Starting phenix.real_space_refine on Fri Feb 16 13:31:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgl_23828/02_2024/7mgl_23828_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgl_23828/02_2024/7mgl_23828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgl_23828/02_2024/7mgl_23828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgl_23828/02_2024/7mgl_23828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgl_23828/02_2024/7mgl_23828_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgl_23828/02_2024/7mgl_23828_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 104 5.16 5 C 10132 2.51 5 N 2564 2.21 5 O 2672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 419": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15476 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3805 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 13, 'TRANS': 458} Chain breaks: 1 Chain: "B" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3805 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 13, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3805 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 13, 'TRANS': 458} Chain breaks: 1 Chain: "D" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3805 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 13, 'TRANS': 458} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'3PE': 1, 'ZB4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'3PE': 2, 'ZB4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'ZB4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'3PE': 1, 'ZB4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Time building chain proxies: 8.36, per 1000 atoms: 0.54 Number of scatterers: 15476 At special positions: 0 Unit cell: (112.86, 112.86, 110.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 4 15.00 O 2672 8.00 N 2564 7.00 C 10132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.04 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.04 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: 5.94 Conformation dependent library (CDL) restraints added in 2.8 seconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 4 sheets defined 58.9% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 64 through 105 removed outlier: 3.696A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 142 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 295 through 337 removed outlier: 4.312A pdb=" N LEU A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 337 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 349 No H-bonds generated for 'chain 'A' and resid 346 through 349' Processing helix chain 'A' and resid 353 through 377 removed outlier: 3.602A pdb=" N MET A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 405 removed outlier: 4.228A pdb=" N VAL A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 447 removed outlier: 3.852A pdb=" N LEU A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Proline residue: A 423 - end of helix Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.803A pdb=" N ASN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 483 removed outlier: 4.479A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 507 Processing helix chain 'A' and resid 510 through 524 Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 64 through 105 removed outlier: 3.695A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 142 Proline residue: B 140 - end of helix Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 295 through 337 removed outlier: 4.311A pdb=" N LEU B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 349 No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 353 through 377 removed outlier: 3.602A pdb=" N MET B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 377 " --> pdb=" O ILE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 405 removed outlier: 4.228A pdb=" N VAL B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE B 402 " --> pdb=" O TRP B 398 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 447 removed outlier: 3.852A pdb=" N LEU B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Proline residue: B 423 - end of helix Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 457 through 469 removed outlier: 3.802A pdb=" N ASN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 removed outlier: 4.479A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 507 Processing helix chain 'B' and resid 510 through 524 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 52 through 58 Processing helix chain 'C' and resid 64 through 105 removed outlier: 3.696A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 142 Proline residue: C 140 - end of helix Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 295 through 337 removed outlier: 4.312A pdb=" N LEU C 299 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN C 337 " --> pdb=" O PHE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 353 through 377 removed outlier: 3.602A pdb=" N MET C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 377 " --> pdb=" O ILE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 405 removed outlier: 4.228A pdb=" N VAL C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE C 402 " --> pdb=" O TRP C 398 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 447 removed outlier: 3.852A pdb=" N LEU C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Proline residue: C 423 - end of helix Processing helix chain 'C' and resid 452 through 454 No H-bonds generated for 'chain 'C' and resid 452 through 454' Processing helix chain 'C' and resid 457 through 469 removed outlier: 3.802A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 483 removed outlier: 4.479A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 507 Processing helix chain 'C' and resid 510 through 524 Processing helix chain 'D' and resid 41 through 49 Processing helix chain 'D' and resid 52 through 58 Processing helix chain 'D' and resid 64 through 105 removed outlier: 3.695A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 142 Proline residue: D 140 - end of helix Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 295 through 337 removed outlier: 4.312A pdb=" N LEU D 299 " --> pdb=" O ASN D 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 353 through 377 removed outlier: 3.601A pdb=" N MET D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 377 " --> pdb=" O ILE D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 405 removed outlier: 4.227A pdb=" N VAL D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 447 removed outlier: 3.851A pdb=" N LEU D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Proline residue: D 423 - end of helix Processing helix chain 'D' and resid 452 through 454 No H-bonds generated for 'chain 'D' and resid 452 through 454' Processing helix chain 'D' and resid 457 through 469 removed outlier: 3.802A pdb=" N ASN D 469 " --> pdb=" O PHE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 removed outlier: 4.481A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 507 Processing helix chain 'D' and resid 510 through 524 Processing sheet with id= A, first strand: chain 'A' and resid 188 through 195 removed outlier: 6.422A pdb=" N TYR A 170 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU A 228 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 188 through 195 removed outlier: 6.422A pdb=" N TYR B 170 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU B 228 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 188 through 195 removed outlier: 6.422A pdb=" N TYR C 170 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU C 228 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 188 through 195 removed outlier: 6.422A pdb=" N TYR D 170 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU D 228 " --> pdb=" O TYR D 170 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4738 1.34 - 1.46: 3917 1.46 - 1.58: 7041 1.58 - 1.71: 8 1.71 - 1.83: 156 Bond restraints: 15860 Sorted by residual: bond pdb=" O02 ZB4 D 601 " pdb=" S01 ZB4 D 601 " ideal model delta sigma weight residual 1.454 1.779 -0.325 2.00e-02 2.50e+03 2.63e+02 bond pdb=" O02 ZB4 C 900 " pdb=" S01 ZB4 C 900 " ideal model delta sigma weight residual 1.454 1.778 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" O02 ZB4 A 601 " pdb=" S01 ZB4 A 601 " ideal model delta sigma weight residual 1.454 1.778 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" O02 ZB4 B 601 " pdb=" S01 ZB4 B 601 " ideal model delta sigma weight residual 1.454 1.778 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" O01 ZB4 B 601 " pdb=" S01 ZB4 B 601 " ideal model delta sigma weight residual 1.454 1.769 -0.315 2.00e-02 2.50e+03 2.48e+02 ... (remaining 15855 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.77: 376 106.77 - 113.59: 8717 113.59 - 120.42: 6470 120.42 - 127.24: 5781 127.24 - 134.06: 152 Bond angle restraints: 21496 Sorted by residual: angle pdb=" C GLU C 249 " pdb=" N ILE C 250 " pdb=" CA ILE C 250 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.15e+01 angle pdb=" C18 ZB4 C 900 " pdb=" O03 ZB4 C 900 " pdb=" C23 ZB4 C 900 " ideal model delta sigma weight residual 118.87 106.41 12.46 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C18 ZB4 A 601 " pdb=" O03 ZB4 A 601 " pdb=" C23 ZB4 A 601 " ideal model delta sigma weight residual 118.87 106.42 12.45 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C18 ZB4 D 601 " pdb=" O03 ZB4 D 601 " pdb=" C23 ZB4 D 601 " ideal model delta sigma weight residual 118.87 106.44 12.43 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C18 ZB4 B 601 " pdb=" O03 ZB4 B 601 " pdb=" C23 ZB4 B 601 " ideal model delta sigma weight residual 118.87 106.47 12.40 3.00e+00 1.11e-01 1.71e+01 ... (remaining 21491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 8129 17.01 - 34.03: 928 34.03 - 51.04: 223 51.04 - 68.06: 64 68.06 - 85.07: 24 Dihedral angle restraints: 9368 sinusoidal: 3840 harmonic: 5528 Sorted by residual: dihedral pdb=" CB CYS B 253 " pdb=" SG CYS B 253 " pdb=" SG CYS B 284 " pdb=" CB CYS B 284 " ideal model delta sinusoidal sigma weight residual 93.00 21.90 71.10 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS D 253 " pdb=" SG CYS D 253 " pdb=" SG CYS D 284 " pdb=" CB CYS D 284 " ideal model delta sinusoidal sigma weight residual 93.00 21.91 71.09 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS A 253 " pdb=" SG CYS A 253 " pdb=" SG CYS A 284 " pdb=" CB CYS A 284 " ideal model delta sinusoidal sigma weight residual 93.00 21.93 71.07 1 1.00e+01 1.00e-02 6.49e+01 ... (remaining 9365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2111 0.064 - 0.128: 304 0.128 - 0.191: 13 0.191 - 0.255: 0 0.255 - 0.319: 4 Chirality restraints: 2432 Sorted by residual: chirality pdb=" C07 ZB4 C 900 " pdb=" C08 ZB4 C 900 " pdb=" C12 ZB4 C 900 " pdb=" N01 ZB4 C 900 " both_signs ideal model delta sigma weight residual False -2.52 -2.84 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C07 ZB4 A 601 " pdb=" C08 ZB4 A 601 " pdb=" C12 ZB4 A 601 " pdb=" N01 ZB4 A 601 " both_signs ideal model delta sigma weight residual False -2.52 -2.84 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C07 ZB4 B 601 " pdb=" C08 ZB4 B 601 " pdb=" C12 ZB4 B 601 " pdb=" N01 ZB4 B 601 " both_signs ideal model delta sigma weight residual False -2.52 -2.84 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 2429 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 62 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO C 63 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 63 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 62 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO B 63 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 63 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 62 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO D 63 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 63 " -0.029 5.00e-02 4.00e+02 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 641 2.72 - 3.27: 15312 3.27 - 3.81: 24826 3.81 - 4.36: 30512 4.36 - 4.90: 52221 Nonbonded interactions: 123512 Sorted by model distance: nonbonded pdb=" NH2 ARG C 455 " pdb=" OE2 GLU D 95 " model vdw 2.177 2.520 nonbonded pdb=" OD1 ASP D 134 " pdb=" OH TYR D 218 " model vdw 2.261 2.440 nonbonded pdb=" OD1 ASP A 134 " pdb=" OH TYR A 218 " model vdw 2.261 2.440 nonbonded pdb=" OD1 ASP C 134 " pdb=" OH TYR C 218 " model vdw 2.261 2.440 nonbonded pdb=" OD1 ASP B 134 " pdb=" OH TYR B 218 " model vdw 2.261 2.440 ... (remaining 123507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 526 or resid 601)) selection = (chain 'B' and (resid 40 through 526 or resid 601)) selection = chain 'C' selection = (chain 'D' and (resid 40 through 526 or resid 601)) } 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 individual isotropic 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.770 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 41.880 Find NCS groups from input model: 1.170 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:16.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.013 0.325 15860 Z= 0.847 Angle : 0.837 12.461 21496 Z= 0.425 Chirality : 0.044 0.319 2432 Planarity : 0.004 0.053 2640 Dihedral : 15.845 85.074 5784 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.10 % Allowed : 4.52 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.17), residues: 1872 helix: 0.19 (0.14), residues: 1112 sheet: -1.09 (0.37), residues: 196 loop : -2.94 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 398 HIS 0.005 0.001 HIS B 451 PHE 0.011 0.001 PHE D 83 TYR 0.024 0.002 TYR A 254 ARG 0.003 0.000 ARG D 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 203 time to evaluate : 1.756 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.5737 (mtpt) REVERT: A 174 HIS cc_start: 0.7357 (m170) cc_final: 0.6506 (t-90) REVERT: A 283 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6594 (mm-30) REVERT: A 322 ARG cc_start: 0.6226 (ttp-170) cc_final: 0.5941 (ttm170) REVERT: B 46 LYS cc_start: 0.6809 (OUTLIER) cc_final: 0.6089 (mmmt) REVERT: B 89 LEU cc_start: 0.8184 (tp) cc_final: 0.7979 (tm) REVERT: B 168 ARG cc_start: 0.6510 (mtm110) cc_final: 0.6215 (mtt180) REVERT: B 276 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7456 (mp0) REVERT: B 283 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6621 (mm-30) REVERT: B 322 ARG cc_start: 0.6304 (ttp-170) cc_final: 0.6014 (ttp-110) REVERT: C 46 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6100 (mmmt) REVERT: C 89 LEU cc_start: 0.8086 (tp) cc_final: 0.7853 (tm) REVERT: C 168 ARG cc_start: 0.6302 (mtm110) cc_final: 0.5983 (mtt90) REVERT: C 322 ARG cc_start: 0.6309 (ttp-170) cc_final: 0.6098 (ttp-110) REVERT: D 46 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6082 (mmmt) REVERT: D 89 LEU cc_start: 0.8137 (tp) cc_final: 0.7900 (tm) REVERT: D 168 ARG cc_start: 0.6494 (mtm110) cc_final: 0.6210 (mtt180) REVERT: D 176 ASP cc_start: 0.7190 (t0) cc_final: 0.6924 (t70) outliers start: 52 outliers final: 5 residues processed: 243 average time/residue: 1.1441 time to fit residues: 310.8070 Evaluate side-chains 141 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain D residue 46 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 6.9990 chunk 142 optimal weight: 0.0060 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.0070 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 147 optimal weight: 0.0970 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.3412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 243 GLN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS B 131 HIS B 243 GLN B 286 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS C 194 GLN C 243 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 481 GLN D 69 GLN D 194 GLN D 243 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 495 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15860 Z= 0.147 Angle : 0.541 8.734 21496 Z= 0.279 Chirality : 0.039 0.141 2432 Planarity : 0.004 0.040 2640 Dihedral : 10.469 79.342 2338 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.85 % Allowed : 10.95 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.20), residues: 1872 helix: 1.91 (0.15), residues: 1108 sheet: -0.45 (0.38), residues: 196 loop : -2.30 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 398 HIS 0.005 0.001 HIS A 451 PHE 0.012 0.001 PHE D 350 TYR 0.011 0.001 TYR C 436 ARG 0.003 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.706 Fit side-chains revert: symmetry clash REVERT: A 174 HIS cc_start: 0.7200 (m170) cc_final: 0.6434 (t-90) REVERT: A 222 THR cc_start: 0.8550 (m) cc_final: 0.8347 (m) REVERT: A 283 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6543 (mm-30) REVERT: A 322 ARG cc_start: 0.6193 (ttp-170) cc_final: 0.5927 (ttm170) REVERT: A 456 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8346 (p) REVERT: B 322 ARG cc_start: 0.6284 (ttp-170) cc_final: 0.5886 (ttp-110) REVERT: C 168 ARG cc_start: 0.6064 (mtm110) cc_final: 0.5792 (mtt180) REVERT: C 322 ARG cc_start: 0.6242 (ttp-170) cc_final: 0.5925 (ttp-110) REVERT: D 168 ARG cc_start: 0.6218 (mtm110) cc_final: 0.5934 (mtt180) REVERT: D 176 ASP cc_start: 0.7062 (t0) cc_final: 0.6862 (t70) REVERT: D 322 ARG cc_start: 0.6084 (ttp-170) cc_final: 0.5779 (ttp-110) outliers start: 31 outliers final: 12 residues processed: 194 average time/residue: 1.0043 time to fit residues: 221.1632 Evaluate side-chains 153 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 0.4980 chunk 142 optimal weight: 0.1980 chunk 116 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 169 optimal weight: 0.2980 chunk 58 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 495 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN D 97 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15860 Z= 0.189 Angle : 0.550 8.693 21496 Z= 0.283 Chirality : 0.040 0.174 2432 Planarity : 0.004 0.040 2640 Dihedral : 9.624 69.094 2317 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.38 % Allowed : 11.37 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1872 helix: 2.41 (0.15), residues: 1104 sheet: 0.01 (0.38), residues: 204 loop : -2.08 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 398 HIS 0.008 0.001 HIS A 451 PHE 0.014 0.001 PHE B 182 TYR 0.019 0.001 TYR D 436 ARG 0.004 0.000 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 1.825 Fit side-chains revert: symmetry clash REVERT: A 174 HIS cc_start: 0.7250 (m170) cc_final: 0.6221 (t-90) REVERT: A 371 MET cc_start: 0.7771 (mtp) cc_final: 0.7569 (mtt) REVERT: B 44 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6874 (mtp85) REVERT: B 322 ARG cc_start: 0.6292 (ttp-170) cc_final: 0.5922 (ttp-110) REVERT: B 467 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8731 (mt) REVERT: C 168 ARG cc_start: 0.6161 (mtm110) cc_final: 0.5854 (mtt180) REVERT: C 322 ARG cc_start: 0.6290 (ttp-170) cc_final: 0.5990 (ttp-110) REVERT: C 467 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8720 (mt) REVERT: D 50 MET cc_start: 0.8119 (mtt) cc_final: 0.7888 (mtm) REVERT: D 168 ARG cc_start: 0.6247 (mtm110) cc_final: 0.5849 (mpt-90) REVERT: D 176 ASP cc_start: 0.7065 (t0) cc_final: 0.6802 (t70) REVERT: D 276 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: D 322 ARG cc_start: 0.6068 (ttp-170) cc_final: 0.5765 (ttp-110) REVERT: D 467 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8708 (mt) outliers start: 40 outliers final: 15 residues processed: 182 average time/residue: 0.9446 time to fit residues: 195.9520 Evaluate side-chains 151 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 495 GLN B 97 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS C 97 ASN C 286 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15860 Z= 0.216 Angle : 0.569 10.823 21496 Z= 0.291 Chirality : 0.041 0.212 2432 Planarity : 0.003 0.040 2640 Dihedral : 8.997 67.481 2316 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.39 % Allowed : 11.90 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.20), residues: 1872 helix: 2.52 (0.15), residues: 1104 sheet: 0.15 (0.38), residues: 204 loop : -1.94 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 398 HIS 0.009 0.001 HIS A 451 PHE 0.014 0.001 PHE A 182 TYR 0.018 0.001 TYR C 254 ARG 0.003 0.000 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 144 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 HIS cc_start: 0.7163 (m170) cc_final: 0.5942 (t-90) REVERT: A 322 ARG cc_start: 0.6571 (ttp-110) cc_final: 0.6328 (ttp-170) REVERT: A 371 MET cc_start: 0.7853 (mtp) cc_final: 0.7642 (mtt) REVERT: B 89 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7812 (tm) REVERT: B 322 ARG cc_start: 0.6324 (ttp-170) cc_final: 0.5946 (ttp-110) REVERT: B 467 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8709 (mt) REVERT: C 89 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7787 (tm) REVERT: C 168 ARG cc_start: 0.6307 (mtm110) cc_final: 0.5737 (mtt90) REVERT: C 322 ARG cc_start: 0.6273 (ttp-170) cc_final: 0.5974 (ttp-110) REVERT: C 467 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8705 (mt) REVERT: D 44 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6821 (mtt-85) REVERT: D 89 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7806 (tm) REVERT: D 168 ARG cc_start: 0.6283 (mtm110) cc_final: 0.5856 (mpt-90) REVERT: D 276 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: D 322 ARG cc_start: 0.6126 (ttp-170) cc_final: 0.5787 (ttp-110) REVERT: D 467 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8707 (mt) outliers start: 57 outliers final: 27 residues processed: 193 average time/residue: 0.9404 time to fit residues: 207.2953 Evaluate side-chains 168 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15860 Z= 0.219 Angle : 0.579 13.918 21496 Z= 0.293 Chirality : 0.041 0.244 2432 Planarity : 0.003 0.041 2640 Dihedral : 8.942 65.400 2316 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.39 % Allowed : 12.62 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.20), residues: 1872 helix: 2.58 (0.15), residues: 1104 sheet: 0.24 (0.38), residues: 204 loop : -1.86 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 398 HIS 0.009 0.001 HIS A 451 PHE 0.014 0.001 PHE C 182 TYR 0.017 0.001 TYR D 436 ARG 0.003 0.000 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 138 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7742 (tm) REVERT: A 371 MET cc_start: 0.7834 (mtp) cc_final: 0.7624 (mtt) REVERT: B 322 ARG cc_start: 0.6328 (ttp-170) cc_final: 0.5951 (ttp-110) REVERT: B 467 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8712 (mt) REVERT: C 168 ARG cc_start: 0.6305 (mtm110) cc_final: 0.5853 (mpt-90) REVERT: C 276 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6214 (mp0) REVERT: C 322 ARG cc_start: 0.6235 (ttp-170) cc_final: 0.5841 (ttp-110) REVERT: C 467 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8707 (mt) REVERT: D 44 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6788 (mtt-85) REVERT: D 168 ARG cc_start: 0.6250 (mtm110) cc_final: 0.5837 (mpt-90) REVERT: D 276 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6286 (mp0) REVERT: D 322 ARG cc_start: 0.6168 (ttp-170) cc_final: 0.5830 (ttp-110) REVERT: D 467 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8708 (mt) outliers start: 57 outliers final: 31 residues processed: 183 average time/residue: 1.0364 time to fit residues: 215.9974 Evaluate side-chains 173 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15860 Z= 0.205 Angle : 0.589 13.955 21496 Z= 0.299 Chirality : 0.041 0.265 2432 Planarity : 0.003 0.041 2640 Dihedral : 8.991 63.640 2316 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.39 % Allowed : 12.86 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1872 helix: 2.44 (0.15), residues: 1136 sheet: 0.07 (0.39), residues: 196 loop : -2.08 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 398 HIS 0.008 0.001 HIS A 451 PHE 0.013 0.001 PHE B 182 TYR 0.015 0.001 TYR D 436 ARG 0.003 0.000 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 138 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7740 (tm) REVERT: A 285 LYS cc_start: 0.6622 (mptt) cc_final: 0.6285 (mptt) REVERT: A 322 ARG cc_start: 0.6523 (ttp-110) cc_final: 0.6313 (ttp80) REVERT: A 371 MET cc_start: 0.7787 (mtp) cc_final: 0.7579 (mtt) REVERT: B 44 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6822 (mtp85) REVERT: B 89 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7737 (tm) REVERT: B 285 LYS cc_start: 0.6557 (mptt) cc_final: 0.6119 (mptt) REVERT: C 89 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7719 (tm) REVERT: C 168 ARG cc_start: 0.6227 (mtm110) cc_final: 0.5820 (mpt-90) REVERT: C 276 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6135 (mp0) REVERT: C 285 LYS cc_start: 0.6639 (mptt) cc_final: 0.6224 (mptt) REVERT: C 322 ARG cc_start: 0.6266 (ttp-170) cc_final: 0.5888 (ttp-110) REVERT: D 44 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6711 (mtt180) REVERT: D 89 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7714 (tm) REVERT: D 168 ARG cc_start: 0.6222 (mtm110) cc_final: 0.5824 (mpt-90) REVERT: D 276 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6174 (mp0) REVERT: D 285 LYS cc_start: 0.6577 (mptt) cc_final: 0.6193 (mptt) REVERT: D 322 ARG cc_start: 0.6184 (ttp-170) cc_final: 0.5789 (ttp-110) REVERT: D 467 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8719 (mt) outliers start: 57 outliers final: 35 residues processed: 183 average time/residue: 0.9979 time to fit residues: 207.5384 Evaluate side-chains 174 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 130 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15860 Z= 0.185 Angle : 0.566 12.941 21496 Z= 0.287 Chirality : 0.040 0.262 2432 Planarity : 0.003 0.041 2640 Dihedral : 8.728 59.322 2316 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.86 % Allowed : 14.05 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.20), residues: 1872 helix: 2.52 (0.15), residues: 1136 sheet: 0.33 (0.40), residues: 196 loop : -2.01 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 398 HIS 0.008 0.001 HIS A 451 PHE 0.014 0.001 PHE B 182 TYR 0.014 0.001 TYR C 436 ARG 0.003 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 133 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.5357 (OUTLIER) cc_final: 0.4213 (mmt) REVERT: A 89 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7717 (tm) REVERT: A 322 ARG cc_start: 0.6549 (ttp-110) cc_final: 0.6345 (ttp80) REVERT: A 452 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8015 (m) REVERT: A 456 SER cc_start: 0.8809 (OUTLIER) cc_final: 0.8504 (p) REVERT: B 89 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7714 (tm) REVERT: B 480 MET cc_start: 0.7766 (mmp) cc_final: 0.7356 (mmp) REVERT: C 89 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7685 (tm) REVERT: C 168 ARG cc_start: 0.6218 (mtm110) cc_final: 0.5801 (mpt-90) REVERT: C 285 LYS cc_start: 0.6490 (mptt) cc_final: 0.6269 (mptt) REVERT: C 322 ARG cc_start: 0.6273 (ttp-170) cc_final: 0.5919 (ttp-110) REVERT: D 89 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7678 (tm) REVERT: D 168 ARG cc_start: 0.6218 (mtm110) cc_final: 0.5819 (mpt-90) REVERT: D 276 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6220 (mp0) REVERT: D 285 LYS cc_start: 0.6579 (mptt) cc_final: 0.6331 (mptt) REVERT: D 322 ARG cc_start: 0.6162 (ttp-170) cc_final: 0.5795 (ttp-110) outliers start: 48 outliers final: 30 residues processed: 169 average time/residue: 1.0806 time to fit residues: 205.8761 Evaluate side-chains 162 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15860 Z= 0.201 Angle : 0.599 13.498 21496 Z= 0.301 Chirality : 0.041 0.270 2432 Planarity : 0.003 0.041 2640 Dihedral : 8.516 59.846 2316 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.80 % Allowed : 14.35 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.20), residues: 1872 helix: 2.53 (0.15), residues: 1136 sheet: 0.40 (0.40), residues: 204 loop : -1.98 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 398 HIS 0.008 0.001 HIS B 451 PHE 0.015 0.001 PHE B 182 TYR 0.015 0.001 TYR A 436 ARG 0.002 0.000 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 127 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.5434 (OUTLIER) cc_final: 0.4261 (mmt) REVERT: A 89 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7706 (tm) REVERT: A 322 ARG cc_start: 0.6560 (ttp-110) cc_final: 0.6358 (ttp80) REVERT: B 89 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7738 (tm) REVERT: B 480 MET cc_start: 0.7788 (mmp) cc_final: 0.7444 (mmp) REVERT: C 89 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7712 (tm) REVERT: C 168 ARG cc_start: 0.6181 (mtm110) cc_final: 0.5786 (mpt-90) REVERT: C 322 ARG cc_start: 0.6245 (ttp-170) cc_final: 0.5899 (ttp-110) REVERT: C 480 MET cc_start: 0.7770 (mmp) cc_final: 0.7329 (mmp) REVERT: D 89 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7703 (tm) REVERT: D 168 ARG cc_start: 0.6225 (mtm110) cc_final: 0.5786 (mpt-90) REVERT: D 276 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6218 (mp0) REVERT: D 322 ARG cc_start: 0.6163 (ttp-170) cc_final: 0.5797 (ttp-110) outliers start: 47 outliers final: 37 residues processed: 164 average time/residue: 1.1572 time to fit residues: 216.5843 Evaluate side-chains 167 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 178 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15860 Z= 0.195 Angle : 0.593 12.661 21496 Z= 0.298 Chirality : 0.040 0.251 2432 Planarity : 0.003 0.040 2640 Dihedral : 8.161 56.892 2316 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.80 % Allowed : 14.52 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.20), residues: 1872 helix: 2.56 (0.15), residues: 1136 sheet: 0.51 (0.41), residues: 196 loop : -2.00 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 398 HIS 0.009 0.001 HIS A 451 PHE 0.015 0.001 PHE B 182 TYR 0.014 0.001 TYR A 436 ARG 0.002 0.000 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 124 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.5390 (OUTLIER) cc_final: 0.4210 (mmt) REVERT: A 89 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7676 (tm) REVERT: A 187 MET cc_start: 0.7324 (tmm) cc_final: 0.7123 (tmt) REVERT: A 322 ARG cc_start: 0.6542 (ttp-110) cc_final: 0.6341 (ttp80) REVERT: A 452 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8002 (m) REVERT: A 480 MET cc_start: 0.7838 (mmp) cc_final: 0.7479 (mmp) REVERT: B 89 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7726 (tm) REVERT: B 322 ARG cc_start: 0.6438 (ttp-110) cc_final: 0.6221 (ttp-170) REVERT: B 452 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.7999 (m) REVERT: B 480 MET cc_start: 0.7830 (mmp) cc_final: 0.7455 (mmp) REVERT: C 89 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7697 (tm) REVERT: C 168 ARG cc_start: 0.6199 (mtm110) cc_final: 0.5807 (mpt-90) REVERT: C 322 ARG cc_start: 0.6252 (ttp-170) cc_final: 0.5913 (ttp-110) REVERT: C 480 MET cc_start: 0.7753 (mmp) cc_final: 0.7337 (mmp) REVERT: D 89 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7679 (tm) REVERT: D 168 ARG cc_start: 0.6207 (mtm110) cc_final: 0.5838 (mpt-90) REVERT: D 276 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: D 322 ARG cc_start: 0.6152 (ttp-170) cc_final: 0.5797 (ttp-110) outliers start: 47 outliers final: 36 residues processed: 159 average time/residue: 1.0355 time to fit residues: 186.6306 Evaluate side-chains 166 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 122 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15860 Z= 0.308 Angle : 0.668 13.849 21496 Z= 0.335 Chirality : 0.043 0.264 2432 Planarity : 0.004 0.039 2640 Dihedral : 8.398 58.309 2316 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.86 % Allowed : 14.35 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1872 helix: 2.39 (0.15), residues: 1136 sheet: 0.43 (0.41), residues: 196 loop : -2.07 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 491 HIS 0.011 0.001 HIS A 451 PHE 0.015 0.001 PHE B 182 TYR 0.018 0.002 TYR A 436 ARG 0.003 0.000 ARG A 455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 126 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.5696 (OUTLIER) cc_final: 0.4660 (mmt) REVERT: A 89 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7758 (tm) REVERT: B 89 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7770 (tm) REVERT: C 89 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7742 (tm) REVERT: C 168 ARG cc_start: 0.6293 (mtm110) cc_final: 0.5859 (mpt-90) REVERT: C 276 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7325 (mp0) REVERT: D 89 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7735 (tm) REVERT: D 168 ARG cc_start: 0.6318 (mtm110) cc_final: 0.5862 (mpt-90) REVERT: D 276 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6320 (mp0) REVERT: D 322 ARG cc_start: 0.6121 (ttp-170) cc_final: 0.5746 (ttp-110) outliers start: 48 outliers final: 37 residues processed: 163 average time/residue: 1.1792 time to fit residues: 216.1701 Evaluate side-chains 166 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 123 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 27 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.162274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.117344 restraints weight = 16187.032| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.83 r_work: 0.3003 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15860 Z= 0.238 Angle : 0.630 13.707 21496 Z= 0.316 Chirality : 0.042 0.258 2432 Planarity : 0.004 0.040 2640 Dihedral : 8.179 59.385 2316 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.62 % Allowed : 14.46 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.20), residues: 1872 helix: 2.44 (0.15), residues: 1136 sheet: 0.49 (0.41), residues: 196 loop : -2.05 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 398 HIS 0.010 0.001 HIS A 451 PHE 0.014 0.001 PHE C 182 TYR 0.016 0.001 TYR A 436 ARG 0.002 0.000 ARG C 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4558.82 seconds wall clock time: 82 minutes 38.41 seconds (4958.41 seconds total)