Starting phenix.real_space_refine on Mon Mar 18 05:57:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/03_2024/5li4_4052.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/03_2024/5li4_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_2024/5li4_4052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/03_2024/5li4_4052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/03_2024/5li4_4052.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/03_2024/5li4_4052.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 ------------------------------------------------------------------------------- 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 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. 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-5265/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: 10.24, per 1000 atoms: 0.51 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: 8.41 Conformation dependent library (CDL) restraints added in 3.3 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: 2.36 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: 6.22 Time building geometry restraints manager: 9.01 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 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: 0.340 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: 2.560 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 53.480 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3172 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 : 3.066 54.579 27396 Z= 2.094 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 % Allowed : 4.50 % Favored : 92.56 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.151 0.053 TRP D 320 HIS 0.009 0.002 HIS F 345 PHE 0.099 0.015 PHE C 351 TYR 0.236 0.016 TYR A 444 ARG 0.004 0.000 ARG D 355 *********************** 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 : 2.276 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 REVERT: A 39 ILE cc_start: 0.5185 (pt) cc_final: 0.4424 (pt) REVERT: A 50 VAL cc_start: 0.7572 (t) cc_final: 0.7067 (t) REVERT: B 39 ILE cc_start: 0.5546 (pt) cc_final: 0.5175 (pt) REVERT: B 153 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.5838 (tp) REVERT: B 450 ASP cc_start: 0.6105 (p0) cc_final: 0.5884 (m-30) REVERT: C 39 ILE cc_start: 0.5845 (pt) cc_final: 0.5540 (pt) REVERT: C 576 VAL cc_start: 0.5496 (t) cc_final: 0.5293 (p) REVERT: D 39 ILE cc_start: 0.5158 (pt) cc_final: 0.4416 (pt) REVERT: D 50 VAL cc_start: 0.7567 (t) cc_final: 0.7068 (t) REVERT: E 39 ILE cc_start: 0.5540 (pt) cc_final: 0.5087 (pt) REVERT: E 153 ILE cc_start: 0.6447 (OUTLIER) cc_final: 0.5781 (tp) REVERT: E 450 ASP cc_start: 0.6113 (p0) cc_final: 0.5852 (m-30) REVERT: F 39 ILE cc_start: 0.5837 (pt) cc_final: 0.5539 (pt) REVERT: F 576 VAL cc_start: 0.5558 (t) cc_final: 0.5351 (p) outliers start: 64 outliers final: 26 residues processed: 624 average time/residue: 0.3850 time to fit residues: 340.4345 Evaluate side-chains 371 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 343 time to evaluate : 2.265 ------------------------------------------------------------------------------- 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: 7.9990 chunk 191 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 228 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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: 0.3329 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20346 Z= 0.389 Angle : 1.173 8.740 27396 Z= 0.631 Chirality : 0.066 0.373 3084 Planarity : 0.007 0.083 3570 Dihedral : 10.149 58.325 2730 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 35.50 Ramachandran Plot: Outliers : 1.96 % Allowed : 14.54 % Favored : 83.50 % Rotamer: Outliers : 0.64 % Allowed : 7.35 % Favored : 92.01 % 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: -4.51 (0.13), residues: 2448 helix: -1.52 (0.17), residues: 690 sheet: -1.63 (0.24), residues: 330 loop : -4.37 (0.11), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP A 76 HIS 0.006 0.002 HIS C 407 PHE 0.030 0.003 PHE D 143 TYR 0.025 0.003 TYR A 112 ARG 0.008 0.001 ARG F 142 *********************** 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 483 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 469 time to evaluate : 2.323 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: A 362 MET cc_start: 0.6610 (pmm) cc_final: 0.5935 (pmm) REVERT: A 458 ILE cc_start: 0.3376 (mm) cc_final: 0.3085 (mm) REVERT: B 39 ILE cc_start: 0.6049 (pt) cc_final: 0.5649 (pt) REVERT: B 362 MET cc_start: 0.7128 (pmm) cc_final: 0.6689 (pmm) REVERT: C 53 LEU cc_start: 0.6715 (mt) cc_final: 0.6106 (mm) REVERT: C 326 LYS cc_start: 0.7828 (mttt) cc_final: 0.7315 (mttt) REVERT: D 362 MET cc_start: 0.6615 (pmm) cc_final: 0.5955 (pmm) REVERT: D 458 ILE cc_start: 0.3433 (mm) cc_final: 0.3063 (mm) REVERT: E 39 ILE cc_start: 0.6015 (pt) cc_final: 0.5573 (pt) REVERT: E 362 MET cc_start: 0.7101 (pmm) cc_final: 0.6667 (pmm) REVERT: F 53 LEU cc_start: 0.6741 (mt) cc_final: 0.6109 (mm) REVERT: F 326 LYS cc_start: 0.7797 (mttt) cc_final: 0.7319 (mttt) outliers start: 14 outliers final: 4 residues processed: 481 average time/residue: 0.3784 time to fit residues: 258.5021 Evaluate side-chains 321 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 317 time to evaluate : 2.375 ------------------------------------------------------------------------------- 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: 5.9990 chunk 71 optimal weight: 30.0000 chunk 190 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 229 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 183 optimal weight: 0.4980 overall best weight: 6.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 120 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN C 407 HIS ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 HIS ** 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** ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN F 407 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3487 moved from start: 0.9087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20346 Z= 0.323 Angle : 1.021 11.488 27396 Z= 0.542 Chirality : 0.058 0.403 3084 Planarity : 0.006 0.066 3570 Dihedral : 8.903 62.378 2730 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 34.92 Ramachandran Plot: Outliers : 1.23 % Allowed : 15.56 % Favored : 83.21 % Rotamer: Outliers : 0.60 % Allowed : 5.74 % Favored : 93.66 % 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: -4.30 (0.13), residues: 2448 helix: -1.33 (0.17), residues: 684 sheet: -0.79 (0.27), residues: 294 loop : -4.37 (0.11), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 76 HIS 0.006 0.002 HIS F 407 PHE 0.029 0.003 PHE B 143 TYR 0.028 0.003 TYR E 566 ARG 0.007 0.001 ARG C 380 *********************** 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 422 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 409 time to evaluate : 2.329 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: A 397 THR cc_start: 0.0155 (OUTLIER) cc_final: -0.0629 (p) REVERT: A 504 LEU cc_start: 0.6139 (mt) cc_final: 0.5434 (mt) REVERT: B 397 THR cc_start: -0.0193 (OUTLIER) cc_final: -0.1107 (p) REVERT: B 524 ILE cc_start: 0.3201 (mp) cc_final: 0.2753 (mp) REVERT: B 525 ILE cc_start: 0.5488 (mt) cc_final: 0.5058 (mt) REVERT: C 397 THR cc_start: -0.0000 (OUTLIER) cc_final: -0.0668 (p) REVERT: C 504 LEU cc_start: 0.5118 (mt) cc_final: 0.4862 (mt) REVERT: C 525 ILE cc_start: 0.5634 (mt) cc_final: 0.5126 (mt) REVERT: D 397 THR cc_start: 0.0189 (OUTLIER) cc_final: -0.0566 (p) REVERT: D 504 LEU cc_start: 0.6141 (mt) cc_final: 0.5452 (mt) REVERT: E 397 THR cc_start: -0.0095 (OUTLIER) cc_final: -0.1089 (p) REVERT: E 524 ILE cc_start: 0.3175 (mp) cc_final: 0.2555 (mp) REVERT: E 525 ILE cc_start: 0.5492 (mt) cc_final: 0.4936 (mt) REVERT: F 53 LEU cc_start: 0.6062 (mt) cc_final: 0.5820 (mm) REVERT: F 397 THR cc_start: -0.0007 (OUTLIER) cc_final: -0.0662 (p) REVERT: F 504 LEU cc_start: 0.5128 (mt) cc_final: 0.4834 (mt) REVERT: F 525 ILE cc_start: 0.5638 (mt) cc_final: 0.5074 (mt) outliers start: 13 outliers final: 2 residues processed: 422 average time/residue: 0.3870 time to fit residues: 236.3187 Evaluate side-chains 332 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 324 time to evaluate : 2.407 ------------------------------------------------------------------------------- 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: 0.9990 chunk 172 optimal weight: 30.0000 chunk 118 optimal weight: 30.0000 chunk 25 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 230 optimal weight: 20.0000 chunk 243 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 218 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 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** C 120 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3528 moved from start: 1.0176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20346 Z= 0.269 Angle : 0.937 11.190 27396 Z= 0.495 Chirality : 0.056 0.459 3084 Planarity : 0.006 0.065 3570 Dihedral : 8.280 57.317 2730 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 31.75 Ramachandran Plot: Outliers : 1.18 % Allowed : 13.73 % Favored : 85.09 % Rotamer: Outliers : 0.14 % Allowed : 5.33 % Favored : 94.54 % 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: -3.97 (0.14), residues: 2448 helix: -0.89 (0.17), residues: 672 sheet: -1.29 (0.28), residues: 306 loop : -4.07 (0.12), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP B 76 HIS 0.003 0.001 HIS D 171 PHE 0.022 0.002 PHE D 143 TYR 0.027 0.002 TYR B 566 ARG 0.007 0.001 ARG E 91 *********************** 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 408 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 405 time to evaluate : 2.327 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: A 525 ILE cc_start: 0.6317 (mt) cc_final: 0.5918 (mt) REVERT: A 561 ILE cc_start: 0.4916 (tt) cc_final: 0.4398 (tt) REVERT: B 53 LEU cc_start: 0.6327 (mm) cc_final: 0.5259 (mm) REVERT: B 56 TYR cc_start: 0.5004 (t80) cc_final: 0.4050 (t80) REVERT: B 525 ILE cc_start: 0.5757 (mt) cc_final: 0.5151 (mm) REVERT: C 504 LEU cc_start: 0.5207 (mt) cc_final: 0.4812 (mt) REVERT: C 524 ILE cc_start: 0.3672 (mp) cc_final: 0.3119 (mt) REVERT: D 525 ILE cc_start: 0.6368 (mt) cc_final: 0.5947 (mt) REVERT: D 561 ILE cc_start: 0.5013 (tt) cc_final: 0.4288 (tt) REVERT: E 53 LEU cc_start: 0.6278 (mm) cc_final: 0.5034 (mm) REVERT: E 381 GLN cc_start: 0.1273 (mm-40) cc_final: 0.0261 (mm110) REVERT: E 524 ILE cc_start: 0.3048 (mp) cc_final: 0.2715 (mp) REVERT: E 525 ILE cc_start: 0.5625 (mt) cc_final: 0.4576 (mm) REVERT: F 504 LEU cc_start: 0.5243 (mt) cc_final: 0.4823 (mt) REVERT: F 524 ILE cc_start: 0.3719 (mp) cc_final: 0.3153 (mt) outliers start: 3 outliers final: 2 residues processed: 407 average time/residue: 0.3899 time to fit residues: 228.6784 Evaluate side-chains 344 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 342 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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: 9.9990 chunk 181 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 218 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 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** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3726 moved from start: 1.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20346 Z= 0.333 Angle : 0.980 10.367 27396 Z= 0.517 Chirality : 0.058 0.606 3084 Planarity : 0.007 0.065 3570 Dihedral : 8.343 55.864 2730 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 37.13 Ramachandran Plot: Outliers : 0.86 % Allowed : 15.97 % Favored : 83.17 % Rotamer: Outliers : 0.37 % Allowed : 5.19 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -4.06 (0.14), residues: 2448 helix: -0.85 (0.17), residues: 672 sheet: -1.48 (0.26), residues: 324 loop : -4.19 (0.12), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP C 76 HIS 0.004 0.001 HIS B 329 PHE 0.037 0.003 PHE E 143 TYR 0.049 0.003 TYR B 56 ARG 0.012 0.001 ARG A 91 *********************** 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 417 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 409 time to evaluate : 2.508 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: A 524 ILE cc_start: 0.3858 (mp) cc_final: 0.3504 (mp) REVERT: A 525 ILE cc_start: 0.6248 (mt) cc_final: 0.5359 (mt) REVERT: B 52 GLU cc_start: 0.5814 (tm-30) cc_final: 0.2908 (tm-30) REVERT: B 53 LEU cc_start: 0.6300 (mm) cc_final: 0.5744 (mm) REVERT: B 87 ILE cc_start: 0.7486 (mp) cc_final: 0.7160 (mp) REVERT: B 397 THR cc_start: 0.0062 (OUTLIER) cc_final: -0.0455 (p) REVERT: B 524 ILE cc_start: 0.3503 (mp) cc_final: 0.2535 (mp) REVERT: B 525 ILE cc_start: 0.7057 (mt) cc_final: 0.5674 (mm) REVERT: B 561 ILE cc_start: 0.4840 (mt) cc_final: 0.4576 (mt) REVERT: C 353 LYS cc_start: 0.6676 (ptpp) cc_final: 0.6216 (ptpp) REVERT: C 524 ILE cc_start: 0.3780 (mp) cc_final: 0.3221 (mp) REVERT: C 525 ILE cc_start: 0.6051 (mt) cc_final: 0.5515 (mt) REVERT: D 524 ILE cc_start: 0.3875 (mp) cc_final: 0.3470 (mp) REVERT: D 525 ILE cc_start: 0.6313 (mt) cc_final: 0.5406 (mt) REVERT: E 52 GLU cc_start: 0.5668 (tm-30) cc_final: 0.2369 (tm-30) REVERT: E 53 LEU cc_start: 0.6256 (mm) cc_final: 0.5290 (mm) REVERT: E 87 ILE cc_start: 0.7455 (mp) cc_final: 0.6941 (mp) REVERT: E 397 THR cc_start: 0.0249 (OUTLIER) cc_final: -0.0231 (p) REVERT: E 447 ILE cc_start: 0.5490 (mp) cc_final: 0.5241 (mp) REVERT: E 524 ILE cc_start: 0.2977 (mp) cc_final: 0.2312 (mp) REVERT: E 525 ILE cc_start: 0.6254 (mt) cc_final: 0.5914 (mm) REVERT: E 561 ILE cc_start: 0.4891 (mt) cc_final: 0.4656 (mt) REVERT: F 353 LYS cc_start: 0.6717 (ptpp) cc_final: 0.6194 (ptpp) REVERT: F 397 THR cc_start: 0.1195 (OUTLIER) cc_final: 0.0971 (p) REVERT: F 504 LEU cc_start: 0.6579 (mt) cc_final: 0.6359 (mt) REVERT: F 524 ILE cc_start: 0.3770 (mp) cc_final: 0.3262 (mp) REVERT: F 525 ILE cc_start: 0.6100 (mt) cc_final: 0.5457 (mm) outliers start: 8 outliers final: 0 residues processed: 417 average time/residue: 0.3675 time to fit residues: 221.9703 Evaluate side-chains 330 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 327 time to evaluate : 2.600 ------------------------------------------------------------------------------- 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: 9.9990 chunk 219 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 60 optimal weight: 0.1980 chunk 243 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** 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** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 114 ASN ** 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: 0.3615 moved from start: 1.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20346 Z= 0.255 Angle : 0.901 10.317 27396 Z= 0.478 Chirality : 0.054 0.426 3084 Planarity : 0.006 0.053 3570 Dihedral : 8.012 53.686 2730 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 30.06 Ramachandran Plot: Outliers : 1.02 % Allowed : 13.11 % Favored : 85.87 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % 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: -3.80 (0.14), residues: 2448 helix: -0.71 (0.18), residues: 672 sheet: -1.41 (0.28), residues: 306 loop : -3.93 (0.12), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP F 76 HIS 0.003 0.001 HIS D 407 PHE 0.036 0.002 PHE A 143 TYR 0.019 0.002 TYR D 532 ARG 0.012 0.001 ARG E 61 *********************** 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 396 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 2.416 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: A 524 ILE cc_start: 0.2986 (mp) cc_final: 0.1919 (mp) REVERT: A 525 ILE cc_start: 0.6174 (mt) cc_final: 0.5739 (mm) REVERT: B 52 GLU cc_start: 0.5911 (tm-30) cc_final: 0.4649 (tm-30) REVERT: B 524 ILE cc_start: 0.2734 (mp) cc_final: 0.2072 (mp) REVERT: B 525 ILE cc_start: 0.6151 (mt) cc_final: 0.5880 (mm) REVERT: C 48 ASN cc_start: 0.7880 (p0) cc_final: 0.7337 (p0) REVERT: C 377 LEU cc_start: 0.5977 (tt) cc_final: 0.4802 (tt) REVERT: C 524 ILE cc_start: 0.2811 (mp) cc_final: 0.2033 (mp) REVERT: C 525 ILE cc_start: 0.6275 (mt) cc_final: 0.4956 (mm) REVERT: C 529 ILE cc_start: 0.6303 (pt) cc_final: 0.5851 (pt) REVERT: D 524 ILE cc_start: 0.3043 (mp) cc_final: 0.1930 (mp) REVERT: D 525 ILE cc_start: 0.6238 (mt) cc_final: 0.5771 (mm) REVERT: E 62 LEU cc_start: 0.6960 (mm) cc_final: 0.6689 (mm) REVERT: E 524 ILE cc_start: 0.3249 (mp) cc_final: 0.2481 (mp) REVERT: E 525 ILE cc_start: 0.5920 (mt) cc_final: 0.5548 (mm) REVERT: F 48 ASN cc_start: 0.7929 (p0) cc_final: 0.7387 (p0) REVERT: F 504 LEU cc_start: 0.6210 (mt) cc_final: 0.5933 (mt) REVERT: F 524 ILE cc_start: 0.2770 (mp) cc_final: 0.1980 (mp) REVERT: F 525 ILE cc_start: 0.6292 (mt) cc_final: 0.4951 (mm) REVERT: F 529 ILE cc_start: 0.6360 (pt) cc_final: 0.5809 (pt) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.3686 time to fit residues: 209.8200 Evaluate side-chains 336 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 2.427 ------------------------------------------------------------------------------- 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: 4.9990 chunk 27 optimal weight: 40.0000 chunk 138 optimal weight: 10.0000 chunk 178 optimal weight: 40.0000 chunk 137 optimal weight: 20.0000 chunk 205 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 242 optimal weight: 8.9990 chunk 152 optimal weight: 0.2980 chunk 148 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- 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 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3688 moved from start: 1.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20346 Z= 0.265 Angle : 0.907 10.319 27396 Z= 0.484 Chirality : 0.053 0.378 3084 Planarity : 0.006 0.077 3570 Dihedral : 7.883 52.755 2730 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 32.13 Ramachandran Plot: Outliers : 1.14 % Allowed : 14.79 % Favored : 84.07 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: -3.88 (0.14), residues: 2448 helix: -0.83 (0.18), residues: 702 sheet: -1.39 (0.27), residues: 324 loop : -4.06 (0.13), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.005 TRP E 76 HIS 0.003 0.001 HIS F 329 PHE 0.030 0.002 PHE A 143 TYR 0.032 0.002 TYR B 411 ARG 0.010 0.001 ARG F 86 *********************** 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 397 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 2.234 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: A 524 ILE cc_start: 0.3383 (mp) cc_final: 0.1963 (mp) REVERT: A 525 ILE cc_start: 0.6706 (mt) cc_final: 0.5979 (mm) REVERT: B 524 ILE cc_start: 0.3412 (mp) cc_final: 0.3101 (mp) REVERT: B 525 ILE cc_start: 0.5785 (mt) cc_final: 0.5448 (mm) REVERT: C 48 ASN cc_start: 0.7838 (p0) cc_final: 0.7436 (p0) REVERT: C 353 LYS cc_start: 0.7119 (ptpp) cc_final: 0.6527 (ptpp) REVERT: C 377 LEU cc_start: 0.6219 (tt) cc_final: 0.5418 (tt) REVERT: C 504 LEU cc_start: 0.6248 (mt) cc_final: 0.6033 (mt) REVERT: C 524 ILE cc_start: 0.3337 (mp) cc_final: 0.1979 (mp) REVERT: C 525 ILE cc_start: 0.5946 (mt) cc_final: 0.5169 (mm) REVERT: C 529 ILE cc_start: 0.6284 (pt) cc_final: 0.5743 (pt) REVERT: D 524 ILE cc_start: 0.3421 (mp) cc_final: 0.1976 (mp) REVERT: D 525 ILE cc_start: 0.6748 (mt) cc_final: 0.5988 (mm) REVERT: E 53 LEU cc_start: 0.5949 (mm) cc_final: 0.5233 (mm) REVERT: E 353 LYS cc_start: 0.4318 (mmtt) cc_final: 0.3762 (mmtt) REVERT: E 524 ILE cc_start: 0.2574 (mp) cc_final: 0.2358 (mp) REVERT: E 525 ILE cc_start: 0.6165 (mt) cc_final: 0.5803 (mm) REVERT: F 48 ASN cc_start: 0.7752 (p0) cc_final: 0.7298 (p0) REVERT: F 353 LYS cc_start: 0.7116 (ptpp) cc_final: 0.6553 (ptpp) REVERT: F 504 LEU cc_start: 0.6220 (mt) cc_final: 0.6004 (mt) REVERT: F 524 ILE cc_start: 0.3296 (mp) cc_final: 0.1897 (mp) REVERT: F 525 ILE cc_start: 0.5932 (mt) cc_final: 0.5200 (mm) REVERT: F 529 ILE cc_start: 0.6216 (pt) cc_final: 0.5681 (pt) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.3686 time to fit residues: 211.2330 Evaluate side-chains 335 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 2.481 ------------------------------------------------------------------------------- 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: 9.9990 chunk 96 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 120 optimal weight: 0.0970 chunk 22 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 386 ASN D 149 ASN ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3618 moved from start: 1.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20346 Z= 0.229 Angle : 0.859 8.692 27396 Z= 0.458 Chirality : 0.052 0.407 3084 Planarity : 0.006 0.095 3570 Dihedral : 7.618 50.884 2730 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 0.98 % Allowed : 14.22 % Favored : 84.80 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: -3.70 (0.15), residues: 2448 helix: -0.64 (0.18), residues: 678 sheet: -1.42 (0.26), residues: 324 loop : -3.88 (0.13), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.005 TRP E 76 HIS 0.002 0.001 HIS C 171 PHE 0.039 0.002 PHE E 143 TYR 0.023 0.002 TYR F 411 ARG 0.010 0.001 ARG B 142 *********************** 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 391 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.363 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: A 326 LYS cc_start: 0.7403 (ptpt) cc_final: 0.7058 (ptpt) REVERT: A 525 ILE cc_start: 0.6491 (mt) cc_final: 0.5822 (mm) REVERT: B 400 MET cc_start: 0.7699 (tmm) cc_final: 0.6619 (tmm) REVERT: B 525 ILE cc_start: 0.6128 (mt) cc_final: 0.5874 (mm) REVERT: C 48 ASN cc_start: 0.7836 (p0) cc_final: 0.7556 (p0) REVERT: C 76 TRP cc_start: 0.4907 (t60) cc_final: 0.4103 (t60) REVERT: C 377 LEU cc_start: 0.6180 (tt) cc_final: 0.5542 (tt) REVERT: C 400 MET cc_start: 0.7355 (tmm) cc_final: 0.6527 (tmm) REVERT: C 524 ILE cc_start: 0.3327 (mp) cc_final: 0.2077 (mp) REVERT: C 525 ILE cc_start: 0.6197 (mt) cc_final: 0.5771 (mm) REVERT: C 529 ILE cc_start: 0.6492 (pt) cc_final: 0.6155 (pt) REVERT: D 326 LYS cc_start: 0.7403 (ptpt) cc_final: 0.7071 (ptpt) REVERT: D 524 ILE cc_start: 0.3255 (mp) cc_final: 0.3026 (mp) REVERT: D 525 ILE cc_start: 0.6500 (mt) cc_final: 0.5800 (mm) REVERT: D 529 ILE cc_start: 0.6264 (pt) cc_final: 0.6043 (pt) REVERT: E 53 LEU cc_start: 0.5858 (mm) cc_final: 0.5616 (mm) REVERT: E 400 MET cc_start: 0.7660 (tmm) cc_final: 0.6932 (tmm) REVERT: E 504 LEU cc_start: 0.6571 (mt) cc_final: 0.6368 (mt) REVERT: E 525 ILE cc_start: 0.6470 (mt) cc_final: 0.6184 (mm) REVERT: E 529 ILE cc_start: 0.6424 (pt) cc_final: 0.6047 (pt) REVERT: F 48 ASN cc_start: 0.7709 (p0) cc_final: 0.7421 (p0) REVERT: F 400 MET cc_start: 0.7428 (tmm) cc_final: 0.6436 (tmm) REVERT: F 524 ILE cc_start: 0.3298 (mp) cc_final: 0.1988 (mp) REVERT: F 525 ILE cc_start: 0.6145 (mt) cc_final: 0.5850 (mm) REVERT: F 529 ILE cc_start: 0.6389 (pt) cc_final: 0.6128 (pt) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.3620 time to fit residues: 204.8591 Evaluate side-chains 320 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.410 ------------------------------------------------------------------------------- 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: 4.9990 chunk 212 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 69 optimal weight: 30.0000 chunk 204 optimal weight: 30.0000 chunk 214 optimal weight: 30.0000 chunk 225 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 ASN D 557 ASN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 ASN ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 453 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3809 moved from start: 1.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20346 Z= 0.293 Angle : 0.923 11.494 27396 Z= 0.488 Chirality : 0.054 0.340 3084 Planarity : 0.007 0.098 3570 Dihedral : 7.942 49.780 2730 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 36.38 Ramachandran Plot: Outliers : 0.98 % Allowed : 16.67 % Favored : 82.35 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: -3.93 (0.14), residues: 2448 helix: -1.04 (0.18), residues: 690 sheet: -1.64 (0.27), residues: 336 loop : -3.91 (0.13), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.005 TRP E 76 HIS 0.007 0.002 HIS F 345 PHE 0.038 0.002 PHE A 143 TYR 0.026 0.003 TYR E 411 ARG 0.009 0.001 ARG F 86 *********************** 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 393 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.122 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: A 60 LYS cc_start: 0.7371 (mtmm) cc_final: 0.6880 (mtmm) REVERT: B 561 ILE cc_start: 0.4764 (mt) cc_final: 0.4483 (mt) REVERT: C 48 ASN cc_start: 0.7832 (p0) cc_final: 0.7548 (p0) REVERT: C 76 TRP cc_start: 0.5486 (t60) cc_final: 0.4762 (t60) REVERT: C 353 LYS cc_start: 0.7623 (ptpp) cc_final: 0.7152 (tppt) REVERT: C 377 LEU cc_start: 0.6339 (tt) cc_final: 0.5613 (tt) REVERT: C 524 ILE cc_start: 0.3335 (mp) cc_final: 0.1977 (mp) REVERT: C 525 ILE cc_start: 0.6222 (mt) cc_final: 0.5586 (mm) REVERT: D 60 LYS cc_start: 0.7273 (mtmm) cc_final: 0.6950 (mtmm) REVERT: E 400 MET cc_start: 0.7714 (tmm) cc_final: 0.6762 (tmm) REVERT: E 529 ILE cc_start: 0.6896 (pt) cc_final: 0.6463 (pt) REVERT: F 48 ASN cc_start: 0.7720 (p0) cc_final: 0.7383 (p0) REVERT: F 353 LYS cc_start: 0.7702 (ptpp) cc_final: 0.7165 (tppt) REVERT: F 366 VAL cc_start: 0.5477 (t) cc_final: 0.5130 (t) REVERT: F 400 MET cc_start: 0.7337 (tmm) cc_final: 0.6610 (tmm) REVERT: F 524 ILE cc_start: 0.3308 (mp) cc_final: 0.1963 (mp) REVERT: F 525 ILE cc_start: 0.6178 (mt) cc_final: 0.5559 (mm) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.3724 time to fit residues: 211.7667 Evaluate side-chains 324 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.421 ------------------------------------------------------------------------------- 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: 9.9990 chunk 146 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 154 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 158 optimal weight: 0.4980 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 345 HIS ** 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 279 ASN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** 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 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN F 279 ASN ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3787 moved from start: 1.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20346 Z= 0.264 Angle : 0.934 12.732 27396 Z= 0.495 Chirality : 0.053 0.302 3084 Planarity : 0.006 0.071 3570 Dihedral : 7.734 42.028 2730 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 32.83 Ramachandran Plot: Outliers : 0.94 % Allowed : 16.01 % Favored : 83.05 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.15), residues: 2448 helix: -1.17 (0.18), residues: 696 sheet: -1.60 (0.29), residues: 306 loop : -3.77 (0.13), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.007 TRP E 76 HIS 0.006 0.001 HIS B 345 PHE 0.038 0.002 PHE A 143 TYR 0.025 0.002 TYR C 411 ARG 0.011 0.001 ARG D 380 ********************** 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 385 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.325 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: B 62 LEU cc_start: 0.6307 (mm) cc_final: 0.6025 (mm) REVERT: C 48 ASN cc_start: 0.7768 (p0) cc_final: 0.7479 (p0) REVERT: C 76 TRP cc_start: 0.5540 (t60) cc_final: 0.4898 (t60) REVERT: C 353 LYS cc_start: 0.7561 (ptpp) cc_final: 0.7123 (tppt) REVERT: C 377 LEU cc_start: 0.6394 (tt) cc_final: 0.5776 (tt) REVERT: C 400 MET cc_start: 0.7356 (tmm) cc_final: 0.6566 (tmm) REVERT: E 400 MET cc_start: 0.7692 (tmm) cc_final: 0.6740 (tmm) REVERT: F 48 ASN cc_start: 0.7630 (p0) cc_final: 0.7333 (p0) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.3739 time to fit residues: 206.6612 Evaluate side-chains 326 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 2.150 ------------------------------------------------------------------------------- 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: 5.9990 chunk 61 optimal weight: 0.0370 chunk 184 optimal weight: 9.9990 chunk 29 optimal weight: 40.0000 chunk 55 optimal weight: 7.9990 chunk 200 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 overall best weight: 5.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN D 345 HIS ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.152105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.141081 restraints weight = 181658.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.141850 restraints weight = 152721.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.142757 restraints weight = 130985.314| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 1.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20346 Z= 0.274 Angle : 0.950 11.850 27396 Z= 0.503 Chirality : 0.054 0.357 3084 Planarity : 0.007 0.069 3570 Dihedral : 7.660 35.758 2730 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 35.90 Ramachandran Plot: Outliers : 0.90 % Allowed : 16.71 % Favored : 82.39 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.15), residues: 2448 helix: -1.32 (0.17), residues: 708 sheet: -1.64 (0.29), residues: 306 loop : -3.74 (0.14), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.008 TRP F 76 HIS 0.004 0.001 HIS C 407 PHE 0.029 0.002 PHE D 143 TYR 0.030 0.002 TYR E 56 ARG 0.013 0.001 ARG B 380 =============================================================================== Job complete usr+sys time: 4509.64 seconds wall clock time: 82 minutes 14.82 seconds (4934.82 seconds total)