" N GLY B 40 " --> pdb=" O ILE B 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AB2, first strand: chain 'B' and resid 143 through 147 removed outlier: 6.856A pdb=" N PHE B 143 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 137 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU B 145 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU B 123 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 131 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE B 119 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 246 through 253 removed outlier: 6.375A pdb=" N GLY B 253 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 460 through 462 Processing sheet with id=AB5, first strand: chain 'B' and resid 561 through 565 Processing sheet with id=AB6, first strand: chain 'C' and resid 52 through 53 removed outlier: 6.489A pdb=" N PHE C 36 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 40 through 41 removed outlier: 7.116A pdb=" N GLY C 40 " --> pdb=" O ILE C 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 106 through 108 Processing sheet with id=AB9, first strand: chain 'C' and resid 143 through 147 removed outlier: 6.856A pdb=" N PHE C 143 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 137 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU C 145 " --> pdb=" O ARG C 135 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU C 123 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 131 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE C 119 " --> pdb=" O SER C 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 246 through 253 removed outlier: 6.375A pdb=" N GLY C 253 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 460 through 462 Processing sheet with id=AC3, first strand: chain 'C' and resid 561 through 565 Processing sheet with id=AC4, first strand: chain 'D' and resid 52 through 53 removed outlier: 6.489A pdb=" N PHE D 36 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 40 through 41 removed outlier: 7.116A pdb=" N GLY D 40 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 106 through 108 Processing sheet with id=AC7, first strand: chain 'D' and resid 143 through 147 removed outlier: 6.856A pdb=" N PHE D 143 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE D 137 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU D 145 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU D 123 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER D 131 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE D 119 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 246 through 253 removed outlier: 6.375A pdb=" N GLY D 253 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 460 through 462 Processing sheet with id=AD1, first strand: chain 'D' and resid 561 through 565 Processing sheet with id=AD2, first strand: chain 'E' and resid 52 through 53 removed outlier: 6.489A pdb=" N PHE E 36 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 40 through 41 removed outlier: 7.116A pdb=" N GLY E 40 " --> pdb=" O ILE E 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 106 through 108 Processing sheet with id=AD5, first strand: chain 'E' and resid 143 through 147 removed outlier: 6.856A pdb=" N PHE E 143 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE E 137 " --> pdb=" O PHE E 143 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU E 145 " --> pdb=" O ARG E 135 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU E 123 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER E 131 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE E 119 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 246 through 253 removed outlier: 6.375A pdb=" N GLY E 253 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 460 through 462 Processing sheet with id=AD8, first strand: chain 'E' and resid 561 through 565 Processing sheet with id=AD9, first strand: chain 'F' and resid 52 through 53 removed outlier: 6.489A pdb=" N PHE F 36 " --> pdb=" O LEU F 88 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 40 through 41 removed outlier: 7.116A pdb=" N GLY F 40 " --> pdb=" O ILE F 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'F' and resid 106 through 108 Processing sheet with id=AE3, first strand: chain 'F' and resid 143 through 147 removed outlier: 6.856A pdb=" N PHE F 143 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE F 137 " --> pdb=" O PHE F 143 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU F 145 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU F 123 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER F 131 " --> pdb=" O ILE F 119 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE F 119 " --> pdb=" O SER F 131 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 246 through 253 removed outlier: 6.375A pdb=" N GLY F 253 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 460 through 462 Processing sheet with id=AE6, first strand: chain 'F' and resid 561 through 565 600 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.78 Time building geometry restraints manager: 9.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.43: 11205 1.43 - 1.74: 9045 1.74 - 2.06: 78 2.06 - 2.37: 12 2.37 - 2.68: 6 Bond restraints: 20346 Sorted by residual: bond pdb=" C ARG E 355 " pdb=" N GLU E 360 " ideal model delta sigma weight residual 1.331 2.676 -1.345 2.07e-02 2.33e+03 4.22e+03 bond pdb=" C ARG B 355 " pdb=" N GLU B 360 " ideal model delta sigma weight residual 1.331 2.676 -1.345 2.07e-02 2.33e+03 4.22e+03 bond pdb=" C ARG C 355 " pdb=" N GLU C 360 " ideal model delta sigma weight residual 1.331 2.676 -1.345 2.07e-02 2.33e+03 4.22e+03 bond pdb=" C ARG F 355 " pdb=" N GLU F 360 " ideal model delta sigma weight residual 1.331 2.676 -1.345 2.07e-02 2.33e+03 4.22e+03 bond pdb=" C ARG A 355 " pdb=" N GLU A 360 " ideal model delta sigma weight residual 1.331 2.676 -1.345 2.07e-02 2.33e+03 4.22e+03 ... (remaining 20341 not shown) Histogram of bond angle deviations from ideal: 67.05 - 85.34: 6 85.34 - 103.63: 402 103.63 - 121.91: 22676 121.91 - 140.20: 4258 140.20 - 158.49: 54 Bond angle restraints: 27396 Sorted by residual: angle pdb=" O ARG C 355 " pdb=" C ARG C 355 " pdb=" N GLU C 360 " ideal model delta sigma weight residual 121.63 67.05 54.58 1.52e+00 4.33e-01 1.29e+03 angle pdb=" O ARG F 355 " pdb=" C ARG F 355 " pdb=" N GLU F 360 " ideal model delta sigma weight residual 121.63 67.05 54.58 1.52e+00 4.33e-01 1.29e+03 angle pdb=" O ARG A 355 " pdb=" C ARG A 355 " pdb=" N GLU A 360 " ideal model delta sigma weight residual 121.63 67.08 54.55 1.52e+00 4.33e-01 1.29e+03 angle pdb=" O ARG D 355 " pdb=" C ARG D 355 " pdb=" N GLU D 360 " ideal model delta sigma weight residual 121.63 67.08 54.55 1.52e+00 4.33e-01 1.29e+03 angle pdb=" O ARG E 355 " pdb=" C ARG E 355 " pdb=" N GLU E 360 " ideal model delta sigma weight residual 121.63 67.08 54.55 1.52e+00 4.33e-01 1.29e+03 ... (remaining 27391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 11562 21.79 - 43.57: 444 43.57 - 65.36: 132 65.36 - 87.15: 48 87.15 - 108.93: 12 Dihedral angle restraints: 12198 sinusoidal: 4884 harmonic: 7314 Sorted by residual: dihedral pdb=" CA SER B 340 " pdb=" C SER B 340 " pdb=" N LYS B 341 " pdb=" CA LYS B 341 " ideal model delta harmonic sigma weight residual -180.00 -71.07 -108.93 0 5.00e+00 4.00e-02 4.75e+02 dihedral pdb=" CA SER E 340 " pdb=" C SER E 340 " pdb=" N LYS E 341 " pdb=" CA LYS E 341 " ideal model delta harmonic sigma weight residual -180.00 -71.07 -108.93 0 5.00e+00 4.00e-02 4.75e+02 dihedral pdb=" CA SER F 340 " pdb=" C SER F 340 " pdb=" N LYS F 341 " pdb=" CA LYS F 341 " ideal model delta harmonic sigma weight residual -180.00 -71.07 -108.93 0 5.00e+00 4.00e-02 4.75e+02 ... (remaining 12195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.989: 3078 0.989 - 1.978: 0 1.978 - 2.967: 0 2.967 - 3.956: 0 3.956 - 4.945: 6 Chirality restraints: 3084 Sorted by residual: chirality pdb=" CA SER C 340 " pdb=" N SER C 340 " pdb=" C SER C 340 " pdb=" CB SER C 340 " both_signs ideal model delta sigma weight residual False 2.51 -2.43 4.94 2.00e-01 2.50e+01 6.11e+02 chirality pdb=" CA SER F 340 " pdb=" N SER F 340 " pdb=" C SER F 340 " pdb=" CB SER F 340 " both_signs ideal model delta sigma weight residual False 2.51 -2.43 4.94 2.00e-01 2.50e+01 6.11e+02 chirality pdb=" CA SER A 340 " pdb=" N SER A 340 " pdb=" C SER A 340 " pdb=" CB SER A 340 " both_signs ideal model delta sigma weight residual False 2.51 -2.43 4.94 2.00e-01 2.50e+01 6.11e+02 ... (remaining 3081 not shown) Planarity restraints: 3570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 355 " -0.211 2.00e-02 2.50e+03 2.83e-01 8.02e+02 pdb=" C ARG E 355 " 0.474 2.00e-02 2.50e+03 pdb=" O ARG E 355 " -0.223 2.00e-02 2.50e+03 pdb=" N GLU E 360 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 355 " -0.211 2.00e-02 2.50e+03 2.83e-01 8.02e+02 pdb=" C ARG A 355 " 0.474 2.00e-02 2.50e+03 pdb=" O ARG A 355 " -0.223 2.00e-02 2.50e+03 pdb=" N GLU A 360 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 355 " -0.211 2.00e-02 2.50e+03 2.83e-01 8.02e+02 pdb=" C ARG D 355 " 0.474 2.00e-02 2.50e+03 pdb=" O ARG D 355 " -0.223 2.00e-02 2.50e+03 pdb=" N GLU D 360 " -0.040 2.00e-02 2.50e+03 ... (remaining 3567 not shown) Histogram of nonbonded interaction distances: 0.11 - 1.07: 66 1.07 - 2.03: 645 2.03 - 2.98: 15310 2.98 - 3.94: 55427 3.94 - 4.90: 100121 Warning: very small nonbonded interaction distances. Nonbonded interactions: 171569 Sorted by model distance: nonbonded pdb=" CD GLU C 93 " pdb=" CB ASP C 140 " model vdw 0.111 3.670 nonbonded pdb=" CD GLU F 93 " pdb=" CB ASP F 140 " model vdw 0.111 3.670 nonbonded pdb=" CD GLU B 93 " pdb=" CB ASP B 140 " model vdw 0.111 3.670 nonbonded pdb=" CD GLU E 93 " pdb=" CB ASP E 140 " model vdw 0.111 3.670 nonbonded pdb=" CD GLU A 93 " pdb=" CB ASP A 140 " model vdw 0.112 3.670 ... (remaining 171564 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 12660 2.51 5 N 3402 2.21 5 O 3966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.160 Check model and map are aligned: 0.280 Process input model: 52.860 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.180 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2997 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 : 0.053 1.345 20346 Z= 3.483 Angle : 3.063 54.579 27396 Z= 2.091 Chirality : 0.336 4.945 3084 Planarity : 0.019 0.283 3570 Dihedral : 14.438 108.931 7482 Min Nonbonded Distance : 0.111 Molprobity Statistics. All-atom Clashscore : 93.07 Ramachandran Plot: Outliers : 6.90 % Allowed : 14.04 % Favored : 79.06 % Rotamer Outliers : 2.94 % Cbeta Deviations : 4.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.47 % Twisted Proline : 11.11 % Twisted General : 2.21 % 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: -4.32 (0.14), residues: 2436 helix: -1.37 (0.21), residues: 612 sheet: -1.70 (0.27), residues: 246 loop : -3.99 (0.11), residues: 1578 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 566 time to evaluate : 2.342 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 26 residues processed: 624 average time/residue: 0.3873 time to fit residues: 341.9240 Evaluate side-chains 367 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 341 time to evaluate : 2.381 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2704 time to fit residues: 14.7622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 197 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 58 GLN ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN A 407 HIS A 530 GLN B 55 ASN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN B 407 HIS B 530 GLN C 55 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN D 55 ASN D 58 GLN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN D 407 HIS D 530 GLN E 55 ASN E 58 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 ASN E 407 HIS E 530 GLN F 55 ASN ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3156 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 20346 Z= 0.404 Angle : 1.215 14.370 27396 Z= 0.637 Chirality : 0.067 0.374 3084 Planarity : 0.007 0.081 3570 Dihedral : 10.188 59.137 2730 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 36.73 Ramachandran Plot: Outliers : 1.96 % Allowed : 14.83 % Favored : 83.21 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 11.11 % Twisted General : 1.23 % 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: -4.54 (0.13), residues: 2448 helix: -1.50 (0.17), residues: 690 sheet: -1.72 (0.24), residues: 330 loop : -4.40 (0.11), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 465 time to evaluate : 2.355 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 485 average time/residue: 0.3994 time to fit residues: 277.9991 Evaluate side-chains 324 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 314 time to evaluate : 2.365 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1759 time to fit residues: 6.6188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 30.0000 chunk 190 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 229 optimal weight: 30.0000 chunk 247 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 120 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN C 120 GLN C 376 GLN C 407 HIS D 117 ASN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN E 120 GLN ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN F 120 GLN F 376 GLN F 407 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3300 moved from start: 0.9182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 20346 Z= 0.318 Angle : 1.043 13.074 27396 Z= 0.538 Chirality : 0.059 0.448 3084 Planarity : 0.007 0.067 3570 Dihedral : 8.938 62.606 2730 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 33.16 Ramachandran Plot: Outliers : 1.23 % Allowed : 15.16 % Favored : 83.62 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 3.70 % Twisted General : 0.74 % 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: -4.27 (0.13), residues: 2448 helix: -1.13 (0.17), residues: 690 sheet: -1.34 (0.24), residues: 324 loop : -4.37 (0.11), residues: 1434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 413 time to evaluate : 2.388 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 425 average time/residue: 0.3633 time to fit residues: 226.4475 Evaluate side-chains 317 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 2.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 153 optimal weight: 50.0000 chunk 230 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 120 optimal weight: 0.0000 chunk 218 optimal weight: 30.0000 chunk 65 optimal weight: 3.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3145 moved from start: 0.9948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 20346 Z= 0.233 Angle : 0.935 12.628 27396 Z= 0.483 Chirality : 0.054 0.413 3084 Planarity : 0.005 0.061 3570 Dihedral : 8.010 58.849 2730 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 1.23 % Allowed : 12.05 % Favored : 86.72 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.74 % 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: -4.01 (0.14), residues: 2448 helix: -0.99 (0.18), residues: 702 sheet: -1.59 (0.26), residues: 336 loop : -4.08 (0.12), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 429 time to evaluate : 2.273 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: 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: 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: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 431 average time/residue: 0.3743 time to fit residues: 233.8968 Evaluate side-chains 339 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.466 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 181 optimal weight: 0.0000 chunk 100 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 124 optimal weight: 0.9990 chunk 218 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 120 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN D 120 GLN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3289 moved from start: 1.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 20346 Z= 0.258 Angle : 0.932 11.101 27396 Z= 0.479 Chirality : 0.054 0.399 3084 Planarity : 0.006 0.059 3570 Dihedral : 7.788 56.733 2730 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 29.69 Ramachandran Plot: Outliers : 0.82 % Allowed : 14.05 % Favored : 85.13 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.94 (0.14), residues: 2448 helix: -0.95 (0.18), residues: 696 sheet: -1.67 (0.25), residues: 324 loop : -3.96 (0.13), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 423 time to evaluate : 2.362 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: 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: 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: symmetry clash outliers start: 2 outliers final: 2 residues processed: 425 average time/residue: 0.3901 time to fit residues: 238.3361 Evaluate side-chains 336 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 334 time to evaluate : 2.329 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1708 time to fit residues: 3.8908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 243 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3316 moved from start: 1.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 20346 Z= 0.265 Angle : 0.923 11.137 27396 Z= 0.474 Chirality : 0.052 0.379 3084 Planarity : 0.006 0.051 3570 Dihedral : 7.698 52.996 2730 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 32.45 Ramachandran Plot: Outliers : 0.98 % Allowed : 13.24 % Favored : 85.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.89 (0.14), residues: 2448 helix: -0.94 (0.18), residues: 678 sheet: -1.88 (0.27), residues: 306 loop : -3.80 (0.13), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 2.632 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.3831 time to fit residues: 225.4224 Evaluate side-chains 322 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 2.422 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 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 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 149 ASN ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3435 moved from start: 1.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 20346 Z= 0.271 Angle : 0.912 10.622 27396 Z= 0.470 Chirality : 0.053 0.339 3084 Planarity : 0.006 0.082 3570 Dihedral : 7.685 52.364 2730 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 32.40 Ramachandran Plot: Outliers : 0.82 % Allowed : 13.89 % Favored : 85.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.95 (0.14), residues: 2448 helix: -0.93 (0.18), residues: 696 sheet: -1.84 (0.25), residues: 336 loop : -3.96 (0.12), residues: 1416 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.338 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.3802 time to fit residues: 215.3425 Evaluate side-chains 316 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 2.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 145 optimal weight: 0.0770 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 165 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 overall best weight: 3.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3360 moved from start: 1.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 20346 Z= 0.233 Angle : 0.896 10.954 27396 Z= 0.459 Chirality : 0.052 0.361 3084 Planarity : 0.006 0.080 3570 Dihedral : 7.577 49.263 2730 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.90 % Allowed : 13.56 % Favored : 85.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.91 (0.14), residues: 2448 helix: -1.03 (0.17), residues: 714 sheet: -1.59 (0.26), residues: 324 loop : -3.93 (0.13), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 2.398 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.3833 time to fit residues: 211.1864 Evaluate side-chains 312 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 2.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 226 optimal weight: 0.3980 chunk 136 optimal weight: 8.9990 chunk 98 optimal weight: 30.0000 chunk 177 optimal weight: 9.9990 chunk 69 optimal weight: 40.0000 chunk 204 optimal weight: 0.9980 chunk 214 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 overall best weight: 4.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 ASN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3448 moved from start: 1.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 20346 Z= 0.248 Angle : 0.905 11.308 27396 Z= 0.465 Chirality : 0.052 0.263 3084 Planarity : 0.006 0.074 3570 Dihedral : 7.527 46.661 2730 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 30.47 Ramachandran Plot: Outliers : 0.90 % Allowed : 14.87 % Favored : 84.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.89 (0.14), residues: 2448 helix: -1.07 (0.17), residues: 714 sheet: -1.66 (0.28), residues: 306 loop : -3.84 (0.13), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.317 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.3848 time to fit residues: 215.5092 Evaluate side-chains 332 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 2.519 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 40.0000 chunk 146 optimal weight: 0.0060 chunk 113 optimal weight: 40.0000 chunk 166 optimal weight: 3.9990 chunk 251 optimal weight: 0.0060 chunk 231 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 20 optimal weight: 0.0060 chunk 154 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.4032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 381 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3244 moved from start: 1.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 20346 Z= 0.220 Angle : 0.917 13.383 27396 Z= 0.468 Chirality : 0.050 0.235 3084 Planarity : 0.006 0.105 3570 Dihedral : 7.066 36.104 2730 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.98 % Allowed : 12.66 % Favored : 86.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.57 (0.15), residues: 2448 helix: -0.81 (0.18), residues: 708 sheet: -1.49 (0.29), residues: 306 loop : -3.62 (0.13), residues: 1434 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 2.421 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: 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: 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 outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.3979 time to fit residues: 218.4548 Evaluate side-chains 304 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.463 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 4.9990 chunk 61 optimal weight: 30.0000 chunk 184 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 25 optimal weight: 0.0980 chunk 36 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 ASN D 279 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.157444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.146552 restraints weight = 182345.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.147552 restraints weight = 148782.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.148089 restraints weight = 129472.301| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5766 moved from start: 1.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 20346 Z= 0.255 Angle : 0.917 12.838 27396 Z= 0.473 Chirality : 0.051 0.276 3084 Planarity : 0.006 0.062 3570 Dihedral : 7.231 37.915 2730 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 29.38 Ramachandran Plot: Outliers : 1.23 % Allowed : 14.34 % Favored : 84.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.15), residues: 2448 helix: -0.95 (0.18), residues: 708 sheet: -1.49 (0.29), residues: 306 loop : -3.63 (0.13), residues: 1434 Sorry: There was an error with writing 5li4_4052_real_space_refined_001.eff. [Errno 28] No space left on device