Starting phenix.real_space_refine (version: dev) on Mon May 16 20:42:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlb_21820/05_2022/6wlb_21820.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlb_21820/05_2022/6wlb_21820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlb_21820/05_2022/6wlb_21820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlb_21820/05_2022/6wlb_21820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlb_21820/05_2022/6wlb_21820.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlb_21820/05_2022/6wlb_21820.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.046 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 34441 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11428 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 42, 'TRANS': 675, 'PCIS': 2} Chain breaks: 2 Chain: "C" Number of atoms: 11417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11417 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 42, 'TRANS': 675, 'PCIS': 2} Chain breaks: 2 Chain: "B" Number of atoms: 11428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11428 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 42, 'TRANS': 675, 'PCIS': 2} Chain breaks: 2 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 16.19, per 1000 atoms: 0.47 Number of scatterers: 34441 At special positions: 0 Unit cell: (136.08, 128.52, 104.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 O 3087 8.00 N 2886 7.00 C 11421 6.00 H 16960 1.00 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 Links applied BETA1-4 " BGC D 1 " - " BGC D 2 " " BGC D 2 " - " BGC D 3 " " BGC D 3 " - " BGC D 4 " " BGC D 4 " - " BGC D 5 " " BGC E 1 " - " BGC E 2 " " BGC E 2 " - " BGC E 3 " " BGC E 3 " - " BGC E 4 " " BGC E 4 " - " BGC E 5 " " BGC F 1 " - " BGC F 2 " " BGC F 2 " - " BGC F 3 " " BGC F 3 " - " BGC F 4 " " BGC F 4 " - " BGC F 5 " Time building additional restraints: 28.24 Conformation dependent library (CDL) restraints added in 3.0 seconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 58.9% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 170 through 194 Processing helix chain 'A' and resid 199 through 222 removed outlier: 3.776A pdb=" N TRP A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'A' and resid 266 through 279 removed outlier: 4.053A pdb=" N THR A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 322 removed outlier: 3.573A pdb=" N PHE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 346 through 373 removed outlier: 3.638A pdb=" N GLU A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 removed outlier: 3.624A pdb=" N ALA A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 4.121A pdb=" N ASP A 480 " --> pdb=" O CYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 removed outlier: 3.925A pdb=" N PHE A 513 " --> pdb=" O ASN A 509 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 611 through 619 Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.735A pdb=" N ILE A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 Processing helix chain 'A' and resid 653 through 657 removed outlier: 4.250A pdb=" N GLU A 657 " --> pdb=" O CYS A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 685 Processing helix chain 'A' and resid 707 through 728 removed outlier: 3.972A pdb=" N ARG A 711 " --> pdb=" O ASN A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 755 Processing helix chain 'A' and resid 756 through 758 No H-bonds generated for 'chain 'A' and resid 756 through 758' Processing helix chain 'A' and resid 759 through 774 removed outlier: 3.845A pdb=" N ALA A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Proline residue: A 770 - end of helix Processing helix chain 'A' and resid 787 through 811 removed outlier: 3.552A pdb=" N ILE A 800 " --> pdb=" O PHE A 796 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 810 " --> pdb=" O GLU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 830 removed outlier: 3.661A pdb=" N LEU A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 846 Processing helix chain 'A' and resid 870 through 875 Processing helix chain 'A' and resid 875 through 899 removed outlier: 3.594A pdb=" N LYS A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 930 removed outlier: 4.163A pdb=" N PHE A 913 " --> pdb=" O GLY A 909 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 914 " --> pdb=" O LYS A 910 " (cutoff:3.500A) Proline residue: A 923 - end of helix removed outlier: 3.512A pdb=" N GLY A 927 " --> pdb=" O PRO A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 958 Processing helix chain 'C' and resid 170 through 194 Processing helix chain 'C' and resid 199 through 222 removed outlier: 3.813A pdb=" N TRP C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 266 through 279 removed outlier: 4.037A pdb=" N THR C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 322 removed outlier: 3.608A pdb=" N PHE C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Proline residue: C 316 - end of helix Processing helix chain 'C' and resid 327 through 333 removed outlier: 3.621A pdb=" N SER C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 373 removed outlier: 3.633A pdb=" N GLU C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 451 removed outlier: 3.572A pdb=" N ALA C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 480 removed outlier: 4.065A pdb=" N ASP C 480 " --> pdb=" O CYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 522 removed outlier: 3.830A pdb=" N PHE C 513 " --> pdb=" O ASN C 509 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 621 through 629 removed outlier: 3.715A pdb=" N ILE C 625 " --> pdb=" O SER C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 652 Processing helix chain 'C' and resid 653 through 657 removed outlier: 4.233A pdb=" N GLU C 657 " --> pdb=" O CYS C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 685 Processing helix chain 'C' and resid 707 through 728 removed outlier: 3.943A pdb=" N ARG C 711 " --> pdb=" O ASN C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 755 Processing helix chain 'C' and resid 756 through 758 No H-bonds generated for 'chain 'C' and resid 756 through 758' Processing helix chain 'C' and resid 759 through 774 removed outlier: 3.831A pdb=" N ALA C 765 " --> pdb=" O LEU C 761 " (cutoff:3.500A) Proline residue: C 770 - end of helix Processing helix chain 'C' and resid 787 through 811 removed outlier: 3.580A pdb=" N ILE C 800 " --> pdb=" O PHE C 796 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 810 " --> pdb=" O GLU C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 830 removed outlier: 3.592A pdb=" N LEU C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP C 818 " --> pdb=" O ILE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 846 Processing helix chain 'C' and resid 870 through 875 Processing helix chain 'C' and resid 875 through 899 removed outlier: 3.579A pdb=" N LYS C 899 " --> pdb=" O ASP C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 930 removed outlier: 4.189A pdb=" N PHE C 913 " --> pdb=" O GLY C 909 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 914 " --> pdb=" O LYS C 910 " (cutoff:3.500A) Proline residue: C 923 - end of helix Processing helix chain 'C' and resid 938 through 958 Processing helix chain 'B' and resid 170 through 194 Processing helix chain 'B' and resid 199 through 222 removed outlier: 3.663A pdb=" N TRP B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.641A pdb=" N LEU B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.971A pdb=" N THR B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 322 removed outlier: 3.641A pdb=" N PHE B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 333 removed outlier: 3.585A pdb=" N SER B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 373 removed outlier: 3.585A pdb=" N GLN B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 removed outlier: 3.742A pdb=" N VAL B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 480 removed outlier: 3.921A pdb=" N ASP B 480 " --> pdb=" O CYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 522 removed outlier: 3.687A pdb=" N PHE B 513 " --> pdb=" O ASN B 509 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 611 through 619 Processing helix chain 'B' and resid 621 through 629 removed outlier: 3.712A pdb=" N ILE B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 652 Processing helix chain 'B' and resid 653 through 657 removed outlier: 4.291A pdb=" N GLU B 657 " --> pdb=" O CYS B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 685 removed outlier: 3.554A pdb=" N GLY B 680 " --> pdb=" O ASP B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 728 removed outlier: 3.995A pdb=" N ARG B 711 " --> pdb=" O ASN B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 Processing helix chain 'B' and resid 756 through 758 No H-bonds generated for 'chain 'B' and resid 756 through 758' Processing helix chain 'B' and resid 759 through 776 removed outlier: 3.887A pdb=" N ALA B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Proline residue: B 770 - end of helix removed outlier: 3.536A pdb=" N LEU B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 809 removed outlier: 3.687A pdb=" N ILE B 800 " --> pdb=" O PHE B 796 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 830 removed outlier: 3.628A pdb=" N LEU B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 846 Processing helix chain 'B' and resid 870 through 875 Processing helix chain 'B' and resid 875 through 899 removed outlier: 3.890A pdb=" N LYS B 899 " --> pdb=" O ASP B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 930 removed outlier: 3.662A pdb=" N GLY B 909 " --> pdb=" O GLY B 905 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 913 " --> pdb=" O GLY B 909 " (cutoff:3.500A) Proline residue: B 923 - end of helix removed outlier: 3.576A pdb=" N GLY B 927 " --> pdb=" O PRO B 923 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 928 " --> pdb=" O PHE B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 958 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 399 through 403 removed outlier: 6.353A pdb=" N VAL A 253 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR A 290 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE A 255 " --> pdb=" O TYR A 290 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N SER A 292 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 257 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 533 " --> pdb=" O ASN A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 465 Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 491 removed outlier: 7.343A pdb=" N ILE A 691 " --> pdb=" O CYS A 488 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 490 " --> pdb=" O ILE A 691 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 160 through 164 Processing sheet with id=AA6, first strand: chain 'C' and resid 399 through 403 removed outlier: 6.344A pdb=" N VAL C 253 " --> pdb=" O SER C 288 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR C 290 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE C 255 " --> pdb=" O TYR C 290 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER C 292 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 257 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS C 533 " --> pdb=" O ASN C 458 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 463 through 464 removed outlier: 6.551A pdb=" N ARG C 495 " --> pdb=" O GLY C 702 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 487 through 491 removed outlier: 7.354A pdb=" N ILE C 691 " --> pdb=" O CYS C 488 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 490 " --> pdb=" O ILE C 691 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 164 removed outlier: 3.702A pdb=" N ILE B 161 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 399 through 403 removed outlier: 6.107A pdb=" N ASP B 254 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU B 459 " --> pdb=" O ASP B 254 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE B 256 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS B 533 " --> pdb=" O ASN B 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 463 through 464 removed outlier: 6.574A pdb=" N ARG B 495 " --> pdb=" O GLY B 702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 487 through 491 removed outlier: 7.534A pdb=" N ILE B 691 " --> pdb=" O CYS B 488 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 490 " --> pdb=" O ILE B 691 " (cutoff:3.500A) 910 hydrogen bonds defined for protein. 2694 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: 13.05 Time building geometry restraints manager: 29.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16921 1.03 - 1.23: 41 1.23 - 1.42: 7631 1.42 - 1.62: 10217 1.62 - 1.82: 135 Bond restraints: 34945 Sorted by residual: bond pdb=" C1 BGC D 5 " pdb=" O5 BGC D 5 " ideal model delta sigma weight residual 1.427 1.503 -0.076 2.80e-02 1.28e+03 7.44e+00 bond pdb=" C1 BGC F 5 " pdb=" O5 BGC F 5 " ideal model delta sigma weight residual 1.427 1.503 -0.076 2.80e-02 1.28e+03 7.44e+00 bond pdb=" C1 BGC E 5 " pdb=" O5 BGC E 5 " ideal model delta sigma weight residual 1.427 1.503 -0.076 2.80e-02 1.28e+03 7.34e+00 bond pdb=" C1 BGC D 4 " pdb=" O5 BGC D 4 " ideal model delta sigma weight residual 1.427 1.502 -0.075 2.80e-02 1.28e+03 7.26e+00 bond pdb=" C1 BGC E 4 " pdb=" O5 BGC E 4 " ideal model delta sigma weight residual 1.427 1.502 -0.075 2.80e-02 1.28e+03 7.25e+00 ... (remaining 34940 not shown) Histogram of bond angle deviations from ideal: 74.10 - 86.10: 50 86.10 - 98.09: 0 98.09 - 110.09: 30932 110.09 - 122.09: 26546 122.09 - 134.09: 5449 Bond angle restraints: 62977 Sorted by residual: angle pdb=" C LEU B 921 " pdb=" CA LEU B 921 " pdb=" HA LEU B 921 " ideal model delta sigma weight residual 109.00 74.10 34.90 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C LEU C 921 " pdb=" CA LEU C 921 " pdb=" HA LEU C 921 " ideal model delta sigma weight residual 109.00 74.22 34.78 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N LEU A 921 " pdb=" CA LEU A 921 " pdb=" HA LEU A 921 " ideal model delta sigma weight residual 110.00 75.24 34.76 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N LEU C 921 " pdb=" CA LEU C 921 " pdb=" HA LEU C 921 " ideal model delta sigma weight residual 110.00 75.25 34.75 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C LEU A 921 " pdb=" CA LEU A 921 " pdb=" HA LEU A 921 " ideal model delta sigma weight residual 109.00 74.25 34.75 3.00e+00 1.11e-01 1.34e+02 ... (remaining 62972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 12958 17.62 - 35.24: 915 35.24 - 52.86: 131 52.86 - 70.48: 37 70.48 - 88.10: 6 Dihedral angle restraints: 14047 sinusoidal: 6340 harmonic: 7707 Sorted by residual: dihedral pdb=" C LEU A 921 " pdb=" N LEU A 921 " pdb=" CA LEU A 921 " pdb=" CB LEU A 921 " ideal model delta harmonic sigma weight residual -122.60 -131.85 9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C LEU C 921 " pdb=" N LEU C 921 " pdb=" CA LEU C 921 " pdb=" CB LEU C 921 " ideal model delta harmonic sigma weight residual -122.60 -131.81 9.21 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" C LEU B 921 " pdb=" N LEU B 921 " pdb=" CA LEU B 921 " pdb=" CB LEU B 921 " ideal model delta harmonic sigma weight residual -122.60 -131.79 9.19 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 14044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.295: 2718 0.295 - 0.590: 3 0.590 - 0.884: 0 0.884 - 1.179: 0 1.179 - 1.474: 3 Chirality restraints: 2724 Sorted by residual: chirality pdb=" CB THR C 872 " pdb=" CA THR C 872 " pdb=" OG1 THR C 872 " pdb=" CG2 THR C 872 " both_signs ideal model delta sigma weight residual False 2.55 1.08 1.47 2.00e-01 2.50e+01 5.43e+01 chirality pdb=" CB THR B 872 " pdb=" CA THR B 872 " pdb=" OG1 THR B 872 " pdb=" CG2 THR B 872 " both_signs ideal model delta sigma weight residual False 2.55 1.08 1.47 2.00e-01 2.50e+01 5.41e+01 chirality pdb=" CB THR A 872 " pdb=" CA THR A 872 " pdb=" OG1 THR A 872 " pdb=" CG2 THR A 872 " both_signs ideal model delta sigma weight residual False 2.55 1.08 1.47 2.00e-01 2.50e+01 5.40e+01 ... (remaining 2721 not shown) Planarity restraints: 5070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 194 " -0.077 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO B 195 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO B 195 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 195 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 194 " -0.075 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO C 195 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO C 195 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 195 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 480 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B 481 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 481 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 481 " -0.031 5.00e-02 4.00e+02 ... (remaining 5067 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.92: 91 1.92 - 2.59: 34213 2.59 - 3.26: 104125 3.26 - 3.93: 124404 3.93 - 4.60: 198179 Nonbonded interactions: 461012 Sorted by model distance: nonbonded pdb=" H ASN B 707 " pdb="HD22 ASN B 707 " model vdw 1.250 2.100 nonbonded pdb=" HA LEU B 921 " pdb=" HB3 LEU B 921 " model vdw 1.610 1.952 nonbonded pdb=" HA LEU C 921 " pdb=" HB3 LEU C 921 " model vdw 1.625 1.952 nonbonded pdb=" HA LEU A 921 " pdb=" HB3 LEU A 921 " model vdw 1.626 1.952 nonbonded pdb=" H LEU A 921 " pdb=" HA LEU A 921 " model vdw 1.641 1.816 ... (remaining 461007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 157 through 424 or (resid 425 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA )) or resid 426 through 958)) selection = (chain 'B' and (resid 157 through 424 or (resid 425 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA )) or resid 426 through 958)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 87 5.16 5 C 11421 2.51 5 N 2886 2.21 5 O 3087 1.98 5 H 16960 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.480 Extract box with map and model: 11.110 Check model and map are aligned: 0.510 Convert atoms to be neutral: 0.300 Process input model: 103.370 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.004 0.086 17985 Z= 0.252 Angle : 0.555 11.704 24465 Z= 0.308 Chirality : 0.063 1.474 2724 Planarity : 0.004 0.113 3054 Dihedral : 13.084 88.098 6426 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.19), residues: 2142 helix: 2.31 (0.16), residues: 1179 sheet: -0.81 (0.38), residues: 162 loop : -0.96 (0.22), residues: 801 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 294 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 297 average time/residue: 0.5720 time to fit residues: 266.3414 Evaluate side-chains 255 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 17985 Z= 0.246 Angle : 0.553 11.573 24465 Z= 0.298 Chirality : 0.063 1.456 2724 Planarity : 0.005 0.098 3054 Dihedral : 3.475 20.305 2352 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.15 (0.19), residues: 2142 helix: 2.18 (0.16), residues: 1188 sheet: -1.02 (0.36), residues: 162 loop : -1.09 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 267 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 277 average time/residue: 0.5728 time to fit residues: 248.3759 Evaluate side-chains 264 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 249 time to evaluate : 2.693 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3847 time to fit residues: 13.9828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN A 640 ASN C 640 ASN B 640 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 17985 Z= 0.241 Angle : 0.547 11.638 24465 Z= 0.290 Chirality : 0.063 1.482 2724 Planarity : 0.005 0.091 3054 Dihedral : 3.597 24.332 2352 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.03 (0.19), residues: 2142 helix: 2.04 (0.15), residues: 1194 sheet: -0.98 (0.35), residues: 165 loop : -1.10 (0.22), residues: 783 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 264 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 268 average time/residue: 0.5828 time to fit residues: 243.6720 Evaluate side-chains 252 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 244 time to evaluate : 2.762 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3766 time to fit residues: 9.0049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 131 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 186 optimal weight: 0.2980 chunk 56 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 17985 Z= 0.161 Angle : 0.521 11.556 24465 Z= 0.272 Chirality : 0.062 1.453 2724 Planarity : 0.005 0.113 3054 Dihedral : 3.531 22.778 2352 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.21 (0.19), residues: 2142 helix: 2.20 (0.15), residues: 1191 sheet: -0.89 (0.35), residues: 165 loop : -1.06 (0.22), residues: 786 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 260 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 252 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 255 average time/residue: 0.6036 time to fit residues: 237.1186 Evaluate side-chains 246 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 239 time to evaluate : 2.744 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.3660 time to fit residues: 8.1467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 155 optimal weight: 0.0040 chunk 86 optimal weight: 0.9990 chunk 178 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 17985 Z= 0.233 Angle : 0.532 11.565 24465 Z= 0.281 Chirality : 0.062 1.461 2724 Planarity : 0.005 0.111 3054 Dihedral : 3.593 23.500 2352 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.16 (0.19), residues: 2142 helix: 2.19 (0.15), residues: 1191 sheet: -0.89 (0.36), residues: 165 loop : -1.12 (0.22), residues: 786 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 251 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 254 average time/residue: 0.6191 time to fit residues: 241.9689 Evaluate side-chains 250 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 244 time to evaluate : 2.738 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4001 time to fit residues: 7.6685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 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 441 ASN B 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 17985 Z= 0.178 Angle : 0.521 11.624 24465 Z= 0.273 Chirality : 0.062 1.464 2724 Planarity : 0.005 0.119 3054 Dihedral : 3.550 20.959 2352 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.19), residues: 2142 helix: 2.32 (0.15), residues: 1182 sheet: -0.80 (0.36), residues: 165 loop : -1.11 (0.22), residues: 795 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 249 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 252 average time/residue: 0.6363 time to fit residues: 245.7443 Evaluate side-chains 239 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 236 time to evaluate : 2.717 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3692 time to fit residues: 5.7943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN A 714 GLN A 820 ASN C 509 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 17985 Z= 0.332 Angle : 0.583 11.626 24465 Z= 0.311 Chirality : 0.063 1.477 2724 Planarity : 0.006 0.119 3054 Dihedral : 3.809 22.529 2352 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.70 % Favored : 94.26 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.91 (0.19), residues: 2142 helix: 2.01 (0.15), residues: 1200 sheet: -0.63 (0.39), residues: 150 loop : -1.43 (0.21), residues: 792 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 246 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 248 average time/residue: 0.6505 time to fit residues: 244.7420 Evaluate side-chains 235 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 2.881 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3806 time to fit residues: 6.3265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 7.9990 chunk 83 optimal weight: 0.2980 chunk 124 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 141 optimal weight: 0.0980 chunk 102 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 17985 Z= 0.163 Angle : 0.531 11.544 24465 Z= 0.279 Chirality : 0.062 1.452 2724 Planarity : 0.006 0.131 3054 Dihedral : 3.648 22.398 2352 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.21 (0.19), residues: 2142 helix: 2.24 (0.15), residues: 1197 sheet: -0.48 (0.38), residues: 150 loop : -1.26 (0.21), residues: 795 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 233 average time/residue: 0.6153 time to fit residues: 221.3943 Evaluate side-chains 228 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 2.977 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3884 time to fit residues: 4.3976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.9990 chunk 181 optimal weight: 0.4980 chunk 194 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 17985 Z= 0.203 Angle : 0.543 11.516 24465 Z= 0.285 Chirality : 0.062 1.449 2724 Planarity : 0.006 0.146 3054 Dihedral : 3.635 22.057 2352 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 2142 helix: 2.34 (0.16), residues: 1182 sheet: -0.50 (0.38), residues: 150 loop : -1.33 (0.21), residues: 810 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 231 average time/residue: 0.6136 time to fit residues: 217.1641 Evaluate side-chains 226 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 2.736 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.3511 time to fit residues: 4.1264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 142 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 chunk 171 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 17985 Z= 0.169 Angle : 0.536 11.528 24465 Z= 0.281 Chirality : 0.062 1.448 2724 Planarity : 0.006 0.143 3054 Dihedral : 3.597 20.214 2352 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.30 (0.19), residues: 2142 helix: 2.41 (0.16), residues: 1182 sheet: -0.46 (0.38), residues: 150 loop : -1.31 (0.21), residues: 810 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 233 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 235 average time/residue: 0.6358 time to fit residues: 231.4532 Evaluate side-chains 230 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 2.753 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.3757 time to fit residues: 4.1751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 176 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.180251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.139254 restraints weight = 72469.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144824 restraints weight = 29841.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.145644 restraints weight = 19228.097| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 17985 Z= 0.187 Angle : 0.538 11.577 24465 Z= 0.282 Chirality : 0.062 1.453 2724 Planarity : 0.006 0.139 3054 Dihedral : 3.563 21.395 2352 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.30 (0.19), residues: 2142 helix: 2.40 (0.16), residues: 1185 sheet: -0.50 (0.38), residues: 150 loop : -1.31 (0.21), residues: 807 =============================================================================== Job complete usr+sys time: 6005.73 seconds wall clock time: 107 minutes 30.18 seconds (6450.18 seconds total)