Starting phenix.real_space_refine on Mon Apr 8 18:26:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvc_0989/04_2024/6lvc_0989.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvc_0989/04_2024/6lvc_0989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvc_0989/04_2024/6lvc_0989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvc_0989/04_2024/6lvc_0989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvc_0989/04_2024/6lvc_0989.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvc_0989/04_2024/6lvc_0989.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 48 5.16 5 C 8916 2.51 5 N 2484 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "C PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14138 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5987 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 39, 'TRANS': 722} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1080 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "C" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5987 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 39, 'TRANS': 722} Chain: "D" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1080 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.42, per 1000 atoms: 0.52 Number of scatterers: 14138 At special positions: 0 Unit cell: (120.91, 123.05, 95.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 48 16.00 O 2688 8.00 N 2484 7.00 C 8916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.18 Conformation dependent library (CDL) restraints added in 2.4 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 18 sheets defined 24.5% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 224 through 228 removed outlier: 4.151A pdb=" N GLY A 227 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.687A pdb=" N ARG A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.527A pdb=" N GLN A 326 " --> pdb=" O CYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 410 through 415 removed outlier: 3.707A pdb=" N ALA A 415 " --> pdb=" O GLY A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.725A pdb=" N VAL A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 475 through 488 removed outlier: 4.366A pdb=" N LEU A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.052A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.739A pdb=" N ASP A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 623 through 631 removed outlier: 3.619A pdb=" N GLN A 626 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N GLU A 628 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG A 629 " --> pdb=" O GLN A 626 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 631 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 688 through 691 removed outlier: 3.609A pdb=" N LYS A 691 " --> pdb=" O PRO A 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 691' Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.726A pdb=" N TRP A 729 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 730 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 731 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 733 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.538A pdb=" N ILE A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.774A pdb=" N TYR B 15 " --> pdb=" O PRO B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 41 removed outlier: 4.374A pdb=" N TRP B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'B' and resid 111 through 130 removed outlier: 3.572A pdb=" N ALA B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 removed outlier: 4.167A pdb=" N GLY C 227 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.687A pdb=" N ARG C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 removed outlier: 3.527A pdb=" N GLN C 326 " --> pdb=" O CYS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 410 through 415 removed outlier: 3.708A pdb=" N ALA C 415 " --> pdb=" O GLY C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 431 removed outlier: 3.725A pdb=" N VAL C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 435 Processing helix chain 'C' and resid 475 through 488 removed outlier: 4.367A pdb=" N LEU C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.051A pdb=" N LEU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 537 removed outlier: 3.745A pdb=" N ASP C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 597 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'C' and resid 623 through 631 removed outlier: 3.618A pdb=" N GLN C 626 " --> pdb=" O PRO C 623 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU C 628 " --> pdb=" O SER C 625 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG C 629 " --> pdb=" O GLN C 626 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 631 " --> pdb=" O GLU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 666 Processing helix chain 'C' and resid 688 through 691 removed outlier: 3.609A pdb=" N LYS C 691 " --> pdb=" O PRO C 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 688 through 691' Processing helix chain 'C' and resid 726 through 733 removed outlier: 3.738A pdb=" N TRP C 729 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 730 " --> pdb=" O ILE C 727 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY C 731 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 733 " --> pdb=" O LEU C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 removed outlier: 3.537A pdb=" N ILE C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.778A pdb=" N TYR D 15 " --> pdb=" O PRO D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 41 removed outlier: 4.375A pdb=" N TRP D 22 " --> pdb=" O ARG D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 60 through 71 Processing helix chain 'D' and resid 111 through 130 removed outlier: 3.572A pdb=" N ALA D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.536A pdb=" N PHE A 346 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 4.939A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 38 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS A 54 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 15 removed outlier: 4.939A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 64 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.770A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL A 239 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TRP A 101 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ALA A 241 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE A 99 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 308 removed outlier: 3.966A pdb=" N SER A 308 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.345A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N MET A 608 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ARG A 660 " --> pdb=" O MET A 608 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 612 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 656 " --> pdb=" O GLY A 612 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N ASP A 614 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N GLY A 654 " --> pdb=" O ASP A 614 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.345A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 611 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 420 through 421 removed outlier: 6.782A pdb=" N ALA B 89 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB1, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.535A pdb=" N PHE C 346 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.938A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU C 38 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS C 54 " --> pdb=" O ILE C 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.938A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 64 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.770A pdb=" N SER C 122 " --> pdb=" O TRP C 116 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP C 116 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP C 124 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER C 114 " --> pdb=" O TRP C 124 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU C 126 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL C 239 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N TRP C 101 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA C 241 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 306 through 308 removed outlier: 3.976A pdb=" N SER C 308 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.357A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N MET C 608 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ARG C 660 " --> pdb=" O MET C 608 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 612 " --> pdb=" O TYR C 656 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR C 656 " --> pdb=" O GLY C 612 " (cutoff:3.500A) removed outlier: 9.480A pdb=" N ASP C 614 " --> pdb=" O GLY C 654 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N GLY C 654 " --> pdb=" O ASP C 614 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.357A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 611 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 420 through 421 removed outlier: 6.781A pdb=" N ALA D 89 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 451 through 453 514 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.06 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4321 1.33 - 1.45: 2735 1.45 - 1.57: 7404 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 14538 Sorted by residual: bond pdb=" C PRO A 577 " pdb=" N PRO A 578 " ideal model delta sigma weight residual 1.334 1.393 -0.059 1.51e-02 4.39e+03 1.51e+01 bond pdb=" C PRO C 577 " pdb=" N PRO C 578 " ideal model delta sigma weight residual 1.334 1.393 -0.058 1.51e-02 4.39e+03 1.50e+01 bond pdb=" CG ARG A 707 " pdb=" CD ARG A 707 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.35e+00 bond pdb=" CG ARG C 707 " pdb=" CD ARG C 707 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.32e+00 bond pdb=" CB VAL A 15 " pdb=" CG1 VAL A 15 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.85e+00 ... (remaining 14533 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.58: 347 105.58 - 112.76: 7039 112.76 - 119.95: 5506 119.95 - 127.13: 6601 127.13 - 134.32: 261 Bond angle restraints: 19754 Sorted by residual: angle pdb=" C GLY A 655 " pdb=" N TYR A 656 " pdb=" CA TYR A 656 " ideal model delta sigma weight residual 121.54 131.84 -10.30 1.91e+00 2.74e-01 2.91e+01 angle pdb=" C GLY C 655 " pdb=" N TYR C 656 " pdb=" CA TYR C 656 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" N PRO C 578 " pdb=" CA PRO C 578 " pdb=" C PRO C 578 " ideal model delta sigma weight residual 113.75 121.61 -7.86 1.49e+00 4.50e-01 2.78e+01 angle pdb=" N PRO A 578 " pdb=" CA PRO A 578 " pdb=" C PRO A 578 " ideal model delta sigma weight residual 113.75 121.59 -7.84 1.49e+00 4.50e-01 2.77e+01 angle pdb=" CA TYR C 24 " pdb=" CB TYR C 24 " pdb=" CG TYR C 24 " ideal model delta sigma weight residual 113.90 120.75 -6.85 1.80e+00 3.09e-01 1.45e+01 ... (remaining 19749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 7992 15.53 - 31.05: 400 31.05 - 46.57: 58 46.57 - 62.10: 6 62.10 - 77.62: 4 Dihedral angle restraints: 8460 sinusoidal: 3394 harmonic: 5066 Sorted by residual: dihedral pdb=" CA PRO A 577 " pdb=" C PRO A 577 " pdb=" N PRO A 578 " pdb=" CA PRO A 578 " ideal model delta harmonic sigma weight residual 180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA PRO C 577 " pdb=" C PRO C 577 " pdb=" N PRO C 578 " pdb=" CA PRO C 578 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA SER C 114 " pdb=" C SER C 114 " pdb=" N ARG C 115 " pdb=" CA ARG C 115 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 8457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1746 0.097 - 0.195: 233 0.195 - 0.292: 17 0.292 - 0.390: 0 0.390 - 0.487: 2 Chirality restraints: 1998 Sorted by residual: chirality pdb=" CB ILE C 283 " pdb=" CA ILE C 283 " pdb=" CG1 ILE C 283 " pdb=" CG2 ILE C 283 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CB ILE A 283 " pdb=" CA ILE A 283 " pdb=" CG1 ILE A 283 " pdb=" CG2 ILE A 283 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CB ILE C 21 " pdb=" CA ILE C 21 " pdb=" CG1 ILE C 21 " pdb=" CG2 ILE C 21 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1995 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 522 " 0.039 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR A 522 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR A 522 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 522 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 522 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 522 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 522 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 522 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 522 " -0.038 2.00e-02 2.50e+03 3.03e-02 1.83e+01 pdb=" CG TYR C 522 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR C 522 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR C 522 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 522 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 522 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 522 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 522 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 440 " 0.030 2.00e-02 2.50e+03 2.95e-02 1.73e+01 pdb=" CG TYR A 440 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 440 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 440 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 440 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 440 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 440 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 440 " -0.001 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 57 2.44 - 3.06: 8092 3.06 - 3.67: 21336 3.67 - 4.29: 34360 4.29 - 4.90: 57880 Nonbonded interactions: 121725 Sorted by model distance: nonbonded pdb=" OH TYR C 440 " pdb="FE FE C 801 " model vdw 1.831 2.260 nonbonded pdb=" OH TYR A 440 " pdb="FE FE A 801 " model vdw 1.833 2.260 nonbonded pdb=" OE1 GLU A 521 " pdb="FE FE A 801 " model vdw 1.915 2.260 nonbonded pdb=" OE1 GLU C 521 " pdb="FE FE C 801 " model vdw 1.918 2.260 nonbonded pdb=" OE2 GLU C 521 " pdb="FE FE C 801 " model vdw 1.959 2.260 ... (remaining 121720 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 7.920 Check model and map are aligned: 0.200 Set scattering table: 0.150 Process input model: 39.940 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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 : 0.011 0.091 14538 Z= 0.740 Angle : 1.001 10.305 19754 Z= 0.561 Chirality : 0.066 0.487 1998 Planarity : 0.008 0.060 2628 Dihedral : 9.662 77.624 5252 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.48 % Allowed : 1.98 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.17), residues: 1764 helix: -2.05 (0.23), residues: 284 sheet: -1.37 (0.28), residues: 326 loop : -2.04 (0.15), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP C 331 HIS 0.021 0.004 HIS A 333 PHE 0.030 0.005 PHE A 358 TYR 0.072 0.005 TYR A 522 ARG 0.014 0.002 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 264 time to evaluate : 1.615 Fit side-chains REVERT: A 4 ILE cc_start: 0.8956 (mm) cc_final: 0.8698 (mp) REVERT: A 170 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8171 (mtmp) REVERT: A 761 ARG cc_start: 0.7403 (mtt-85) cc_final: 0.7201 (mmm-85) REVERT: B 32 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8079 (mtmm) REVERT: B 116 MET cc_start: 0.8895 (mtt) cc_final: 0.8647 (mtm) REVERT: C 4 ILE cc_start: 0.8953 (mm) cc_final: 0.8682 (mp) REVERT: C 170 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8171 (mtmp) REVERT: D 32 LYS cc_start: 0.8391 (mtmt) cc_final: 0.8076 (mtmm) REVERT: D 116 MET cc_start: 0.8882 (mtt) cc_final: 0.8632 (mtm) outliers start: 7 outliers final: 1 residues processed: 271 average time/residue: 1.5248 time to fit residues: 446.9523 Evaluate side-chains 151 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 121 GLN A 422 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN A 695 HIS B 14 ASN C 71 GLN C 422 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 ASN C 695 HIS D 14 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14538 Z= 0.187 Angle : 0.559 7.013 19754 Z= 0.306 Chirality : 0.045 0.205 1998 Planarity : 0.005 0.049 2628 Dihedral : 5.413 36.061 1983 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.53 % Allowed : 7.79 % Favored : 89.69 % 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: -1.63 (0.18), residues: 1764 helix: -0.15 (0.27), residues: 304 sheet: -0.84 (0.28), residues: 336 loop : -1.48 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 22 HIS 0.004 0.001 HIS D 67 PHE 0.015 0.002 PHE C 332 TYR 0.022 0.002 TYR A 661 ARG 0.008 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 1.740 Fit side-chains REVERT: A 170 LYS cc_start: 0.8557 (mtpt) cc_final: 0.8185 (mtmp) REVERT: A 402 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: A 422 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8526 (p0) REVERT: A 721 MET cc_start: 0.9231 (tpt) cc_final: 0.8819 (tpt) REVERT: B 116 MET cc_start: 0.8774 (mtt) cc_final: 0.8540 (mtm) REVERT: C 4 ILE cc_start: 0.8885 (mm) cc_final: 0.8682 (mp) REVERT: C 170 LYS cc_start: 0.8562 (mtpt) cc_final: 0.8185 (mtmp) REVERT: C 402 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6703 (tm-30) REVERT: C 634 MET cc_start: 0.8346 (mmt) cc_final: 0.8101 (mmt) REVERT: C 721 MET cc_start: 0.9266 (tpt) cc_final: 0.8782 (tpt) REVERT: D 116 MET cc_start: 0.8776 (mtt) cc_final: 0.8535 (mtm) outliers start: 37 outliers final: 21 residues processed: 178 average time/residue: 1.3953 time to fit residues: 271.8023 Evaluate side-chains 162 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 512 LYS Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 37 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN C 225 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14538 Z= 0.303 Angle : 0.581 7.399 19754 Z= 0.315 Chirality : 0.047 0.208 1998 Planarity : 0.005 0.053 2628 Dihedral : 5.288 38.376 1983 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.42 % Allowed : 9.08 % Favored : 87.50 % 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: -1.12 (0.19), residues: 1764 helix: 0.81 (0.29), residues: 304 sheet: -0.66 (0.28), residues: 340 loop : -1.25 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 22 HIS 0.008 0.002 HIS B 67 PHE 0.015 0.002 PHE A 75 TYR 0.027 0.002 TYR C 661 ARG 0.007 0.000 ARG C 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 144 time to evaluate : 1.784 Fit side-chains REVERT: A 65 GLN cc_start: 0.8091 (mt0) cc_final: 0.7792 (mt0) REVERT: A 170 LYS cc_start: 0.8545 (mtpt) cc_final: 0.8130 (mtmp) REVERT: A 364 ARG cc_start: 0.7943 (tpp80) cc_final: 0.7707 (ttm-80) REVERT: A 402 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6784 (tm-30) REVERT: A 420 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8889 (t) REVERT: A 592 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.7986 (ptt-90) REVERT: B 72 MET cc_start: 0.9021 (ptm) cc_final: 0.8751 (ptp) REVERT: B 116 MET cc_start: 0.8851 (mtt) cc_final: 0.8640 (mtm) REVERT: C 65 GLN cc_start: 0.8089 (mt0) cc_final: 0.7794 (mt0) REVERT: C 170 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8131 (mtmp) REVERT: C 364 ARG cc_start: 0.7948 (tpp80) cc_final: 0.7709 (ttm-80) REVERT: C 402 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: C 420 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8905 (t) REVERT: C 592 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7989 (ptt-90) REVERT: D 72 MET cc_start: 0.9019 (ptm) cc_final: 0.8750 (ptp) REVERT: D 116 MET cc_start: 0.8851 (mtt) cc_final: 0.8639 (mtm) outliers start: 50 outliers final: 26 residues processed: 173 average time/residue: 1.3716 time to fit residues: 260.9740 Evaluate side-chains 166 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 512 LYS Chi-restraints excluded: chain C residue 592 ARG Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 107 optimal weight: 0.0040 chunk 160 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14538 Z= 0.397 Angle : 0.615 7.277 19754 Z= 0.334 Chirality : 0.048 0.217 1998 Planarity : 0.006 0.053 2628 Dihedral : 5.405 42.218 1983 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.87 % Allowed : 10.25 % Favored : 86.89 % 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: -0.90 (0.19), residues: 1764 helix: 1.38 (0.30), residues: 304 sheet: -0.80 (0.28), residues: 340 loop : -1.13 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 22 HIS 0.009 0.002 HIS D 67 PHE 0.018 0.002 PHE C 187 TYR 0.028 0.002 TYR C 661 ARG 0.007 0.001 ARG C 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 148 time to evaluate : 1.562 Fit side-chains REVERT: A 65 GLN cc_start: 0.8183 (mt0) cc_final: 0.7835 (mt0) REVERT: A 170 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8127 (mtmp) REVERT: A 364 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7666 (ttm-80) REVERT: A 402 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6817 (tm-30) REVERT: A 592 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7919 (ptt-90) REVERT: A 717 ASN cc_start: 0.8848 (t0) cc_final: 0.8562 (t0) REVERT: B 72 MET cc_start: 0.9036 (ptm) cc_final: 0.8761 (ptp) REVERT: B 100 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: C 65 GLN cc_start: 0.8182 (mt0) cc_final: 0.7834 (mt0) REVERT: C 170 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8125 (mtmp) REVERT: C 364 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7667 (ttm-80) REVERT: C 402 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: C 420 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8924 (t) REVERT: C 592 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7927 (ptt-90) REVERT: D 72 MET cc_start: 0.9040 (ptm) cc_final: 0.8764 (ptp) REVERT: D 100 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7294 (mp0) outliers start: 42 outliers final: 25 residues processed: 174 average time/residue: 1.4444 time to fit residues: 274.3427 Evaluate side-chains 167 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 592 ARG Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 112 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 0.0070 chunk 70 optimal weight: 0.9980 chunk 145 optimal weight: 0.0570 chunk 117 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 152 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14538 Z= 0.140 Angle : 0.482 6.721 19754 Z= 0.261 Chirality : 0.043 0.183 1998 Planarity : 0.004 0.048 2628 Dihedral : 4.734 39.827 1983 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.87 % Allowed : 11.68 % Favored : 85.45 % 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: -0.48 (0.20), residues: 1764 helix: 1.80 (0.30), residues: 314 sheet: -0.30 (0.28), residues: 346 loop : -0.98 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 22 HIS 0.002 0.001 HIS C 333 PHE 0.013 0.001 PHE B 53 TYR 0.016 0.001 TYR A 661 ARG 0.005 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 1.542 Fit side-chains REVERT: A 65 GLN cc_start: 0.8139 (mt0) cc_final: 0.7780 (mt0) REVERT: A 170 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8034 (mtmp) REVERT: A 402 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6738 (tm-30) REVERT: B 28 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: B 72 MET cc_start: 0.9026 (ptm) cc_final: 0.8798 (ptp) REVERT: C 65 GLN cc_start: 0.8136 (mt0) cc_final: 0.7779 (mt0) REVERT: C 170 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8029 (mtmp) REVERT: C 402 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6736 (tm-30) REVERT: D 28 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: D 72 MET cc_start: 0.9028 (ptm) cc_final: 0.8793 (ptp) outliers start: 42 outliers final: 21 residues processed: 179 average time/residue: 1.4179 time to fit residues: 278.6057 Evaluate side-chains 163 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 83 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14538 Z= 0.391 Angle : 0.603 7.171 19754 Z= 0.327 Chirality : 0.048 0.212 1998 Planarity : 0.005 0.049 2628 Dihedral : 5.181 42.205 1983 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.87 % Allowed : 11.89 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1764 helix: 1.90 (0.30), residues: 302 sheet: -0.61 (0.28), residues: 340 loop : -0.95 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 101 HIS 0.008 0.002 HIS D 67 PHE 0.019 0.002 PHE D 53 TYR 0.028 0.002 TYR A 661 ARG 0.008 0.001 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 133 time to evaluate : 1.652 Fit side-chains REVERT: A 65 GLN cc_start: 0.8237 (mt0) cc_final: 0.7834 (mt0) REVERT: A 170 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8113 (mtmp) REVERT: A 364 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.7281 (ttp80) REVERT: A 402 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: A 592 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7881 (ptt-90) REVERT: A 717 ASN cc_start: 0.8845 (t0) cc_final: 0.8551 (t0) REVERT: B 27 ASP cc_start: 0.8567 (t0) cc_final: 0.8329 (t0) REVERT: B 72 MET cc_start: 0.9056 (ptm) cc_final: 0.8777 (ptp) REVERT: B 100 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: C 65 GLN cc_start: 0.8235 (mt0) cc_final: 0.7832 (mt0) REVERT: C 170 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8110 (mtmp) REVERT: C 364 ARG cc_start: 0.7752 (ttm-80) cc_final: 0.7316 (ttp80) REVERT: C 402 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: C 592 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7873 (ptt-90) REVERT: D 27 ASP cc_start: 0.8577 (t0) cc_final: 0.8333 (t0) REVERT: D 72 MET cc_start: 0.9044 (ptm) cc_final: 0.8761 (ptp) REVERT: D 100 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7291 (mp0) outliers start: 42 outliers final: 25 residues processed: 164 average time/residue: 1.4292 time to fit residues: 257.2311 Evaluate side-chains 163 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 592 ARG Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14538 Z= 0.232 Angle : 0.532 6.812 19754 Z= 0.289 Chirality : 0.045 0.196 1998 Planarity : 0.005 0.043 2628 Dihedral : 4.982 43.170 1983 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.73 % Allowed : 12.91 % Favored : 84.36 % 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: -0.49 (0.20), residues: 1764 helix: 2.01 (0.30), residues: 302 sheet: -0.58 (0.27), residues: 364 loop : -0.93 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 22 HIS 0.004 0.001 HIS B 67 PHE 0.018 0.002 PHE B 53 TYR 0.021 0.001 TYR C 661 ARG 0.008 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 1.729 Fit side-chains REVERT: A 65 GLN cc_start: 0.8206 (mt0) cc_final: 0.7814 (mt0) REVERT: A 170 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8055 (mtmp) REVERT: A 364 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7313 (ttp80) REVERT: A 402 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6778 (tm-30) REVERT: B 27 ASP cc_start: 0.8500 (t0) cc_final: 0.8204 (t0) REVERT: B 72 MET cc_start: 0.9039 (ptm) cc_final: 0.8793 (ptp) REVERT: C 65 GLN cc_start: 0.8205 (mt0) cc_final: 0.7818 (mt0) REVERT: C 170 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8053 (mtmp) REVERT: C 364 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7322 (ttp80) REVERT: C 402 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: D 27 ASP cc_start: 0.8503 (t0) cc_final: 0.8204 (t0) REVERT: D 72 MET cc_start: 0.9024 (ptm) cc_final: 0.8773 (ptp) outliers start: 40 outliers final: 31 residues processed: 167 average time/residue: 1.3878 time to fit residues: 253.7159 Evaluate side-chains 169 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 83 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 154 optimal weight: 0.0670 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14538 Z= 0.270 Angle : 0.546 6.994 19754 Z= 0.296 Chirality : 0.046 0.198 1998 Planarity : 0.005 0.043 2628 Dihedral : 5.016 43.470 1983 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.53 % Allowed : 12.77 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.20), residues: 1764 helix: 2.01 (0.30), residues: 302 sheet: -0.57 (0.27), residues: 364 loop : -0.92 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 22 HIS 0.005 0.001 HIS B 67 PHE 0.017 0.002 PHE B 53 TYR 0.022 0.001 TYR A 661 ARG 0.007 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 1.385 Fit side-chains REVERT: A 65 GLN cc_start: 0.8211 (mt0) cc_final: 0.7820 (mt0) REVERT: A 170 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8106 (mtmp) REVERT: A 364 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7302 (ttp80) REVERT: A 402 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6717 (tm-30) REVERT: B 27 ASP cc_start: 0.8517 (t0) cc_final: 0.8219 (t0) REVERT: B 72 MET cc_start: 0.9049 (ptm) cc_final: 0.8799 (ptp) REVERT: C 65 GLN cc_start: 0.8211 (mt0) cc_final: 0.7823 (mt0) REVERT: C 170 LYS cc_start: 0.8503 (mtpt) cc_final: 0.8103 (mtmp) REVERT: C 364 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7307 (ttp80) REVERT: C 402 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6701 (tm-30) REVERT: D 27 ASP cc_start: 0.8528 (t0) cc_final: 0.8230 (t0) REVERT: D 72 MET cc_start: 0.9049 (ptm) cc_final: 0.8798 (ptp) outliers start: 37 outliers final: 33 residues processed: 161 average time/residue: 1.3188 time to fit residues: 233.0771 Evaluate side-chains 167 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 83 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14538 Z= 0.363 Angle : 0.591 7.207 19754 Z= 0.321 Chirality : 0.047 0.207 1998 Planarity : 0.005 0.047 2628 Dihedral : 5.228 46.732 1983 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.39 % Allowed : 12.91 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1764 helix: 1.90 (0.30), residues: 302 sheet: -0.62 (0.27), residues: 364 loop : -0.95 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 22 HIS 0.007 0.002 HIS D 67 PHE 0.020 0.002 PHE D 53 TYR 0.026 0.002 TYR A 661 ARG 0.007 0.000 ARG C 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.617 Fit side-chains REVERT: A 65 GLN cc_start: 0.8234 (mt0) cc_final: 0.7834 (mt0) REVERT: A 170 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8124 (mtmp) REVERT: A 364 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7286 (ttp80) REVERT: A 402 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6738 (tm-30) REVERT: A 717 ASN cc_start: 0.8844 (t0) cc_final: 0.8516 (t0) REVERT: B 27 ASP cc_start: 0.8565 (t0) cc_final: 0.8279 (t0) REVERT: B 72 MET cc_start: 0.9072 (ptm) cc_final: 0.8843 (ptp) REVERT: C 65 GLN cc_start: 0.8230 (mt0) cc_final: 0.7834 (mt0) REVERT: C 170 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8122 (mtmp) REVERT: C 364 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7286 (ttp80) REVERT: C 402 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: C 717 ASN cc_start: 0.8833 (t0) cc_final: 0.8506 (t0) REVERT: D 27 ASP cc_start: 0.8566 (t0) cc_final: 0.8277 (t0) REVERT: D 72 MET cc_start: 0.9073 (ptm) cc_final: 0.8840 (ptp) outliers start: 35 outliers final: 31 residues processed: 155 average time/residue: 1.3382 time to fit residues: 228.5872 Evaluate side-chains 162 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 83 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 0.1980 chunk 175 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14538 Z= 0.245 Angle : 0.540 6.987 19754 Z= 0.293 Chirality : 0.045 0.194 1998 Planarity : 0.005 0.043 2628 Dihedral : 5.047 47.470 1983 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.12 % Allowed : 12.98 % Favored : 84.90 % 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: -0.45 (0.20), residues: 1764 helix: 2.00 (0.30), residues: 302 sheet: -0.52 (0.27), residues: 364 loop : -0.90 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 22 HIS 0.004 0.001 HIS D 67 PHE 0.016 0.002 PHE D 53 TYR 0.021 0.001 TYR A 661 ARG 0.007 0.000 ARG C 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.669 Fit side-chains REVERT: A 65 GLN cc_start: 0.8204 (mt0) cc_final: 0.7827 (mt0) REVERT: A 170 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8061 (mtmp) REVERT: A 364 ARG cc_start: 0.7693 (ttm-80) cc_final: 0.7387 (ttp80) REVERT: A 402 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6782 (tm-30) REVERT: A 717 ASN cc_start: 0.8826 (t0) cc_final: 0.8489 (t0) REVERT: B 27 ASP cc_start: 0.8538 (t0) cc_final: 0.8193 (t0) REVERT: B 72 MET cc_start: 0.9049 (ptm) cc_final: 0.8813 (ptp) REVERT: C 65 GLN cc_start: 0.8200 (mt0) cc_final: 0.7830 (mt0) REVERT: C 170 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8058 (mtmp) REVERT: C 364 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7395 (ttp80) REVERT: C 402 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6785 (tm-30) REVERT: C 717 ASN cc_start: 0.8818 (t0) cc_final: 0.8485 (t0) REVERT: D 27 ASP cc_start: 0.8590 (t0) cc_final: 0.8273 (t0) outliers start: 31 outliers final: 31 residues processed: 153 average time/residue: 1.3059 time to fit residues: 220.3240 Evaluate side-chains 160 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 83 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 20 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.091775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.071179 restraints weight = 19777.503| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 1.82 r_work: 0.2567 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14538 Z= 0.206 Angle : 0.522 6.879 19754 Z= 0.283 Chirality : 0.044 0.190 1998 Planarity : 0.004 0.043 2628 Dihedral : 4.905 47.142 1983 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.12 % Allowed : 12.98 % Favored : 84.90 % 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: -0.37 (0.20), residues: 1764 helix: 2.11 (0.30), residues: 302 sheet: -0.46 (0.27), residues: 364 loop : -0.86 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 22 HIS 0.004 0.001 HIS C 582 PHE 0.017 0.002 PHE B 53 TYR 0.019 0.001 TYR A 661 ARG 0.007 0.000 ARG A 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4903.06 seconds wall clock time: 92 minutes 50.71 seconds (5570.71 seconds total)