Starting phenix.real_space_refine on Thu Aug 8 13:23:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzl_36746/08_2024/8jzl_36746.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzl_36746/08_2024/8jzl_36746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzl_36746/08_2024/8jzl_36746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzl_36746/08_2024/8jzl_36746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzl_36746/08_2024/8jzl_36746.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzl_36746/08_2024/8jzl_36746.cif" } resolution = 2.62 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= 0.007 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 90 5.16 5 C 14538 2.51 5 N 4212 2.21 5 O 4344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 138": "NH1" <-> "NH2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 138": "NH1" <-> "NH2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 381": "OE1" <-> "OE2" Residue "C TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 381": "OE1" <-> "OE2" Residue "D TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 138": "NH1" <-> "NH2" Residue "E TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 138": "NH1" <-> "NH2" Residue "F TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 381": "OE1" <-> "OE2" Residue "F TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23184 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3864 Classifications: {'peptide': 498} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 478} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3864 Classifications: {'peptide': 498} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 478} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3864 Classifications: {'peptide': 498} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 478} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3864 Classifications: {'peptide': 498} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 478} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3864 Classifications: {'peptide': 498} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 478} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3864 Classifications: {'peptide': 498} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 478} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 13.88, per 1000 atoms: 0.60 Number of scatterers: 23184 At special positions: 0 Unit cell: (156.782, 144.896, 125.086, 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 90 16.00 O 4344 8.00 N 4212 7.00 C 14538 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: 8.58 Conformation dependent library (CDL) restraints added in 3.9 seconds 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 12 sheets defined 56.0% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 72 through 92 removed outlier: 3.588A pdb=" N LEU A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 81 " --> pdb=" O TYR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 169 removed outlier: 3.518A pdb=" N GLN A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 280 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.623A pdb=" N SER A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 406 Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.770A pdb=" N ARG A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 483 removed outlier: 3.848A pdb=" N GLN A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 509 removed outlier: 3.631A pdb=" N LEU A 507 " --> pdb=" O GLN A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 520 Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.596A pdb=" N ASN A 536 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 4.131A pdb=" N ARG A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 555 through 559 removed outlier: 3.752A pdb=" N ILE A 559 " --> pdb=" O SER A 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 92 removed outlier: 3.588A pdb=" N LEU B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 143 removed outlier: 4.648A pdb=" N LYS B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 169 removed outlier: 3.519A pdb=" N GLN B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 280 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 371 through 388 removed outlier: 3.624A pdb=" N SER B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 406 Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 430 through 433 Processing helix chain 'B' and resid 439 through 452 removed outlier: 3.770A pdb=" N ARG B 444 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 483 removed outlier: 3.848A pdb=" N GLN B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.632A pdb=" N LEU B 507 " --> pdb=" O GLN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 520 Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.595A pdb=" N ASN B 536 " --> pdb=" O GLU B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 4.131A pdb=" N ARG B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 553 Processing helix chain 'B' and resid 555 through 559 removed outlier: 3.752A pdb=" N ILE B 559 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 92 removed outlier: 3.588A pdb=" N LEU C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG C 81 " --> pdb=" O TYR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LYS C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 169 removed outlier: 3.519A pdb=" N GLN C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 280 Processing helix chain 'C' and resid 281 through 290 Processing helix chain 'C' and resid 312 through 328 removed outlier: 3.726A pdb=" N MET C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 371 through 388 removed outlier: 3.624A pdb=" N SER C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 406 Processing helix chain 'C' and resid 411 through 429 Processing helix chain 'C' and resid 430 through 433 Processing helix chain 'C' and resid 439 through 452 removed outlier: 3.771A pdb=" N ARG C 444 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 483 removed outlier: 3.849A pdb=" N GLN C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.632A pdb=" N LEU C 507 " --> pdb=" O GLN C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 520 Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.595A pdb=" N ASN C 536 " --> pdb=" O GLU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 removed outlier: 4.130A pdb=" N ARG C 542 " --> pdb=" O SER C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 553 Processing helix chain 'C' and resid 555 through 559 removed outlier: 3.752A pdb=" N ILE C 559 " --> pdb=" O SER C 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 92 removed outlier: 3.587A pdb=" N LEU D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG D 81 " --> pdb=" O TYR D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LYS D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 169 removed outlier: 3.519A pdb=" N GLN D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 280 Processing helix chain 'D' and resid 281 through 290 Processing helix chain 'D' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET D 316 " --> pdb=" O LYS D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 371 through 388 removed outlier: 3.623A pdb=" N SER D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU D 381 " --> pdb=" O SER D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 406 Processing helix chain 'D' and resid 411 through 429 Processing helix chain 'D' and resid 430 through 433 Processing helix chain 'D' and resid 439 through 452 removed outlier: 3.771A pdb=" N ARG D 444 " --> pdb=" O LYS D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 483 removed outlier: 3.850A pdb=" N GLN D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 509 removed outlier: 3.631A pdb=" N LEU D 507 " --> pdb=" O GLN D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 520 Processing helix chain 'D' and resid 532 through 536 removed outlier: 3.595A pdb=" N ASN D 536 " --> pdb=" O GLU D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 removed outlier: 4.130A pdb=" N ARG D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 553 Processing helix chain 'D' and resid 555 through 559 removed outlier: 3.752A pdb=" N ILE D 559 " --> pdb=" O SER D 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 92 removed outlier: 3.589A pdb=" N LEU E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG E 81 " --> pdb=" O TYR E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS E 128 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 169 removed outlier: 3.518A pdb=" N GLN E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 280 Processing helix chain 'E' and resid 281 through 290 Processing helix chain 'E' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET E 316 " --> pdb=" O LYS E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 371 through 388 removed outlier: 3.624A pdb=" N SER E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 406 Processing helix chain 'E' and resid 411 through 429 Processing helix chain 'E' and resid 430 through 433 Processing helix chain 'E' and resid 439 through 452 removed outlier: 3.770A pdb=" N ARG E 444 " --> pdb=" O LYS E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 483 removed outlier: 3.849A pdb=" N GLN E 483 " --> pdb=" O ILE E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 509 removed outlier: 3.632A pdb=" N LEU E 507 " --> pdb=" O GLN E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 520 Processing helix chain 'E' and resid 532 through 536 removed outlier: 3.595A pdb=" N ASN E 536 " --> pdb=" O GLU E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 543 removed outlier: 4.131A pdb=" N ARG E 542 " --> pdb=" O SER E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 553 Processing helix chain 'E' and resid 555 through 559 removed outlier: 3.753A pdb=" N ILE E 559 " --> pdb=" O SER E 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 92 removed outlier: 3.589A pdb=" N LEU F 76 " --> pdb=" O SER F 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG F 81 " --> pdb=" O TYR F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 169 removed outlier: 3.518A pdb=" N GLN F 169 " --> pdb=" O GLN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 280 Processing helix chain 'F' and resid 281 through 290 Processing helix chain 'F' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET F 316 " --> pdb=" O LYS F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 371 through 388 removed outlier: 3.623A pdb=" N SER F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU F 381 " --> pdb=" O SER F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 406 Processing helix chain 'F' and resid 411 through 429 Processing helix chain 'F' and resid 430 through 433 Processing helix chain 'F' and resid 439 through 452 removed outlier: 3.771A pdb=" N ARG F 444 " --> pdb=" O LYS F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 483 removed outlier: 3.849A pdb=" N GLN F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 509 removed outlier: 3.631A pdb=" N LEU F 507 " --> pdb=" O GLN F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 520 Processing helix chain 'F' and resid 532 through 536 removed outlier: 3.594A pdb=" N ASN F 536 " --> pdb=" O GLU F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 4.131A pdb=" N ARG F 542 " --> pdb=" O SER F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 553 Processing helix chain 'F' and resid 555 through 559 removed outlier: 3.753A pdb=" N ILE F 559 " --> pdb=" O SER F 556 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 180 removed outlier: 5.071A pdb=" N HIS A 184 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 233 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR A 241 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU A 235 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 294 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP A 353 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 296 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA A 355 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 298 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE A 357 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER A 300 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 197 removed outlier: 3.902A pdb=" N ILE A 197 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 200 " --> pdb=" O ILE A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 174 through 180 removed outlier: 5.070A pdb=" N HIS B 184 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B 233 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR B 241 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU B 235 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 294 " --> pdb=" O LYS B 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP B 353 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 296 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA B 355 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 298 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE B 357 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 300 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 196 through 197 removed outlier: 3.901A pdb=" N ILE B 197 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS B 200 " --> pdb=" O ILE B 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 174 through 180 removed outlier: 5.071A pdb=" N HIS C 184 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL C 233 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR C 241 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU C 235 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 294 " --> pdb=" O LYS C 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP C 353 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 296 " --> pdb=" O ASP C 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA C 355 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 298 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE C 357 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 300 " --> pdb=" O PHE C 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 196 through 197 removed outlier: 3.901A pdb=" N ILE C 197 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS C 200 " --> pdb=" O ILE C 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 174 through 180 removed outlier: 5.070A pdb=" N HIS D 184 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 233 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR D 241 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU D 235 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL D 294 " --> pdb=" O LYS D 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP D 353 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU D 296 " --> pdb=" O ASP D 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA D 355 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU D 298 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE D 357 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER D 300 " --> pdb=" O PHE D 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 196 through 197 removed outlier: 3.902A pdb=" N ILE D 197 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS D 200 " --> pdb=" O ILE D 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 174 through 180 removed outlier: 5.070A pdb=" N HIS E 184 " --> pdb=" O HIS E 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 233 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR E 241 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU E 235 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL E 294 " --> pdb=" O LYS E 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP E 353 " --> pdb=" O VAL E 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU E 296 " --> pdb=" O ASP E 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA E 355 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU E 298 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE E 357 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER E 300 " --> pdb=" O PHE E 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 196 through 197 removed outlier: 3.902A pdb=" N ILE E 197 " --> pdb=" O LYS E 200 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS E 200 " --> pdb=" O ILE E 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 174 through 180 removed outlier: 5.071A pdb=" N HIS F 184 " --> pdb=" O HIS F 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL F 233 " --> pdb=" O THR F 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR F 241 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU F 235 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL F 294 " --> pdb=" O LYS F 351 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASP F 353 " --> pdb=" O VAL F 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU F 296 " --> pdb=" O ASP F 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA F 355 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU F 298 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE F 357 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER F 300 " --> pdb=" O PHE F 357 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 196 through 197 removed outlier: 3.901A pdb=" N ILE F 197 " --> pdb=" O LYS F 200 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS F 200 " --> pdb=" O ILE F 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1320 hydrogen bonds defined for protein. 3816 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: 7.50 Time building geometry restraints manager: 9.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7772 1.33 - 1.45: 2449 1.45 - 1.57: 13245 1.57 - 1.68: 0 1.68 - 1.80: 162 Bond restraints: 23628 Sorted by residual: bond pdb=" C LEU E 251 " pdb=" N SER E 252 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.59e-02 3.96e+03 4.75e+00 bond pdb=" C LEU D 251 " pdb=" N SER D 252 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.59e-02 3.96e+03 4.73e+00 bond pdb=" C LEU A 251 " pdb=" N SER A 252 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.59e-02 3.96e+03 4.73e+00 bond pdb=" C LEU F 251 " pdb=" N SER F 252 " ideal model delta sigma weight residual 1.333 1.298 0.034 1.59e-02 3.96e+03 4.70e+00 bond pdb=" C LEU C 251 " pdb=" N SER C 252 " ideal model delta sigma weight residual 1.333 1.298 0.034 1.59e-02 3.96e+03 4.70e+00 ... (remaining 23623 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.55: 690 106.55 - 113.46: 13616 113.46 - 120.37: 8742 120.37 - 127.28: 8554 127.28 - 134.19: 342 Bond angle restraints: 31944 Sorted by residual: angle pdb=" C LEU F 76 " pdb=" N TYR F 77 " pdb=" CA TYR F 77 " ideal model delta sigma weight residual 120.82 125.22 -4.40 1.50e+00 4.44e-01 8.59e+00 angle pdb=" C LEU C 76 " pdb=" N TYR C 77 " pdb=" CA TYR C 77 " ideal model delta sigma weight residual 120.82 125.21 -4.39 1.50e+00 4.44e-01 8.56e+00 angle pdb=" C LEU D 76 " pdb=" N TYR D 77 " pdb=" CA TYR D 77 " ideal model delta sigma weight residual 120.82 125.20 -4.38 1.50e+00 4.44e-01 8.51e+00 angle pdb=" C LEU E 76 " pdb=" N TYR E 77 " pdb=" CA TYR E 77 " ideal model delta sigma weight residual 120.82 125.14 -4.32 1.50e+00 4.44e-01 8.31e+00 angle pdb=" C LEU B 76 " pdb=" N TYR B 77 " pdb=" CA TYR B 77 " ideal model delta sigma weight residual 120.82 125.14 -4.32 1.50e+00 4.44e-01 8.29e+00 ... (remaining 31939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 13174 17.48 - 34.96: 980 34.96 - 52.44: 168 52.44 - 69.92: 42 69.92 - 87.40: 12 Dihedral angle restraints: 14376 sinusoidal: 5796 harmonic: 8580 Sorted by residual: dihedral pdb=" CA TYR D 254 " pdb=" C TYR D 254 " pdb=" N HIS D 255 " pdb=" CA HIS D 255 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA TYR B 254 " pdb=" C TYR B 254 " pdb=" N HIS B 255 " pdb=" CA HIS B 255 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA TYR A 254 " pdb=" C TYR A 254 " pdb=" N HIS A 255 " pdb=" CA HIS A 255 " ideal model delta harmonic sigma weight residual -180.00 -161.56 -18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 14373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1871 0.031 - 0.062: 1120 0.062 - 0.093: 368 0.093 - 0.124: 134 0.124 - 0.154: 53 Chirality restraints: 3546 Sorted by residual: chirality pdb=" CA GLU A 318 " pdb=" N GLU A 318 " pdb=" C GLU A 318 " pdb=" CB GLU A 318 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA GLU D 318 " pdb=" N GLU D 318 " pdb=" C GLU D 318 " pdb=" CB GLU D 318 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA GLU F 318 " pdb=" N GLU F 318 " pdb=" C GLU F 318 " pdb=" CB GLU F 318 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 3543 not shown) Planarity restraints: 4164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 351 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO E 352 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 352 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 352 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 351 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO F 352 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO F 352 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 352 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 351 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO C 352 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 352 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 352 " -0.019 5.00e-02 4.00e+02 ... (remaining 4161 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 8046 2.86 - 3.37: 22625 3.37 - 3.88: 37210 3.88 - 4.39: 42374 4.39 - 4.90: 72167 Nonbonded interactions: 182422 Sorted by model distance: nonbonded pdb=" O LYS A 464 " pdb=" NE2 GLN A 515 " model vdw 2.353 3.120 nonbonded pdb=" O LYS F 464 " pdb=" NE2 GLN F 515 " model vdw 2.353 3.120 nonbonded pdb=" O LYS C 464 " pdb=" NE2 GLN C 515 " model vdw 2.354 3.120 nonbonded pdb=" O LYS E 464 " pdb=" NE2 GLN E 515 " model vdw 2.354 3.120 nonbonded pdb=" O LYS D 464 " pdb=" NE2 GLN D 515 " model vdw 2.354 3.120 ... (remaining 182417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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=1.00 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: 5.660 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: 1.100 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 60.840 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 0.009 0.040 23628 Z= 0.562 Angle : 0.670 8.247 31944 Z= 0.357 Chirality : 0.045 0.154 3546 Planarity : 0.003 0.034 4164 Dihedral : 12.906 87.398 8832 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 1.22 (0.16), residues: 2976 helix: 1.93 (0.13), residues: 1542 sheet: 1.15 (0.26), residues: 396 loop : -1.09 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 227 HIS 0.006 0.001 HIS F 482 PHE 0.017 0.002 PHE C 502 TYR 0.015 0.002 TYR D 77 ARG 0.003 0.001 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.9232 (m110) cc_final: 0.8920 (m-40) REVERT: A 105 MET cc_start: 0.9170 (tpt) cc_final: 0.8908 (tmt) REVERT: A 547 ASN cc_start: 0.9250 (m-40) cc_final: 0.8981 (m110) REVERT: B 546 GLU cc_start: 0.8600 (tp30) cc_final: 0.8399 (tp30) REVERT: C 465 ASP cc_start: 0.8410 (m-30) cc_final: 0.8159 (m-30) REVERT: D 105 MET cc_start: 0.9272 (tpt) cc_final: 0.8421 (tmm) REVERT: D 220 ILE cc_start: 0.9376 (pt) cc_final: 0.9161 (pp) REVERT: E 105 MET cc_start: 0.9148 (tpt) cc_final: 0.8245 (tmm) REVERT: E 547 ASN cc_start: 0.9360 (m-40) cc_final: 0.9115 (m-40) REVERT: F 543 VAL cc_start: 0.8805 (t) cc_final: 0.8506 (p) outliers start: 0 outliers final: 1 residues processed: 235 average time/residue: 1.2732 time to fit residues: 345.6310 Evaluate side-chains 173 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 548 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 266 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 432 HIS A 540 GLN B 103 ASN B 325 GLN B 432 HIS C 103 ASN C 432 HIS D 103 ASN D 432 HIS E 103 ASN E 432 HIS E 515 GLN F 103 ASN F 432 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23628 Z= 0.162 Angle : 0.564 7.006 31944 Z= 0.292 Chirality : 0.040 0.163 3546 Planarity : 0.003 0.031 4164 Dihedral : 4.206 14.254 3140 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.69 % Allowed : 6.84 % Favored : 92.48 % 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: 1.74 (0.16), residues: 2976 helix: 2.57 (0.13), residues: 1518 sheet: 1.19 (0.25), residues: 420 loop : -1.11 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 549 HIS 0.003 0.001 HIS D 485 PHE 0.011 0.001 PHE E 357 TYR 0.019 0.001 TYR D 77 ARG 0.006 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 217 time to evaluate : 2.712 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: A 80 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.8951 (mp10) REVERT: A 81 ARG cc_start: 0.8733 (ptp-110) cc_final: 0.7900 (ptp-110) REVERT: A 105 MET cc_start: 0.9129 (tpt) cc_final: 0.8864 (tmt) REVERT: A 547 ASN cc_start: 0.9319 (m-40) cc_final: 0.9025 (m110) REVERT: C 316 MET cc_start: 0.8507 (mtt) cc_final: 0.8010 (mtt) REVERT: D 105 MET cc_start: 0.9175 (tpt) cc_final: 0.8300 (tmm) REVERT: D 220 ILE cc_start: 0.9465 (pt) cc_final: 0.9263 (pp) REVERT: D 316 MET cc_start: 0.8661 (mtt) cc_final: 0.8262 (mtt) REVERT: D 551 SER cc_start: 0.9567 (t) cc_final: 0.9134 (p) REVERT: E 80 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.8988 (mp10) REVERT: E 316 MET cc_start: 0.8382 (mtt) cc_final: 0.8044 (mtt) REVERT: E 547 ASN cc_start: 0.9367 (m-40) cc_final: 0.9132 (m-40) outliers start: 17 outliers final: 2 residues processed: 223 average time/residue: 1.3084 time to fit residues: 336.4374 Evaluate side-chains 194 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 548 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 288 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 23628 Z= 0.361 Angle : 0.606 7.763 31944 Z= 0.311 Chirality : 0.042 0.159 3546 Planarity : 0.003 0.051 4164 Dihedral : 4.395 17.153 3140 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.53 % Allowed : 9.75 % Favored : 89.72 % 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: 1.74 (0.16), residues: 2976 helix: 2.52 (0.13), residues: 1560 sheet: 1.09 (0.26), residues: 402 loop : -1.08 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 549 HIS 0.007 0.001 HIS E 485 PHE 0.013 0.002 PHE B 203 TYR 0.019 0.002 TYR A 77 ARG 0.006 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 193 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.9117 (tpt) cc_final: 0.8600 (tmm) REVERT: A 547 ASN cc_start: 0.9316 (m-40) cc_final: 0.9043 (m110) REVERT: B 547 ASN cc_start: 0.9275 (m-40) cc_final: 0.8990 (m-40) REVERT: D 105 MET cc_start: 0.9106 (tpt) cc_final: 0.8218 (tmm) REVERT: D 515 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: E 80 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8999 (mp10) REVERT: E 547 ASN cc_start: 0.9350 (m-40) cc_final: 0.9145 (m-40) outliers start: 13 outliers final: 2 residues processed: 198 average time/residue: 1.3779 time to fit residues: 312.8914 Evaluate side-chains 175 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain D residue 515 GLN Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 548 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 5.9990 chunk 201 optimal weight: 0.0040 chunk 138 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23628 Z= 0.211 Angle : 0.549 8.274 31944 Z= 0.277 Chirality : 0.039 0.166 3546 Planarity : 0.003 0.034 4164 Dihedral : 4.104 15.208 3140 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.97 % Allowed : 11.57 % Favored : 87.46 % 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: 1.89 (0.16), residues: 2976 helix: 2.64 (0.13), residues: 1566 sheet: 1.13 (0.26), residues: 402 loop : -1.02 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 549 HIS 0.004 0.001 HIS E 482 PHE 0.008 0.001 PHE A 357 TYR 0.019 0.001 TYR A 77 ARG 0.006 0.000 ARG E 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 197 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.9135 (tpt) cc_final: 0.8592 (tmm) REVERT: A 267 GLU cc_start: 0.8494 (tp30) cc_final: 0.8056 (mm-30) REVERT: A 547 ASN cc_start: 0.9338 (m-40) cc_final: 0.9125 (m-40) REVERT: B 547 ASN cc_start: 0.9278 (m-40) cc_final: 0.9010 (m-40) REVERT: D 105 MET cc_start: 0.9128 (tpt) cc_final: 0.8920 (tpt) REVERT: D 318 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: D 515 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7558 (mt0) REVERT: E 80 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8830 (mp10) REVERT: E 105 MET cc_start: 0.9300 (mmp) cc_final: 0.9094 (tpt) REVERT: F 318 GLU cc_start: 0.8017 (mp0) cc_final: 0.7748 (mp0) REVERT: F 368 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8575 (pp) outliers start: 24 outliers final: 3 residues processed: 212 average time/residue: 1.3848 time to fit residues: 335.7851 Evaluate side-chains 193 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 515 GLN Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 211 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 242 optimal weight: 0.7980 chunk 196 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 145 optimal weight: 9.9990 chunk 255 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23628 Z= 0.251 Angle : 0.563 9.332 31944 Z= 0.284 Chirality : 0.040 0.176 3546 Planarity : 0.003 0.031 4164 Dihedral : 4.097 15.606 3138 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.38 % Allowed : 11.81 % Favored : 86.81 % 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: 2.03 (0.16), residues: 2976 helix: 2.90 (0.13), residues: 1518 sheet: 1.13 (0.26), residues: 402 loop : -1.00 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 549 HIS 0.005 0.001 HIS E 482 PHE 0.010 0.001 PHE F 203 TYR 0.016 0.001 TYR A 77 ARG 0.007 0.000 ARG E 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9408 (OUTLIER) cc_final: 0.8947 (mp10) REVERT: A 82 ASP cc_start: 0.9145 (m-30) cc_final: 0.8929 (m-30) REVERT: A 105 MET cc_start: 0.9156 (tpt) cc_final: 0.8626 (tmm) REVERT: A 267 GLU cc_start: 0.8475 (tp30) cc_final: 0.8021 (mm-30) REVERT: A 547 ASN cc_start: 0.9332 (m-40) cc_final: 0.9081 (m110) REVERT: B 547 ASN cc_start: 0.9279 (m-40) cc_final: 0.9022 (m-40) REVERT: D 105 MET cc_start: 0.9141 (tpt) cc_final: 0.8919 (tpt) REVERT: D 318 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: D 515 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7585 (mt0) REVERT: E 80 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.8757 (mp10) REVERT: E 105 MET cc_start: 0.9306 (mmp) cc_final: 0.9067 (tpt) REVERT: F 101 MET cc_start: 0.9162 (pmm) cc_final: 0.8760 (pmm) REVERT: F 105 MET cc_start: 0.8812 (tpt) cc_final: 0.8406 (ppp) REVERT: F 368 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8591 (pp) outliers start: 34 outliers final: 11 residues processed: 215 average time/residue: 1.3576 time to fit residues: 334.4934 Evaluate side-chains 201 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 515 GLN Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 519 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 284 optimal weight: 0.7980 chunk 236 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN E 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23628 Z= 0.209 Angle : 0.553 9.270 31944 Z= 0.279 Chirality : 0.039 0.179 3546 Planarity : 0.003 0.031 4164 Dihedral : 4.001 14.756 3138 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.29 % Allowed : 12.78 % Favored : 85.92 % 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: 2.09 (0.16), residues: 2976 helix: 2.94 (0.13), residues: 1518 sheet: 1.13 (0.26), residues: 402 loop : -0.95 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 549 HIS 0.004 0.001 HIS A 485 PHE 0.007 0.001 PHE F 203 TYR 0.014 0.001 TYR C 77 ARG 0.008 0.000 ARG E 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 193 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9403 (OUTLIER) cc_final: 0.8934 (mp10) REVERT: A 82 ASP cc_start: 0.9133 (m-30) cc_final: 0.8907 (m-30) REVERT: A 105 MET cc_start: 0.9149 (tpt) cc_final: 0.8621 (tmm) REVERT: A 267 GLU cc_start: 0.8458 (tp30) cc_final: 0.8008 (mm-30) REVERT: A 547 ASN cc_start: 0.9327 (m-40) cc_final: 0.9083 (m110) REVERT: B 547 ASN cc_start: 0.9261 (m-40) cc_final: 0.9031 (m-40) REVERT: C 318 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: D 105 MET cc_start: 0.9143 (tpt) cc_final: 0.8914 (tpt) REVERT: D 318 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: D 515 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: E 80 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.9052 (mp10) REVERT: F 80 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: F 105 MET cc_start: 0.8841 (tpt) cc_final: 0.8429 (ppp) REVERT: F 368 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8562 (pp) outliers start: 32 outliers final: 14 residues processed: 211 average time/residue: 1.3744 time to fit residues: 334.1801 Evaluate side-chains 210 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 515 GLN Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 519 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 160 optimal weight: 0.0980 chunk 239 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23628 Z= 0.236 Angle : 0.562 9.449 31944 Z= 0.282 Chirality : 0.039 0.196 3546 Planarity : 0.003 0.030 4164 Dihedral : 4.019 15.270 3138 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.50 % Allowed : 12.86 % Favored : 85.64 % 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: 2.12 (0.16), residues: 2976 helix: 2.96 (0.13), residues: 1518 sheet: 1.12 (0.26), residues: 402 loop : -0.92 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 549 HIS 0.005 0.001 HIS A 485 PHE 0.009 0.001 PHE F 203 TYR 0.014 0.001 TYR C 77 ARG 0.003 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.8931 (mp10) REVERT: A 82 ASP cc_start: 0.9135 (m-30) cc_final: 0.8904 (m-30) REVERT: A 105 MET cc_start: 0.9150 (tpt) cc_final: 0.8640 (tmm) REVERT: A 267 GLU cc_start: 0.8448 (tp30) cc_final: 0.8031 (mm-30) REVERT: A 547 ASN cc_start: 0.9324 (m-40) cc_final: 0.9075 (m110) REVERT: B 547 ASN cc_start: 0.9263 (m-40) cc_final: 0.9041 (m-40) REVERT: C 318 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: D 105 MET cc_start: 0.9140 (tpt) cc_final: 0.8909 (tpt) REVERT: D 316 MET cc_start: 0.8166 (mtt) cc_final: 0.7892 (mtm) REVERT: D 318 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: D 515 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: E 80 GLN cc_start: 0.9399 (OUTLIER) cc_final: 0.8923 (mp10) REVERT: F 80 GLN cc_start: 0.8945 (mp10) cc_final: 0.8711 (mp10) REVERT: F 101 MET cc_start: 0.9474 (mpp) cc_final: 0.9101 (pmm) REVERT: F 318 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: F 368 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8563 (pp) outliers start: 37 outliers final: 14 residues processed: 219 average time/residue: 1.2666 time to fit residues: 321.0180 Evaluate side-chains 211 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 515 GLN Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 519 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23628 Z= 0.221 Angle : 0.559 9.627 31944 Z= 0.283 Chirality : 0.039 0.198 3546 Planarity : 0.003 0.031 4164 Dihedral : 3.984 15.581 3138 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.29 % Allowed : 13.03 % Favored : 85.68 % 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: 2.16 (0.16), residues: 2976 helix: 3.03 (0.13), residues: 1512 sheet: 1.12 (0.26), residues: 402 loop : -0.93 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 549 HIS 0.005 0.001 HIS A 485 PHE 0.008 0.001 PHE F 203 TYR 0.013 0.001 TYR C 77 ARG 0.003 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9177 (mp) cc_final: 0.8948 (mp) REVERT: A 80 GLN cc_start: 0.9387 (OUTLIER) cc_final: 0.8897 (mp10) REVERT: A 82 ASP cc_start: 0.9135 (m-30) cc_final: 0.8918 (m-30) REVERT: A 105 MET cc_start: 0.9155 (tpt) cc_final: 0.8634 (tmm) REVERT: A 267 GLU cc_start: 0.8443 (tp30) cc_final: 0.7988 (mm-30) REVERT: A 316 MET cc_start: 0.8197 (mtt) cc_final: 0.7923 (mtm) REVERT: A 547 ASN cc_start: 0.9326 (m-40) cc_final: 0.9079 (m110) REVERT: B 547 ASN cc_start: 0.9273 (m-40) cc_final: 0.9056 (m-40) REVERT: C 318 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: D 105 MET cc_start: 0.9145 (tpt) cc_final: 0.8911 (tpt) REVERT: D 318 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: D 515 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: E 80 GLN cc_start: 0.9398 (OUTLIER) cc_final: 0.9016 (mp10) REVERT: E 316 MET cc_start: 0.8532 (mtm) cc_final: 0.8299 (mtm) REVERT: F 80 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8541 (mp10) REVERT: F 318 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: F 368 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8562 (pp) outliers start: 32 outliers final: 15 residues processed: 213 average time/residue: 1.3503 time to fit residues: 331.0159 Evaluate side-chains 213 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 515 GLN Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 519 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 0.9980 chunk 271 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 264 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 115 optimal weight: 0.0270 chunk 207 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 249 optimal weight: 20.0000 chunk 263 optimal weight: 0.8980 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 23628 Z= 0.142 Angle : 0.551 9.940 31944 Z= 0.274 Chirality : 0.038 0.209 3546 Planarity : 0.003 0.030 4164 Dihedral : 3.800 13.985 3138 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.05 % Allowed : 13.47 % Favored : 85.48 % 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: 2.15 (0.16), residues: 2976 helix: 3.03 (0.13), residues: 1518 sheet: 0.97 (0.26), residues: 432 loop : -0.96 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 549 HIS 0.004 0.000 HIS A 485 PHE 0.007 0.001 PHE D 357 TYR 0.012 0.001 TYR C 77 ARG 0.003 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9168 (mp) cc_final: 0.8937 (mp) REVERT: A 80 GLN cc_start: 0.9379 (OUTLIER) cc_final: 0.8897 (mp10) REVERT: A 82 ASP cc_start: 0.9140 (m-30) cc_final: 0.8921 (m-30) REVERT: A 105 MET cc_start: 0.9149 (tpt) cc_final: 0.8628 (tmm) REVERT: A 267 GLU cc_start: 0.8408 (tp30) cc_final: 0.8020 (mm-30) REVERT: A 316 MET cc_start: 0.8132 (mtt) cc_final: 0.7893 (mtm) REVERT: A 547 ASN cc_start: 0.9316 (m-40) cc_final: 0.9072 (m110) REVERT: B 547 ASN cc_start: 0.9269 (m-40) cc_final: 0.9050 (m-40) REVERT: C 316 MET cc_start: 0.8660 (mpp) cc_final: 0.8428 (mtm) REVERT: C 318 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: D 105 MET cc_start: 0.9128 (tpt) cc_final: 0.8923 (tpt) REVERT: D 318 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: E 80 GLN cc_start: 0.9392 (OUTLIER) cc_final: 0.8916 (mp10) REVERT: E 316 MET cc_start: 0.8435 (mtm) cc_final: 0.8148 (mtm) REVERT: F 80 GLN cc_start: 0.8994 (mp10) cc_final: 0.8637 (mp10) REVERT: F 101 MET cc_start: 0.9477 (mpp) cc_final: 0.9124 (pmm) REVERT: F 105 MET cc_start: 0.8868 (tpt) cc_final: 0.8431 (ppp) REVERT: F 318 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7749 (mp0) outliers start: 26 outliers final: 13 residues processed: 218 average time/residue: 1.2544 time to fit residues: 318.2176 Evaluate side-chains 205 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 531 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.615 > 50: distance: 95 - 120: 18.293 distance: 99 - 128: 21.432 distance: 105 - 111: 6.629 distance: 106 - 137: 19.815 distance: 111 - 112: 18.212 distance: 112 - 113: 7.065 distance: 112 - 115: 7.790 distance: 113 - 114: 13.452 distance: 113 - 120: 19.862 distance: 114 - 146: 11.364 distance: 115 - 116: 15.655 distance: 116 - 117: 6.209 distance: 117 - 118: 8.455 distance: 117 - 119: 20.179 distance: 120 - 121: 8.849 distance: 121 - 122: 7.424 distance: 121 - 124: 11.819 distance: 122 - 123: 3.906 distance: 122 - 128: 18.801 distance: 123 - 155: 18.473 distance: 124 - 125: 20.589 distance: 124 - 126: 25.590 distance: 125 - 127: 22.909 distance: 128 - 129: 6.686 distance: 129 - 130: 5.000 distance: 129 - 132: 11.454 distance: 130 - 131: 4.004 distance: 130 - 137: 6.852 distance: 131 - 163: 27.843 distance: 132 - 133: 13.995 distance: 133 - 134: 9.130 distance: 134 - 135: 6.259 distance: 134 - 136: 22.968 distance: 137 - 138: 13.485 distance: 138 - 139: 10.724 distance: 138 - 141: 19.151 distance: 139 - 140: 14.577 distance: 139 - 146: 21.300 distance: 140 - 170: 50.559 distance: 141 - 142: 19.980 distance: 142 - 143: 16.927 distance: 143 - 144: 11.608 distance: 144 - 145: 14.976 distance: 146 - 147: 15.063 distance: 147 - 148: 27.748 distance: 147 - 150: 20.444 distance: 148 - 149: 11.964 distance: 148 - 155: 31.295 distance: 150 - 151: 31.844 distance: 151 - 152: 13.795 distance: 152 - 153: 21.678 distance: 152 - 154: 34.354 distance: 155 - 156: 6.802 distance: 156 - 157: 43.489 distance: 156 - 159: 24.528 distance: 157 - 158: 25.333 distance: 157 - 163: 13.840 distance: 159 - 160: 21.002 distance: 160 - 161: 19.042 distance: 160 - 162: 14.798 distance: 163 - 164: 17.744 distance: 164 - 165: 31.636 distance: 164 - 167: 29.096 distance: 165 - 166: 14.176 distance: 165 - 170: 6.175 distance: 167 - 168: 4.225 distance: 167 - 169: 29.325 distance: 170 - 171: 26.725 distance: 171 - 172: 6.328 distance: 172 - 173: 37.787 distance: 172 - 174: 15.671 distance: 174 - 175: 21.452 distance: 175 - 176: 32.863 distance: 176 - 177: 16.302 distance: 176 - 178: 21.470 distance: 178 - 179: 17.960 distance: 179 - 180: 8.257 distance: 179 - 182: 20.490 distance: 180 - 181: 22.922 distance: 180 - 183: 14.403