Starting phenix.real_space_refine on Sat Mar 16 03:16:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afh_15398/03_2024/8afh_15398.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afh_15398/03_2024/8afh_15398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afh_15398/03_2024/8afh_15398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afh_15398/03_2024/8afh_15398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afh_15398/03_2024/8afh_15398.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afh_15398/03_2024/8afh_15398.pdb" } resolution = 3.9 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= 0.001 sd= 0.017 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 46 5.16 5 C 8248 2.51 5 N 2564 2.21 5 O 2712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 431": "OE1" <-> "OE2" Residue "D ARG 808": "NH1" <-> "NH2" Residue "D ARG 839": "NH1" <-> "NH2" Residue "D ARG 873": "NH1" <-> "NH2" Residue "C ARG 808": "NH1" <-> "NH2" Residue "C ARG 839": "NH1" <-> "NH2" Residue "C ARG 873": "NH1" <-> "NH2" Residue "H GLU 431": "OE1" <-> "OE2" Residue "I ARG 808": "NH1" <-> "NH2" Residue "I ARG 839": "NH1" <-> "NH2" Residue "I ARG 873": "NH1" <-> "NH2" Residue "J ARG 808": "NH1" <-> "NH2" Residue "J ARG 839": "NH1" <-> "NH2" Residue "J ARG 873": "NH1" <-> "NH2" Residue "L GLU 431": "OE1" <-> "OE2" Residue "N ARG 808": "NH1" <-> "NH2" Residue "N ARG 839": "NH1" <-> "NH2" Residue "N ARG 873": "NH1" <-> "NH2" Residue "M ARG 808": "NH1" <-> "NH2" Residue "M ARG 839": "NH1" <-> "NH2" Residue "M ARG 873": "NH1" <-> "NH2" Residue "R GLU 431": "OE1" <-> "OE2" Residue "S ARG 808": "NH1" <-> "NH2" Residue "S ARG 839": "NH1" <-> "NH2" Residue "S ARG 873": "NH1" <-> "NH2" Residue "T ARG 808": "NH1" <-> "NH2" Residue "T ARG 839": "NH1" <-> "NH2" Residue "T ARG 873": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13570 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'TRANS': 95} Chain: "B" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 747 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 333 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "H" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 299 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "I" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 860 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "K" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'TRANS': 95} Chain: "L" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 747 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "N" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "M" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "O" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "P" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 333 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "R" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 299 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 860 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "T" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Time building chain proxies: 7.25, per 1000 atoms: 0.53 Number of scatterers: 13570 At special positions: 0 Unit cell: (99.375, 271.625, 88.775, 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 46 16.00 O 2712 8.00 N 2564 7.00 C 8248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 795 " - pdb=" SG CYS D 868 " distance=2.03 Simple disulfide: pdb=" SG CYS C 795 " - pdb=" SG CYS C 868 " distance=2.03 Simple disulfide: pdb=" SG CYS I 795 " - pdb=" SG CYS I 868 " distance=2.03 Simple disulfide: pdb=" SG CYS J 795 " - pdb=" SG CYS J 868 " distance=2.03 Simple disulfide: pdb=" SG CYS N 795 " - pdb=" SG CYS N 868 " distance=2.03 Simple disulfide: pdb=" SG CYS M 795 " - pdb=" SG CYS M 868 " distance=2.03 Simple disulfide: pdb=" SG CYS S 795 " - pdb=" SG CYS S 868 " distance=2.03 Simple disulfide: pdb=" SG CYS T 795 " - pdb=" SG CYS T 868 " distance=2.03 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: 5.76 Conformation dependent library (CDL) restraints added in 2.5 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 26 sheets defined 50.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.961A pdb=" N ASP A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 441 removed outlier: 3.646A pdb=" N GLU A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 432 removed outlier: 3.876A pdb=" N ALA B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 442 Processing helix chain 'B' and resid 443 through 446 Processing helix chain 'D' and resid 859 through 863 removed outlier: 3.554A pdb=" N THR D 863 " --> pdb=" O PRO D 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 863 removed outlier: 3.891A pdb=" N THR C 863 " --> pdb=" O PRO C 860 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 163 removed outlier: 3.828A pdb=" N LEU E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 163 removed outlier: 3.592A pdb=" N ALA F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 3.796A pdb=" N ALA G 411 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS G 412 " --> pdb=" O THR G 408 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU G 426 " --> pdb=" O ARG G 422 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA G 427 " --> pdb=" O LEU G 423 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU G 429 " --> pdb=" O SER G 425 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA G 433 " --> pdb=" O LEU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 444 Processing helix chain 'H' and resid 405 through 431 removed outlier: 3.649A pdb=" N HIS H 409 " --> pdb=" O ASP H 405 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU H 410 " --> pdb=" O SER H 406 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE H 420 " --> pdb=" O LEU H 416 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU H 421 " --> pdb=" O GLN H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 441 removed outlier: 3.588A pdb=" N ASP H 440 " --> pdb=" O ALA H 436 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG H 441 " --> pdb=" O ALA H 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 859 through 863 removed outlier: 3.603A pdb=" N THR I 863 " --> pdb=" O PRO I 860 " (cutoff:3.500A) Processing helix chain 'J' and resid 859 through 863 removed outlier: 3.819A pdb=" N THR J 863 " --> pdb=" O PRO J 860 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 357 removed outlier: 3.571A pdb=" N THR K 355 " --> pdb=" O ALA K 351 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG K 357 " --> pdb=" O VAL K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 441 removed outlier: 3.647A pdb=" N GLU K 362 " --> pdb=" O ALA K 358 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG K 363 " --> pdb=" O THR K 359 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA K 364 " --> pdb=" O ALA K 360 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA K 368 " --> pdb=" O ALA K 364 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS K 369 " --> pdb=" O ASP K 365 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL K 372 " --> pdb=" O ALA K 368 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER K 425 " --> pdb=" O GLU K 421 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU K 426 " --> pdb=" O ARG K 422 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG K 441 " --> pdb=" O ALA K 437 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 432 removed outlier: 3.876A pdb=" N ALA L 356 " --> pdb=" O GLY L 352 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU L 362 " --> pdb=" O ALA L 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU L 367 " --> pdb=" O ARG L 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA L 371 " --> pdb=" O LEU L 367 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL L 372 " --> pdb=" O ALA L 368 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU L 383 " --> pdb=" O LYS L 379 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG L 404 " --> pdb=" O ASP L 400 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE L 420 " --> pdb=" O LEU L 416 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 429 " --> pdb=" O SER L 425 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 442 Processing helix chain 'L' and resid 443 through 446 Processing helix chain 'N' and resid 859 through 863 removed outlier: 3.554A pdb=" N THR N 863 " --> pdb=" O PRO N 860 " (cutoff:3.500A) Processing helix chain 'M' and resid 859 through 863 removed outlier: 3.892A pdb=" N THR M 863 " --> pdb=" O PRO M 860 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 163 removed outlier: 3.828A pdb=" N LEU O 115 " --> pdb=" O VAL O 111 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA O 116 " --> pdb=" O SER O 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 163 removed outlier: 3.592A pdb=" N ALA P 92 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 404 through 439 removed outlier: 3.796A pdb=" N ALA Q 411 " --> pdb=" O ALA Q 407 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS Q 412 " --> pdb=" O THR Q 408 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA Q 418 " --> pdb=" O ALA Q 414 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU Q 426 " --> pdb=" O ARG Q 422 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA Q 427 " --> pdb=" O LEU Q 423 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA Q 433 " --> pdb=" O LEU Q 429 " (cutoff:3.500A) Processing helix chain 'Q' and resid 440 through 444 Processing helix chain 'R' and resid 405 through 431 removed outlier: 3.648A pdb=" N HIS R 409 " --> pdb=" O ASP R 405 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU R 410 " --> pdb=" O SER R 406 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE R 420 " --> pdb=" O LEU R 416 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU R 421 " --> pdb=" O GLN R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 432 through 441 removed outlier: 3.588A pdb=" N ASP R 440 " --> pdb=" O ALA R 436 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG R 441 " --> pdb=" O ALA R 437 " (cutoff:3.500A) Processing helix chain 'S' and resid 859 through 863 removed outlier: 3.602A pdb=" N THR S 863 " --> pdb=" O PRO S 860 " (cutoff:3.500A) Processing helix chain 'T' and resid 859 through 863 removed outlier: 3.819A pdb=" N THR T 863 " --> pdb=" O PRO T 860 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.710A pdb=" N VAL D 851 " --> pdb=" O CYS D 795 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 850 " --> pdb=" O ASP D 845 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY D 10 " --> pdb=" O THR D 885 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET D 807 " --> pdb=" O VAL D 823 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL D 823 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP D 809 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 870 through 872 Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.550A pdb=" N VAL C 12 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 830 through 832 removed outlier: 7.030A pdb=" N TRP C 809 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL C 823 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET C 807 " --> pdb=" O VAL C 823 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.613A pdb=" N VAL I 851 " --> pdb=" O CYS I 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.808A pdb=" N MET I 807 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL I 823 " --> pdb=" O MET I 807 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP I 809 " --> pdb=" O VAL I 821 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 870 through 872 removed outlier: 3.572A pdb=" N TYR I 872 " --> pdb=" O SER I 875 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N GLY J 10 " --> pdb=" O THR J 885 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N GLY J 10 " --> pdb=" O THR J 885 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 792 through 793 Processing sheet with id=AB5, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.711A pdb=" N VAL N 851 " --> pdb=" O CYS N 795 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR N 850 " --> pdb=" O ASP N 845 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY N 10 " --> pdb=" O THR N 885 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET N 807 " --> pdb=" O VAL N 823 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL N 823 " --> pdb=" O MET N 807 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP N 809 " --> pdb=" O VAL N 821 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 870 through 872 Processing sheet with id=AB8, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AB9, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.551A pdb=" N VAL M 12 " --> pdb=" O THR M 885 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 830 through 832 removed outlier: 7.030A pdb=" N TRP M 809 " --> pdb=" O VAL M 821 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL M 823 " --> pdb=" O MET M 807 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET M 807 " --> pdb=" O VAL M 823 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 5 through 6 removed outlier: 3.613A pdb=" N VAL S 851 " --> pdb=" O CYS S 795 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.810A pdb=" N MET S 807 " --> pdb=" O VAL S 823 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL S 823 " --> pdb=" O MET S 807 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP S 809 " --> pdb=" O VAL S 821 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 870 through 872 removed outlier: 3.571A pdb=" N TYR S 872 " --> pdb=" O SER S 875 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'T' and resid 10 through 12 removed outlier: 6.545A pdb=" N GLY T 10 " --> pdb=" O THR T 885 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 10 through 12 removed outlier: 6.545A pdb=" N GLY T 10 " --> pdb=" O THR T 885 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 792 through 793 926 hydrogen bonds defined for protein. 2586 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: 4.30 Time building geometry restraints manager: 6.23 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: 4856 1.34 - 1.46: 2135 1.46 - 1.58: 6615 1.58 - 1.70: 0 1.70 - 1.81: 76 Bond restraints: 13682 Sorted by residual: bond pdb=" CB TRP M 827 " pdb=" CG TRP M 827 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.81e+00 bond pdb=" CB TRP C 827 " pdb=" CG TRP C 827 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.79e+00 bond pdb=" C TYR T 832 " pdb=" N VAL T 833 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.29e-02 6.01e+03 1.74e+00 bond pdb=" CG1 ILE N 806 " pdb=" CD1 ILE N 806 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.69e+00 bond pdb=" CG1 ILE D 806 " pdb=" CD1 ILE D 806 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 ... (remaining 13677 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.74: 90 105.74 - 112.81: 7438 112.81 - 119.87: 4420 119.87 - 126.93: 6383 126.93 - 133.99: 87 Bond angle restraints: 18418 Sorted by residual: angle pdb=" N ILE J 806 " pdb=" CA ILE J 806 " pdb=" C ILE J 806 " ideal model delta sigma weight residual 108.93 113.32 -4.39 1.35e+00 5.49e-01 1.06e+01 angle pdb=" N ILE T 806 " pdb=" CA ILE T 806 " pdb=" C ILE T 806 " ideal model delta sigma weight residual 108.93 113.32 -4.39 1.35e+00 5.49e-01 1.06e+01 angle pdb=" N ILE D 806 " pdb=" CA ILE D 806 " pdb=" C ILE D 806 " ideal model delta sigma weight residual 109.30 113.41 -4.11 1.31e+00 5.83e-01 9.83e+00 angle pdb=" N ILE N 806 " pdb=" CA ILE N 806 " pdb=" C ILE N 806 " ideal model delta sigma weight residual 109.30 113.37 -4.07 1.31e+00 5.83e-01 9.65e+00 angle pdb=" C ALA E 118 " pdb=" N GLU E 119 " pdb=" CA GLU E 119 " ideal model delta sigma weight residual 120.68 115.79 4.89 1.70e+00 3.46e-01 8.27e+00 ... (remaining 18413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 7573 17.25 - 34.51: 761 34.51 - 51.76: 92 51.76 - 69.02: 12 69.02 - 86.27: 28 Dihedral angle restraints: 8466 sinusoidal: 3382 harmonic: 5084 Sorted by residual: dihedral pdb=" CB CYS M 795 " pdb=" SG CYS M 795 " pdb=" SG CYS M 868 " pdb=" CB CYS M 868 " ideal model delta sinusoidal sigma weight residual 93.00 43.72 49.28 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS C 795 " pdb=" SG CYS C 795 " pdb=" SG CYS C 868 " pdb=" CB CYS C 868 " ideal model delta sinusoidal sigma weight residual 93.00 43.76 49.24 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CB CYS I 795 " pdb=" SG CYS I 795 " pdb=" SG CYS I 868 " pdb=" CB CYS I 868 " ideal model delta sinusoidal sigma weight residual 93.00 44.87 48.13 1 1.00e+01 1.00e-02 3.19e+01 ... (remaining 8463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1438 0.040 - 0.080: 476 0.080 - 0.120: 152 0.120 - 0.161: 7 0.161 - 0.201: 9 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CB ILE J 842 " pdb=" CA ILE J 842 " pdb=" CG1 ILE J 842 " pdb=" CG2 ILE J 842 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE T 842 " pdb=" CA ILE T 842 " pdb=" CG1 ILE T 842 " pdb=" CG2 ILE T 842 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CB ILE S 842 " pdb=" CA ILE S 842 " pdb=" CG1 ILE S 842 " pdb=" CG2 ILE S 842 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 2079 not shown) Planarity restraints: 2438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS M 859 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO M 860 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO M 860 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO M 860 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 859 " 0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO C 860 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 860 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 860 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 417 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" CD GLN L 417 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN L 417 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN L 417 " -0.013 2.00e-02 2.50e+03 ... (remaining 2435 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 549 2.71 - 3.26: 13767 3.26 - 3.80: 20842 3.80 - 4.35: 26626 4.35 - 4.90: 44512 Nonbonded interactions: 106296 Sorted by model distance: nonbonded pdb=" O THR L 424 " pdb=" ND2 ASN M 831 " model vdw 2.160 2.520 nonbonded pdb=" O THR B 424 " pdb=" ND2 ASN C 831 " model vdw 2.161 2.520 nonbonded pdb=" NH1 ARG D 799 " pdb=" OG SER D 800 " model vdw 2.201 2.520 nonbonded pdb=" NH1 ARG N 799 " pdb=" OG SER N 800 " model vdw 2.202 2.520 nonbonded pdb=" OD1 ASP I 802 " pdb=" NH2 ARG I 844 " model vdw 2.245 2.520 ... (remaining 106291 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 350 through 445) selection = chain 'K' selection = (chain 'L' and resid 350 through 445) } ncs_group { reference = (chain 'C' and resid 2 through 887) selection = (chain 'D' and resid 2 through 887) selection = chain 'I' selection = (chain 'J' and resid 2 through 887) selection = (chain 'M' and resid 2 through 887) selection = (chain 'N' and resid 2 through 887) selection = chain 'S' selection = (chain 'T' and resid 2 through 887) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'O' selection = chain 'P' } ncs_group { reference = (chain 'G' and resid 403 through 441) selection = chain 'H' selection = (chain 'Q' and resid 403 through 441) selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 6.860 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 38.720 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 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 : 0.006 0.052 13682 Z= 0.378 Angle : 0.699 5.869 18418 Z= 0.430 Chirality : 0.044 0.201 2082 Planarity : 0.004 0.086 2438 Dihedral : 14.167 86.270 5146 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.29 (0.20), residues: 1704 helix: -0.24 (0.18), residues: 758 sheet: -2.06 (0.22), residues: 478 loop : 0.03 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 827 HIS 0.005 0.002 HIS K 350 PHE 0.006 0.001 PHE I 840 TYR 0.018 0.002 TYR T 13 ARG 0.013 0.001 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 369 LYS cc_start: 0.6832 (mtmm) cc_final: 0.6493 (mtmm) REVERT: B 376 LYS cc_start: 0.7593 (tppp) cc_final: 0.7317 (tppp) REVERT: D 792 ARG cc_start: 0.7445 (ttt180) cc_final: 0.7223 (ttm-80) REVERT: C 863 THR cc_start: 0.7906 (m) cc_final: 0.7567 (p) REVERT: G 415 GLU cc_start: 0.7209 (tp30) cc_final: 0.6804 (tp30) REVERT: G 419 THR cc_start: 0.7582 (t) cc_final: 0.7374 (p) REVERT: I 829 SER cc_start: 0.8178 (t) cc_final: 0.7899 (p) REVERT: I 854 GLN cc_start: 0.6504 (tp40) cc_final: 0.6114 (tp40) REVERT: J 855 MET cc_start: 0.7018 (mmm) cc_final: 0.6259 (mmm) REVERT: J 858 LEU cc_start: 0.6366 (mt) cc_final: 0.6031 (tt) REVERT: L 380 ARG cc_start: 0.7396 (ptp90) cc_final: 0.6907 (mtm110) REVERT: L 395 MET cc_start: 0.5951 (ttm) cc_final: 0.5577 (mmm) REVERT: L 416 LEU cc_start: 0.7606 (tp) cc_final: 0.7129 (mp) REVERT: N 860 PRO cc_start: 0.8040 (Cg_exo) cc_final: 0.7816 (Cg_endo) REVERT: M 820 MET cc_start: 0.7789 (ttp) cc_final: 0.7550 (ttp) REVERT: R 413 ILE cc_start: 0.7276 (mm) cc_final: 0.6827 (mm) REVERT: R 426 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6323 (mt-10) REVERT: T 807 MET cc_start: 0.7422 (mmm) cc_final: 0.7205 (mtt) REVERT: T 871 ILE cc_start: 0.7862 (mp) cc_final: 0.7516 (mt) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.3516 time to fit residues: 151.7002 Evaluate side-chains 305 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.7980 chunk 125 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 130 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN D 869 ASN C 831 ASN E 93 ASN N 856 ASN N 869 ASN M 854 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13682 Z= 0.214 Angle : 0.570 6.774 18418 Z= 0.315 Chirality : 0.040 0.172 2082 Planarity : 0.005 0.085 2438 Dihedral : 4.710 20.729 1962 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.29 % Allowed : 11.82 % Favored : 85.89 % 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: 0.26 (0.21), residues: 1704 helix: 1.53 (0.18), residues: 754 sheet: -1.72 (0.22), residues: 470 loop : 0.33 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 827 HIS 0.006 0.001 HIS Q 409 PHE 0.007 0.002 PHE M 840 TYR 0.017 0.002 TYR T 810 ARG 0.010 0.001 ARG R 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 309 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: B 379 LYS cc_start: 0.8363 (tmtt) cc_final: 0.7826 (tmmt) REVERT: D 835 SER cc_start: 0.8409 (t) cc_final: 0.8202 (p) REVERT: C 844 ARG cc_start: 0.6572 (mtp85) cc_final: 0.6213 (mmm-85) REVERT: F 115 LEU cc_start: 0.7501 (tp) cc_final: 0.7289 (tp) REVERT: G 419 THR cc_start: 0.7500 (t) cc_final: 0.7221 (p) REVERT: I 807 MET cc_start: 0.7056 (mpp) cc_final: 0.6838 (mpp) REVERT: I 817 GLN cc_start: 0.5605 (mp10) cc_final: 0.5262 (mp10) REVERT: I 829 SER cc_start: 0.8456 (t) cc_final: 0.8084 (p) REVERT: I 854 GLN cc_start: 0.6453 (tp40) cc_final: 0.6217 (tp40) REVERT: I 872 TYR cc_start: 0.7397 (t80) cc_final: 0.7144 (t80) REVERT: J 858 LEU cc_start: 0.6184 (mt) cc_final: 0.5648 (tt) REVERT: L 384 ARG cc_start: 0.6760 (mtm180) cc_final: 0.6532 (mtp180) REVERT: L 395 MET cc_start: 0.5507 (ttm) cc_final: 0.5179 (mmm) REVERT: L 416 LEU cc_start: 0.7841 (tp) cc_final: 0.7588 (mp) REVERT: M 13 TYR cc_start: 0.5367 (m-80) cc_final: 0.5075 (m-80) REVERT: M 792 ARG cc_start: 0.7835 (ttt90) cc_final: 0.7598 (ttm-80) REVERT: M 820 MET cc_start: 0.7937 (ttp) cc_final: 0.7461 (ttp) REVERT: M 839 ARG cc_start: 0.5603 (mtm-85) cc_final: 0.5365 (ttp-110) REVERT: M 865 VAL cc_start: 0.7887 (m) cc_final: 0.7501 (t) REVERT: M 866 TYR cc_start: 0.8074 (m-80) cc_final: 0.7735 (m-10) REVERT: O 107 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6723 (tm-30) REVERT: P 107 GLU cc_start: 0.7480 (tt0) cc_final: 0.7153 (tt0) REVERT: R 413 ILE cc_start: 0.7754 (mm) cc_final: 0.7415 (mm) REVERT: R 426 GLU cc_start: 0.6499 (mt-10) cc_final: 0.5821 (mt-10) REVERT: T 7 SER cc_start: 0.6916 (m) cc_final: 0.6474 (t) REVERT: T 807 MET cc_start: 0.7096 (mmm) cc_final: 0.6884 (mtt) REVERT: T 820 MET cc_start: 0.7198 (mmm) cc_final: 0.6908 (mmm) REVERT: T 871 ILE cc_start: 0.7977 (mp) cc_final: 0.7693 (mt) REVERT: T 877 TYR cc_start: 0.7229 (m-80) cc_final: 0.6841 (m-80) outliers start: 32 outliers final: 19 residues processed: 323 average time/residue: 0.3086 time to fit residues: 135.6004 Evaluate side-chains 308 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 289 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 824 VAL Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain T residue 857 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN L 374 GLN N 869 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13682 Z= 0.230 Angle : 0.547 8.409 18418 Z= 0.300 Chirality : 0.040 0.156 2082 Planarity : 0.004 0.061 2438 Dihedral : 4.522 21.602 1962 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.37 % Allowed : 14.26 % Favored : 81.38 % 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: 0.80 (0.21), residues: 1704 helix: 2.06 (0.18), residues: 756 sheet: -1.52 (0.22), residues: 474 loop : 0.54 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 827 HIS 0.005 0.001 HIS Q 409 PHE 0.006 0.001 PHE M 840 TYR 0.016 0.002 TYR D 832 ARG 0.006 0.001 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 315 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7098 (tpt90) cc_final: 0.6730 (tpp-160) REVERT: A 423 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7929 (mt) REVERT: B 416 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8245 (mp) REVERT: H 426 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: I 817 GLN cc_start: 0.6004 (mp10) cc_final: 0.5685 (mp10) REVERT: I 829 SER cc_start: 0.8458 (t) cc_final: 0.8069 (p) REVERT: I 855 MET cc_start: 0.5978 (ttp) cc_final: 0.5725 (ttp) REVERT: J 805 ASN cc_start: 0.3945 (OUTLIER) cc_final: 0.3669 (t0) REVERT: J 858 LEU cc_start: 0.6880 (mt) cc_final: 0.5973 (tt) REVERT: K 350 HIS cc_start: 0.3526 (OUTLIER) cc_final: 0.3171 (m90) REVERT: L 363 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.7185 (mmm-85) REVERT: L 374 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6987 (tp40) REVERT: L 416 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7775 (mp) REVERT: N 810 TYR cc_start: 0.8007 (m-80) cc_final: 0.7688 (m-80) REVERT: M 820 MET cc_start: 0.7874 (ttp) cc_final: 0.7417 (ttp) REVERT: M 866 TYR cc_start: 0.8249 (m-80) cc_final: 0.7969 (m-80) REVERT: O 107 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6559 (tm-30) REVERT: O 156 LYS cc_start: 0.7417 (mttt) cc_final: 0.7061 (mttt) REVERT: P 107 GLU cc_start: 0.7605 (tt0) cc_final: 0.6638 (tt0) REVERT: R 413 ILE cc_start: 0.7796 (mm) cc_final: 0.7360 (mm) REVERT: R 426 GLU cc_start: 0.6396 (mt-10) cc_final: 0.6063 (mt-10) REVERT: T 7 SER cc_start: 0.7528 (m) cc_final: 0.7041 (t) REVERT: T 809 TRP cc_start: 0.7485 (m100) cc_final: 0.7244 (m100) REVERT: T 820 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6698 (ttm) REVERT: T 871 ILE cc_start: 0.7972 (mp) cc_final: 0.7748 (mt) outliers start: 61 outliers final: 36 residues processed: 341 average time/residue: 0.2855 time to fit residues: 134.9773 Evaluate side-chains 351 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 307 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 876 GLU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain H residue 434 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 805 ASN Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 831 ASN Chi-restraints excluded: chain J residue 833 VAL Chi-restraints excluded: chain K residue 350 HIS Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 875 SER Chi-restraints excluded: chain N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 797 SER Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain S residue 790 SER Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 857 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.7980 chunk 113 optimal weight: 0.0770 chunk 78 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 143 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN D 3 GLN C 3 GLN C 5 GLN ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 350 HIS L 374 GLN P 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13682 Z= 0.170 Angle : 0.488 6.248 18418 Z= 0.266 Chirality : 0.038 0.139 2082 Planarity : 0.003 0.053 2438 Dihedral : 4.173 19.893 1962 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.15 % Allowed : 17.41 % Favored : 78.44 % 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: 1.28 (0.21), residues: 1704 helix: 2.56 (0.17), residues: 758 sheet: -1.31 (0.23), residues: 486 loop : 0.65 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 827 HIS 0.003 0.001 HIS K 350 PHE 0.003 0.001 PHE M 840 TYR 0.012 0.001 TYR C 810 ARG 0.006 0.000 ARG M 792 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 311 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7142 (tpt90) cc_final: 0.6858 (tpp-160) REVERT: C 6 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6605 (mm-30) REVERT: C 820 MET cc_start: 0.8429 (tmm) cc_final: 0.8117 (ttp) REVERT: C 827 TRP cc_start: 0.8092 (p90) cc_final: 0.7725 (p90) REVERT: C 855 MET cc_start: 0.7303 (mtm) cc_final: 0.6823 (mtp) REVERT: H 435 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7524 (mt-10) REVERT: I 817 GLN cc_start: 0.6029 (mp10) cc_final: 0.5748 (mp10) REVERT: I 829 SER cc_start: 0.8342 (t) cc_final: 0.7946 (p) REVERT: J 805 ASN cc_start: 0.4068 (OUTLIER) cc_final: 0.3666 (t0) REVERT: J 855 MET cc_start: 0.7522 (mmm) cc_final: 0.7311 (mmm) REVERT: K 412 LYS cc_start: 0.7535 (ttmm) cc_final: 0.7264 (ttmm) REVERT: L 363 ARG cc_start: 0.7344 (mmm-85) cc_final: 0.7011 (mmm-85) REVERT: L 374 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6433 (mm110) REVERT: L 416 LEU cc_start: 0.8054 (tp) cc_final: 0.7764 (mp) REVERT: N 810 TYR cc_start: 0.8014 (m-80) cc_final: 0.7635 (m-80) REVERT: N 839 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.6351 (ttp80) REVERT: M 13 TYR cc_start: 0.6022 (OUTLIER) cc_final: 0.4856 (t80) REVERT: M 820 MET cc_start: 0.7817 (ttp) cc_final: 0.7455 (ttp) REVERT: M 866 TYR cc_start: 0.8104 (m-80) cc_final: 0.7848 (m-80) REVERT: O 156 LYS cc_start: 0.7354 (mttt) cc_final: 0.7028 (mttt) REVERT: Q 429 LEU cc_start: 0.8137 (mp) cc_final: 0.7932 (tp) REVERT: R 413 ILE cc_start: 0.7828 (mm) cc_final: 0.7420 (mm) REVERT: R 426 GLU cc_start: 0.6447 (mt-10) cc_final: 0.5759 (mt-10) REVERT: T 7 SER cc_start: 0.7540 (m) cc_final: 0.7018 (t) REVERT: T 809 TRP cc_start: 0.7479 (m100) cc_final: 0.7062 (m100) REVERT: T 820 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6523 (ttm) outliers start: 58 outliers final: 33 residues processed: 338 average time/residue: 0.3032 time to fit residues: 139.0234 Evaluate side-chains 344 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 306 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 876 GLU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 412 LYS Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 805 ASN Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 833 VAL Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 839 ARG Chi-restraints excluded: chain N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 857 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN C 831 ASN E 139 ASN L 374 GLN L 409 HIS ** M 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13682 Z= 0.245 Angle : 0.546 8.579 18418 Z= 0.294 Chirality : 0.040 0.142 2082 Planarity : 0.004 0.051 2438 Dihedral : 4.346 18.778 1962 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.80 % Allowed : 18.34 % Favored : 76.86 % 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: 1.27 (0.21), residues: 1704 helix: 2.57 (0.17), residues: 756 sheet: -1.28 (0.23), residues: 474 loop : 0.50 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 809 HIS 0.004 0.001 HIS L 350 PHE 0.004 0.001 PHE N 840 TYR 0.017 0.002 TYR D 832 ARG 0.006 0.001 ARG L 438 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 314 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6558 (mm-30) REVERT: C 809 TRP cc_start: 0.8394 (m100) cc_final: 0.8189 (m100) REVERT: C 820 MET cc_start: 0.8437 (tmm) cc_final: 0.8073 (ttp) REVERT: C 827 TRP cc_start: 0.8192 (p90) cc_final: 0.7901 (p90) REVERT: C 855 MET cc_start: 0.7386 (mtm) cc_final: 0.6844 (mtp) REVERT: H 435 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7568 (mt-10) REVERT: I 817 GLN cc_start: 0.6125 (mp10) cc_final: 0.5830 (mp10) REVERT: J 805 ASN cc_start: 0.4130 (OUTLIER) cc_final: 0.3866 (t0) REVERT: K 412 LYS cc_start: 0.7564 (ttmm) cc_final: 0.7278 (ttmm) REVERT: L 363 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.7061 (mmm-85) REVERT: L 374 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6929 (tt0) REVERT: L 416 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7794 (mp) REVERT: L 431 GLU cc_start: 0.6626 (tp30) cc_final: 0.6392 (tp30) REVERT: L 439 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7405 (mtt180) REVERT: N 810 TYR cc_start: 0.7956 (m-80) cc_final: 0.7686 (m-80) REVERT: M 13 TYR cc_start: 0.6144 (OUTLIER) cc_final: 0.5262 (t80) REVERT: M 792 ARG cc_start: 0.7893 (tpt-90) cc_final: 0.7416 (ttm-80) REVERT: M 820 MET cc_start: 0.7869 (ttp) cc_final: 0.7518 (ttp) REVERT: M 866 TYR cc_start: 0.8023 (m-80) cc_final: 0.7772 (m-80) REVERT: O 156 LYS cc_start: 0.7379 (mttt) cc_final: 0.7038 (mttt) REVERT: P 107 GLU cc_start: 0.7482 (tt0) cc_final: 0.6584 (tt0) REVERT: P 146 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6956 (tp) REVERT: R 413 ILE cc_start: 0.7891 (mm) cc_final: 0.7505 (mm) REVERT: R 426 GLU cc_start: 0.6368 (mt-10) cc_final: 0.5838 (mt-10) REVERT: S 820 MET cc_start: 0.7978 (ttp) cc_final: 0.7691 (ttp) REVERT: T 7 SER cc_start: 0.7606 (m) cc_final: 0.7026 (t) REVERT: T 809 TRP cc_start: 0.7573 (m100) cc_final: 0.7063 (m100) REVERT: T 820 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6703 (ttm) REVERT: T 886 VAL cc_start: 0.7509 (p) cc_final: 0.7298 (t) outliers start: 67 outliers final: 44 residues processed: 344 average time/residue: 0.3115 time to fit residues: 145.4469 Evaluate side-chains 358 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 308 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 876 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 798 SER Chi-restraints excluded: chain J residue 805 ASN Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 833 VAL Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 420 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 857 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN L 374 GLN P 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13682 Z= 0.212 Angle : 0.514 8.710 18418 Z= 0.280 Chirality : 0.039 0.147 2082 Planarity : 0.003 0.048 2438 Dihedral : 4.242 18.836 1962 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.23 % Allowed : 19.99 % Favored : 74.79 % 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: 1.41 (0.21), residues: 1704 helix: 2.69 (0.17), residues: 768 sheet: -1.22 (0.23), residues: 474 loop : 0.50 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 827 HIS 0.005 0.001 HIS K 350 PHE 0.004 0.001 PHE D 840 TYR 0.016 0.001 TYR C 810 ARG 0.005 0.000 ARG F 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 323 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 384 ARG cc_start: 0.7218 (mtp180) cc_final: 0.6642 (mtp-110) REVERT: D 855 MET cc_start: 0.6375 (mtp) cc_final: 0.6112 (mtt) REVERT: C 6 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6413 (mm-30) REVERT: C 809 TRP cc_start: 0.8366 (m100) cc_final: 0.7496 (m100) REVERT: C 855 MET cc_start: 0.7470 (mtm) cc_final: 0.6848 (mtp) REVERT: F 115 LEU cc_start: 0.6324 (tp) cc_final: 0.6004 (tp) REVERT: G 416 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7940 (mp) REVERT: H 435 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7470 (mt-10) REVERT: I 817 GLN cc_start: 0.6154 (mp10) cc_final: 0.5823 (mp10) REVERT: I 829 SER cc_start: 0.8317 (t) cc_final: 0.7919 (p) REVERT: I 855 MET cc_start: 0.6325 (ttt) cc_final: 0.6103 (ttp) REVERT: J 805 ASN cc_start: 0.4107 (OUTLIER) cc_final: 0.3864 (t0) REVERT: J 855 MET cc_start: 0.7761 (mmm) cc_final: 0.7442 (mmm) REVERT: L 416 LEU cc_start: 0.8137 (tp) cc_final: 0.7866 (mp) REVERT: N 810 TYR cc_start: 0.7961 (m-80) cc_final: 0.7721 (m-80) REVERT: M 13 TYR cc_start: 0.5605 (OUTLIER) cc_final: 0.4951 (t80) REVERT: M 832 TYR cc_start: 0.7604 (m-80) cc_final: 0.7260 (m-80) REVERT: O 156 LYS cc_start: 0.7330 (mttt) cc_final: 0.7006 (mttt) REVERT: Q 429 LEU cc_start: 0.8142 (mp) cc_final: 0.7839 (tp) REVERT: R 413 ILE cc_start: 0.7960 (mm) cc_final: 0.7591 (mm) REVERT: R 426 GLU cc_start: 0.6393 (mt-10) cc_final: 0.5807 (mt-10) REVERT: S 820 MET cc_start: 0.8019 (ttp) cc_final: 0.7689 (ttp) REVERT: T 7 SER cc_start: 0.7633 (m) cc_final: 0.7079 (t) REVERT: T 809 TRP cc_start: 0.7543 (m100) cc_final: 0.7118 (m100) outliers start: 73 outliers final: 53 residues processed: 353 average time/residue: 0.3017 time to fit residues: 144.7151 Evaluate side-chains 378 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 322 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 876 GLU Chi-restraints excluded: chain D residue 882 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 861 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 798 SER Chi-restraints excluded: chain J residue 805 ASN Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 831 ASN Chi-restraints excluded: chain J residue 833 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 403 ARG Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 875 SER Chi-restraints excluded: chain N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 797 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 857 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 159 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 98 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13682 Z= 0.196 Angle : 0.505 8.737 18418 Z= 0.274 Chirality : 0.038 0.141 2082 Planarity : 0.003 0.047 2438 Dihedral : 4.153 18.278 1962 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.80 % Allowed : 20.34 % Favored : 74.86 % 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: 1.57 (0.21), residues: 1704 helix: 2.88 (0.17), residues: 768 sheet: -1.26 (0.25), residues: 408 loop : 0.33 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 809 HIS 0.004 0.001 HIS K 350 PHE 0.003 0.001 PHE N 840 TYR 0.025 0.001 TYR M 866 ARG 0.006 0.000 ARG N 792 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 315 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 384 ARG cc_start: 0.7203 (mtp180) cc_final: 0.6620 (mtp-110) REVERT: C 6 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6330 (mm-30) REVERT: C 799 ARG cc_start: 0.7011 (ptp-110) cc_final: 0.6768 (ptp-110) REVERT: C 809 TRP cc_start: 0.8341 (m100) cc_final: 0.7758 (m100) REVERT: C 855 MET cc_start: 0.7435 (mtm) cc_final: 0.6879 (mtp) REVERT: C 866 TYR cc_start: 0.8237 (m-80) cc_final: 0.7863 (m-80) REVERT: G 416 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7934 (mp) REVERT: H 416 LEU cc_start: 0.7587 (tp) cc_final: 0.7380 (mt) REVERT: H 435 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7514 (mt-10) REVERT: I 817 GLN cc_start: 0.6110 (mp10) cc_final: 0.5826 (mp10) REVERT: I 829 SER cc_start: 0.8401 (t) cc_final: 0.7989 (p) REVERT: I 855 MET cc_start: 0.6349 (ttt) cc_final: 0.6074 (ttp) REVERT: J 855 MET cc_start: 0.7795 (mmm) cc_final: 0.7438 (mmm) REVERT: L 416 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7866 (mp) REVERT: N 810 TYR cc_start: 0.7964 (m-80) cc_final: 0.7727 (m-80) REVERT: M 13 TYR cc_start: 0.5740 (OUTLIER) cc_final: 0.5158 (t80) REVERT: M 832 TYR cc_start: 0.7622 (m-80) cc_final: 0.7270 (m-80) REVERT: O 156 LYS cc_start: 0.7290 (mttt) cc_final: 0.6993 (mttt) REVERT: P 146 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6919 (tp) REVERT: Q 429 LEU cc_start: 0.8081 (mp) cc_final: 0.7846 (tp) REVERT: R 413 ILE cc_start: 0.7977 (mm) cc_final: 0.7595 (mm) REVERT: R 426 GLU cc_start: 0.6424 (mt-10) cc_final: 0.5799 (mt-10) REVERT: T 7 SER cc_start: 0.7639 (m) cc_final: 0.7138 (t) outliers start: 67 outliers final: 55 residues processed: 339 average time/residue: 0.3118 time to fit residues: 143.8987 Evaluate side-chains 373 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 314 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 876 GLU Chi-restraints excluded: chain D residue 882 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 861 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 798 SER Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 831 ASN Chi-restraints excluded: chain J residue 833 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 875 SER Chi-restraints excluded: chain N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 797 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 835 SER Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 857 ASN Chi-restraints excluded: chain T residue 875 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 30 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN O 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13682 Z= 0.204 Angle : 0.515 8.599 18418 Z= 0.278 Chirality : 0.039 0.140 2082 Planarity : 0.003 0.046 2438 Dihedral : 4.165 18.356 1962 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.94 % Allowed : 20.56 % Favored : 74.50 % 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: 1.62 (0.21), residues: 1704 helix: 2.92 (0.17), residues: 774 sheet: -1.15 (0.24), residues: 450 loop : 0.39 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 827 HIS 0.004 0.001 HIS K 350 PHE 0.005 0.001 PHE D 840 TYR 0.019 0.001 TYR C 810 ARG 0.006 0.000 ARG M 792 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 319 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 384 ARG cc_start: 0.7210 (mtp180) cc_final: 0.6610 (mtp-110) REVERT: D 855 MET cc_start: 0.6228 (mtp) cc_final: 0.5974 (mtt) REVERT: C 6 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6362 (mm-30) REVERT: C 809 TRP cc_start: 0.8349 (m100) cc_final: 0.7760 (m100) REVERT: C 855 MET cc_start: 0.7216 (mtm) cc_final: 0.6547 (mtp) REVERT: C 866 TYR cc_start: 0.8245 (m-80) cc_final: 0.7925 (m-80) REVERT: G 416 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7854 (mp) REVERT: G 426 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6823 (mt-10) REVERT: H 426 GLU cc_start: 0.7306 (mp0) cc_final: 0.6827 (mp0) REVERT: H 435 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7469 (mt-10) REVERT: I 817 GLN cc_start: 0.6145 (mp10) cc_final: 0.5804 (mp10) REVERT: I 855 MET cc_start: 0.6388 (ttt) cc_final: 0.6143 (ttp) REVERT: J 855 MET cc_start: 0.7896 (mmm) cc_final: 0.7593 (mmm) REVERT: L 413 ILE cc_start: 0.7443 (mm) cc_final: 0.7200 (mm) REVERT: L 416 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7884 (mp) REVERT: N 810 TYR cc_start: 0.7962 (m-80) cc_final: 0.7701 (m-80) REVERT: M 13 TYR cc_start: 0.5746 (OUTLIER) cc_final: 0.5271 (t80) REVERT: M 832 TYR cc_start: 0.7672 (m-80) cc_final: 0.7187 (m-80) REVERT: M 865 VAL cc_start: 0.8030 (m) cc_final: 0.7694 (t) REVERT: M 866 TYR cc_start: 0.8180 (m-80) cc_final: 0.7925 (m-80) REVERT: O 156 LYS cc_start: 0.7293 (mttt) cc_final: 0.6987 (mttt) REVERT: P 107 GLU cc_start: 0.7421 (tt0) cc_final: 0.7210 (tt0) REVERT: Q 429 LEU cc_start: 0.8089 (mp) cc_final: 0.7827 (tp) REVERT: R 413 ILE cc_start: 0.8007 (mm) cc_final: 0.7622 (mm) REVERT: R 426 GLU cc_start: 0.6390 (mt-10) cc_final: 0.5800 (mt-10) REVERT: T 7 SER cc_start: 0.7636 (m) cc_final: 0.7134 (t) outliers start: 69 outliers final: 57 residues processed: 348 average time/residue: 0.3114 time to fit residues: 147.0173 Evaluate side-chains 377 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 317 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 876 GLU Chi-restraints excluded: chain D residue 882 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 798 SER Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 829 SER Chi-restraints excluded: chain J residue 831 ASN Chi-restraints excluded: chain J residue 833 VAL Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 875 SER Chi-restraints excluded: chain N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 797 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 835 SER Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 857 ASN Chi-restraints excluded: chain T residue 875 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 89 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 134 optimal weight: 0.0980 chunk 141 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13682 Z= 0.183 Angle : 0.516 8.844 18418 Z= 0.277 Chirality : 0.038 0.147 2082 Planarity : 0.003 0.046 2438 Dihedral : 4.109 19.464 1962 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.66 % Allowed : 21.56 % Favored : 73.78 % 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: 1.78 (0.21), residues: 1704 helix: 3.09 (0.17), residues: 770 sheet: -1.16 (0.24), residues: 450 loop : 0.51 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 809 HIS 0.004 0.001 HIS K 350 PHE 0.004 0.001 PHE D 840 TYR 0.022 0.001 TYR C 810 ARG 0.008 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 314 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 384 ARG cc_start: 0.7204 (mtp180) cc_final: 0.6608 (mtp-110) REVERT: D 855 MET cc_start: 0.6242 (mtp) cc_final: 0.5973 (mtt) REVERT: C 6 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6380 (mm-30) REVERT: C 809 TRP cc_start: 0.8350 (m100) cc_final: 0.7775 (m100) REVERT: C 855 MET cc_start: 0.7104 (mtm) cc_final: 0.6469 (mtp) REVERT: C 866 TYR cc_start: 0.8181 (m-80) cc_final: 0.7891 (m-80) REVERT: E 128 ARG cc_start: 0.5786 (tpm170) cc_final: 0.5478 (tpm170) REVERT: F 151 LEU cc_start: 0.7152 (mt) cc_final: 0.6922 (mm) REVERT: G 416 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7913 (mp) REVERT: H 426 GLU cc_start: 0.7271 (mp0) cc_final: 0.6881 (mp0) REVERT: H 435 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7443 (mt-10) REVERT: I 817 GLN cc_start: 0.6088 (mp10) cc_final: 0.5789 (mp10) REVERT: I 855 MET cc_start: 0.6397 (ttt) cc_final: 0.6140 (ttp) REVERT: J 855 MET cc_start: 0.7883 (mmm) cc_final: 0.7584 (mmm) REVERT: L 416 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7887 (mp) REVERT: N 810 TYR cc_start: 0.7933 (m-80) cc_final: 0.7718 (m-80) REVERT: M 13 TYR cc_start: 0.5800 (OUTLIER) cc_final: 0.5302 (t80) REVERT: M 832 TYR cc_start: 0.7666 (m-80) cc_final: 0.7230 (m-80) REVERT: M 866 TYR cc_start: 0.8147 (m-80) cc_final: 0.7920 (m-80) REVERT: O 107 GLU cc_start: 0.7036 (tt0) cc_final: 0.6432 (tt0) REVERT: O 128 ARG cc_start: 0.6071 (tpm170) cc_final: 0.5701 (mmm160) REVERT: O 156 LYS cc_start: 0.7303 (mttt) cc_final: 0.7001 (mttt) REVERT: Q 429 LEU cc_start: 0.8060 (mp) cc_final: 0.7803 (tp) REVERT: R 413 ILE cc_start: 0.7979 (mm) cc_final: 0.7606 (mm) REVERT: R 426 GLU cc_start: 0.6321 (mt-10) cc_final: 0.5730 (mt-10) REVERT: T 7 SER cc_start: 0.7647 (m) cc_final: 0.7124 (t) outliers start: 65 outliers final: 54 residues processed: 340 average time/residue: 0.3013 time to fit residues: 139.9080 Evaluate side-chains 365 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 308 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 876 GLU Chi-restraints excluded: chain D residue 882 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 798 SER Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 829 SER Chi-restraints excluded: chain J residue 831 ASN Chi-restraints excluded: chain J residue 833 VAL Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 845 ASP Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 875 SER Chi-restraints excluded: chain N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 835 SER Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 857 ASN Chi-restraints excluded: chain T residue 861 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN I 856 ASN N 854 GLN N 856 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13682 Z= 0.269 Angle : 0.585 9.333 18418 Z= 0.313 Chirality : 0.041 0.205 2082 Planarity : 0.004 0.047 2438 Dihedral : 4.455 21.701 1962 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.44 % Allowed : 21.99 % Favored : 73.57 % 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: 1.43 (0.21), residues: 1704 helix: 2.76 (0.17), residues: 766 sheet: -1.30 (0.23), residues: 450 loop : 0.43 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 827 HIS 0.005 0.001 HIS K 350 PHE 0.004 0.001 PHE N 840 TYR 0.025 0.002 TYR C 810 ARG 0.008 0.001 ARG B 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 315 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 ARG cc_start: 0.6561 (mpt-90) cc_final: 0.5956 (mtt90) REVERT: B 384 ARG cc_start: 0.7231 (mtp180) cc_final: 0.6672 (mtp-110) REVERT: D 855 MET cc_start: 0.6390 (mtp) cc_final: 0.6112 (mtt) REVERT: C 6 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6787 (mp0) REVERT: C 855 MET cc_start: 0.7064 (mtm) cc_final: 0.6508 (mtp) REVERT: C 866 TYR cc_start: 0.8277 (m-80) cc_final: 0.7903 (m-80) REVERT: E 128 ARG cc_start: 0.5952 (tpm170) cc_final: 0.5397 (tpm170) REVERT: G 426 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6916 (mt-10) REVERT: H 426 GLU cc_start: 0.7262 (mp0) cc_final: 0.6874 (mp0) REVERT: H 435 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7644 (mt-10) REVERT: I 6 GLU cc_start: 0.6340 (mp0) cc_final: 0.5794 (mp0) REVERT: I 817 GLN cc_start: 0.6282 (mp10) cc_final: 0.5967 (mp10) REVERT: J 855 MET cc_start: 0.7839 (mmm) cc_final: 0.7581 (mmm) REVERT: J 875 SER cc_start: 0.8261 (t) cc_final: 0.7831 (m) REVERT: L 416 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7904 (mp) REVERT: N 810 TYR cc_start: 0.7923 (m-80) cc_final: 0.7676 (m-80) REVERT: N 865 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8535 (t) REVERT: M 13 TYR cc_start: 0.5692 (OUTLIER) cc_final: 0.5365 (t80) REVERT: M 794 SER cc_start: 0.7678 (p) cc_final: 0.7426 (t) REVERT: M 832 TYR cc_start: 0.7738 (m-80) cc_final: 0.7212 (m-80) REVERT: O 156 LYS cc_start: 0.7301 (mttt) cc_final: 0.7024 (mttt) REVERT: R 413 ILE cc_start: 0.8002 (mm) cc_final: 0.7612 (mm) REVERT: R 426 GLU cc_start: 0.6260 (mt-10) cc_final: 0.5659 (mt-10) REVERT: T 7 SER cc_start: 0.7730 (m) cc_final: 0.7144 (t) REVERT: T 820 MET cc_start: 0.6583 (ttm) cc_final: 0.6348 (ttt) outliers start: 62 outliers final: 54 residues processed: 340 average time/residue: 0.2961 time to fit residues: 137.5610 Evaluate side-chains 367 residues out of total 1396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 310 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 876 GLU Chi-restraints excluded: chain D residue 882 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 798 SER Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 831 ASN Chi-restraints excluded: chain J residue 833 VAL Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 845 ASP Chi-restraints excluded: chain N residue 854 GLN Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 875 SER Chi-restraints excluded: chain N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain R residue 420 ILE Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 835 SER Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 857 ASN Chi-restraints excluded: chain T residue 875 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 121 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 16 optimal weight: 0.0370 chunk 24 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN N 854 GLN P 98 GLN R 417 GLN T 831 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.178840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.166320 restraints weight = 19181.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.169374 restraints weight = 11223.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.171387 restraints weight = 7333.847| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13682 Z= 0.182 Angle : 0.543 10.455 18418 Z= 0.288 Chirality : 0.039 0.223 2082 Planarity : 0.003 0.044 2438 Dihedral : 4.307 28.791 1962 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.87 % Allowed : 22.92 % Favored : 73.21 % 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 (0.21), residues: 1704 helix: 3.06 (0.17), residues: 770 sheet: -1.30 (0.23), residues: 450 loop : 0.49 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 809 HIS 0.004 0.001 HIS K 350 PHE 0.004 0.001 PHE N 840 TYR 0.021 0.001 TYR C 810 ARG 0.008 0.000 ARG B 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3212.26 seconds wall clock time: 58 minutes 19.54 seconds (3499.54 seconds total)