Starting phenix.real_space_refine on Mon May 26 03:49:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yro_39546/05_2025/8yro_39546.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yro_39546/05_2025/8yro_39546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yro_39546/05_2025/8yro_39546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yro_39546/05_2025/8yro_39546.map" model { file = "/net/cci-nas-00/data/ceres_data/8yro_39546/05_2025/8yro_39546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yro_39546/05_2025/8yro_39546.cif" } resolution = 3.27 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= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 17669 2.51 5 N 4656 2.21 5 O 5332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27775 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7535 Classifications: {'peptide': 970} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 48, 'TRANS': 921} Chain breaks: 13 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 7547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7547 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 47, 'TRANS': 919} Chain breaks: 14 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 3, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "P" Number of atoms: 7491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7491 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 45, 'TRANS': 913} Chain breaks: 16 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 939 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 795 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "B" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 939 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 795 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 939 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "F" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 795 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Time building chain proxies: 17.30, per 1000 atoms: 0.62 Number of scatterers: 27775 At special positions: 0 Unit cell: (157.151, 150.511, 187.032, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 5332 8.00 N 4656 7.00 C 17669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.05 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.02 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.02 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 166 " distance=2.03 Simple disulfide: pdb=" SG CYS P 291 " - pdb=" SG CYS P 301 " distance=2.03 Simple disulfide: pdb=" SG CYS P 336 " - pdb=" SG CYS P 361 " distance=2.03 Simple disulfide: pdb=" SG CYS P 379 " - pdb=" SG CYS P 432 " distance=2.04 Simple disulfide: pdb=" SG CYS P 480 " - pdb=" SG CYS P 488 " distance=2.03 Simple disulfide: pdb=" SG CYS P 538 " - pdb=" SG CYS P 590 " distance=2.02 Simple disulfide: pdb=" SG CYS P 617 " - pdb=" SG CYS P 649 " distance=2.03 Simple disulfide: pdb=" SG CYS P 662 " - pdb=" SG CYS P 671 " distance=2.03 Simple disulfide: pdb=" SG CYS P 738 " - pdb=" SG CYS P 760 " distance=2.03 Simple disulfide: pdb=" SG CYS P 743 " - pdb=" SG CYS P 749 " distance=2.02 Simple disulfide: pdb=" SG CYS P1032 " - pdb=" SG CYS P1043 " distance=2.03 Simple disulfide: pdb=" SG CYS P1082 " - pdb=" SG CYS P1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 97 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 97 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 7.01 Conformation dependent library (CDL) restraints added in 3.8 seconds 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6654 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 64 sheets defined 18.2% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.513A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.886A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.310A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 390' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 759 through 782 removed outlier: 3.611A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 871 removed outlier: 3.504A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.519A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 936 Processing helix chain 'A' and resid 946 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.733A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.780A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.528A pdb=" N GLU D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.661A pdb=" N TYR D 421 " --> pdb=" O LYS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 737 through 742 Processing helix chain 'D' and resid 747 through 755 Processing helix chain 'D' and resid 759 through 782 removed outlier: 3.612A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.537A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 890 removed outlier: 3.675A pdb=" N ALA D 890 " --> pdb=" O THR D 887 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 removed outlier: 4.104A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 935 Processing helix chain 'D' and resid 946 through 965 Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 removed outlier: 3.916A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 1032 Processing helix chain 'P' and resid 294 through 304 Processing helix chain 'P' and resid 338 through 343 Processing helix chain 'P' and resid 384 through 388 removed outlier: 3.615A pdb=" N LEU P 387 " --> pdb=" O PRO P 384 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN P 388 " --> pdb=" O THR P 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 384 through 388' Processing helix chain 'P' and resid 416 through 421 removed outlier: 3.606A pdb=" N TYR P 421 " --> pdb=" O LYS P 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 438 through 443 Processing helix chain 'P' and resid 737 through 742 Processing helix chain 'P' and resid 746 through 755 removed outlier: 3.934A pdb=" N SER P 750 " --> pdb=" O SER P 746 " (cutoff:3.500A) Processing helix chain 'P' and resid 758 through 783 removed outlier: 3.627A pdb=" N GLN P 762 " --> pdb=" O SER P 758 " (cutoff:3.500A) Processing helix chain 'P' and resid 816 through 826 removed outlier: 3.585A pdb=" N VAL P 826 " --> pdb=" O LEU P 822 " (cutoff:3.500A) Processing helix chain 'P' and resid 872 through 883 Processing helix chain 'P' and resid 897 through 908 removed outlier: 4.939A pdb=" N ALA P 903 " --> pdb=" O ALA P 899 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR P 904 " --> pdb=" O MET P 900 " (cutoff:3.500A) Processing helix chain 'P' and resid 913 through 918 removed outlier: 3.522A pdb=" N TYR P 917 " --> pdb=" O GLN P 913 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU P 918 " --> pdb=" O ASN P 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 913 through 918' Processing helix chain 'P' and resid 919 through 939 removed outlier: 3.678A pdb=" N ALA P 924 " --> pdb=" O GLN P 920 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASN P 925 " --> pdb=" O LYS P 921 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN P 926 " --> pdb=" O LEU P 922 " (cutoff:3.500A) Processing helix chain 'P' and resid 946 through 964 Processing helix chain 'P' and resid 965 through 968 Processing helix chain 'P' and resid 977 through 984 removed outlier: 3.502A pdb=" N LEU P 981 " --> pdb=" O LEU P 977 " (cutoff:3.500A) Processing helix chain 'P' and resid 985 through 1032 removed outlier: 4.792A pdb=" N VAL P 991 " --> pdb=" O PRO P 987 " (cutoff:3.500A) Processing helix chain 'P' and resid 1116 through 1120 removed outlier: 3.868A pdb=" N ASN P1119 " --> pdb=" O THR P1116 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR P1120 " --> pdb=" O THR P1117 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 1116 through 1120' Processing helix chain 'L' and resid 88 through 92 removed outlier: 3.896A pdb=" N GLU L 92 " --> pdb=" O SER L 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.524A pdb=" N SER B 32 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS B 33 " --> pdb=" O PHE B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 33' Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.672A pdb=" N ASP F 91 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU F 92 " --> pdb=" O SER F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 88 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.782A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.776A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.172A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.743A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 191 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 190 through 191 current: chain 'A' and resid 200 through 207 removed outlier: 6.173A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.349A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.496A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.112A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.453A pdb=" N PHE A 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.264A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 7.916A pdb=" N ASN A 703 " --> pdb=" O LYS D 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 718 through 728 current: chain 'A' and resid 1059 through 1069 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.595A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1088 through 1089 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.839A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 50 through 55 removed outlier: 3.863A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.540A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 117 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 120 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 90 through 92 current: chain 'D' and resid 188 through 194 removed outlier: 3.556A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 311 through 314 Processing sheet with id=AC5, first strand: chain 'D' and resid 318 through 319 Processing sheet with id=AC6, first strand: chain 'D' and resid 325 through 328 removed outlier: 6.557A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 585 " --> pdb=" O VAL D 576 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 357 through 358 removed outlier: 4.348A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR D 430 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.006A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER D 691 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 666 " --> pdb=" O ILE D 670 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 711 through 713 Processing sheet with id=AD2, first strand: chain 'D' and resid 719 through 728 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 719 through 728 current: chain 'D' and resid 1059 through 1068 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 734 through 735 Processing sheet with id=AD4, first strand: chain 'D' and resid 1095 through 1097 Processing sheet with id=AD5, first strand: chain 'P' and resid 28 through 31 removed outlier: 3.904A pdb=" N SER P 60 " --> pdb=" O SER P 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 50 through 52 removed outlier: 3.583A pdb=" N ASP P 287 " --> pdb=" O LYS P 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'P' and resid 92 through 94 removed outlier: 3.549A pdb=" N ALA P 93 " --> pdb=" O TYR P 266 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 118 through 120 Processing sheet with id=AE1, first strand: chain 'P' and resid 190 through 191 removed outlier: 6.440A pdb=" N SER P 205 " --> pdb=" O PRO P 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 311 through 314 Processing sheet with id=AE3, first strand: chain 'P' and resid 318 through 319 Processing sheet with id=AE4, first strand: chain 'P' and resid 325 through 328 removed outlier: 6.612A pdb=" N ILE P 326 " --> pdb=" O ASN P 542 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 376 through 380 removed outlier: 4.113A pdb=" N THR P 430 " --> pdb=" O PHE P 515 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU P 516 " --> pdb=" O ASN P 394 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN P 394 " --> pdb=" O GLU P 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'P' and resid 654 through 655 removed outlier: 6.104A pdb=" N GLU P 654 " --> pdb=" O ALA P 694 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N THR P 696 " --> pdb=" O GLU P 654 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE P 670 " --> pdb=" O ILE P 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 711 through 719 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 711 through 719 current: chain 'P' and resid 1059 through 1077 removed outlier: 3.783A pdb=" N THR P1076 " --> pdb=" O SER P1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 735 through 736 Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.548A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 101 through 103 Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AF5, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF6, first strand: chain 'L' and resid 50 through 54 removed outlier: 6.339A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AF9, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AG1, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AG2, first strand: chain 'C' and resid 9 through 11 Processing sheet with id=AG3, first strand: chain 'C' and resid 19 through 24 Processing sheet with id=AG4, first strand: chain 'C' and resid 50 through 54 removed outlier: 6.202A pdb=" N TRP C 41 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AG6, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AG7, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AG8, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.600A pdb=" N SER F 24 " --> pdb=" O THR F 5 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 9 through 11 Processing sheet with id=AH1, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.340A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) 853 hydrogen bonds defined for protein. 2304 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: 11.30 Time building geometry restraints manager: 8.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 4578 1.29 - 1.43: 7708 1.43 - 1.58: 15949 1.58 - 1.72: 0 1.72 - 1.86: 144 Bond restraints: 28379 Sorted by residual: bond pdb=" C PHE P 802 " pdb=" O PHE P 802 " ideal model delta sigma weight residual 1.235 1.146 0.089 1.26e-02 6.30e+03 5.04e+01 bond pdb=" C ASN P 801 " pdb=" O ASN P 801 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.26e-02 6.30e+03 1.46e+01 bond pdb=" N VAL P 781 " pdb=" CA VAL P 781 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.06e-02 8.90e+03 1.41e+01 bond pdb=" N PHE P 802 " pdb=" CA PHE P 802 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.22e+01 bond pdb=" C ALA A1056 " pdb=" N PRO A1057 " ideal model delta sigma weight residual 1.332 1.370 -0.038 1.12e-02 7.97e+03 1.16e+01 ... (remaining 28374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 37762 2.94 - 5.88: 714 5.88 - 8.82: 73 8.82 - 11.76: 19 11.76 - 14.70: 10 Bond angle restraints: 38578 Sorted by residual: angle pdb=" CA ILE P 805 " pdb=" C ILE P 805 " pdb=" O ILE P 805 " ideal model delta sigma weight residual 120.78 107.48 13.30 1.25e+00 6.40e-01 1.13e+02 angle pdb=" N THR A 618 " pdb=" CA THR A 618 " pdb=" C THR A 618 " ideal model delta sigma weight residual 113.23 100.58 12.65 1.24e+00 6.50e-01 1.04e+02 angle pdb=" CA ASN P 801 " pdb=" CB ASN P 801 " pdb=" CG ASN P 801 " ideal model delta sigma weight residual 112.60 122.22 -9.62 1.00e+00 1.00e+00 9.25e+01 angle pdb=" CA PHE P 802 " pdb=" CB PHE P 802 " pdb=" CG PHE P 802 " ideal model delta sigma weight residual 113.80 104.99 8.81 1.00e+00 1.00e+00 7.77e+01 angle pdb=" CA ILE P 805 " pdb=" C ILE P 805 " pdb=" N LEU P 806 " ideal model delta sigma weight residual 116.60 128.92 -12.32 1.45e+00 4.76e-01 7.22e+01 ... (remaining 38573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 15012 18.03 - 36.07: 1445 36.07 - 54.10: 289 54.10 - 72.13: 73 72.13 - 90.17: 36 Dihedral angle restraints: 16855 sinusoidal: 6509 harmonic: 10346 Sorted by residual: dihedral pdb=" N PHE P 802 " pdb=" C PHE P 802 " pdb=" CA PHE P 802 " pdb=" CB PHE P 802 " ideal model delta harmonic sigma weight residual 122.80 148.33 -25.53 0 2.50e+00 1.60e-01 1.04e+02 dihedral pdb=" CB CYS P 336 " pdb=" SG CYS P 336 " pdb=" SG CYS P 361 " pdb=" CB CYS P 361 " ideal model delta sinusoidal sigma weight residual 93.00 -176.83 -90.17 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS D 291 " pdb=" SG CYS D 291 " pdb=" SG CYS D 301 " pdb=" CB CYS D 301 " ideal model delta sinusoidal sigma weight residual 93.00 -179.72 -87.28 1 1.00e+01 1.00e-02 9.14e+01 ... (remaining 16852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.201: 4348 0.201 - 0.401: 27 0.401 - 0.602: 1 0.602 - 0.802: 0 0.802 - 1.003: 1 Chirality restraints: 4377 Sorted by residual: chirality pdb=" CA PHE P 802 " pdb=" N PHE P 802 " pdb=" C PHE P 802 " pdb=" CB PHE P 802 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CB VAL P1128 " pdb=" CA VAL P1128 " pdb=" CG1 VAL P1128 " pdb=" CG2 VAL P1128 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CA ILE D 896 " pdb=" N ILE D 896 " pdb=" C ILE D 896 " pdb=" CB ILE D 896 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 4374 not shown) Planarity restraints: 4987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE P 802 " -0.068 2.00e-02 2.50e+03 4.78e-02 4.00e+01 pdb=" CG PHE P 802 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 PHE P 802 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE P 802 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE P 802 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE P 802 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE P 802 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE P 800 " -0.025 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C PHE P 800 " 0.088 2.00e-02 2.50e+03 pdb=" O PHE P 800 " -0.034 2.00e-02 2.50e+03 pdb=" N ASN P 801 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 617 " 0.022 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C CYS A 617 " -0.082 2.00e-02 2.50e+03 pdb=" O CYS A 617 " 0.032 2.00e-02 2.50e+03 pdb=" N THR A 618 " 0.028 2.00e-02 2.50e+03 ... (remaining 4984 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 7 1.92 - 2.67: 660 2.67 - 3.41: 36920 3.41 - 4.16: 68082 4.16 - 4.90: 117397 Nonbonded interactions: 223066 Sorted by model distance: nonbonded pdb=" CD1 ILE P 805 " pdb=" CG1 ILE P 818 " model vdw 1.176 3.860 nonbonded pdb=" CG1 ILE P 805 " pdb=" CB ILE P 818 " model vdw 1.379 3.870 nonbonded pdb=" O HIS H 110 " pdb=" O GLY H 111 " model vdw 1.539 3.040 nonbonded pdb=" CG1 ILE P 805 " pdb=" CG1 ILE P 818 " model vdw 1.611 3.840 nonbonded pdb=" O ALA A 363 " pdb=" CG PRO A 527 " model vdw 1.722 3.440 ... (remaining 223061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 141 or (resid 142 and (name N or name CA or nam \ e C or name O or name CB )) or resid 166 through 274 or (resid 275 and (name N o \ r name CA or name C or name O or name CB )) or resid 276 through 475 or resid 48 \ 7 through 526 or resid 529 through 707 or resid 710 through 785 or resid 788 thr \ ough 865 or resid 871 through 884 or resid 893 through 935 or resid 945 through \ 1069 or resid 1073 through 1089 or resid 1094 through 1120 or (resid 1121 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1122 through 1123 or \ resid 1125 through 1140)) selection = (chain 'D' and (resid 27 through 68 or resid 80 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 122 or resi \ d 125 through 142 or resid 166 through 209 or resid 216 through 243 or resid 263 \ through 475 or resid 487 through 526 or resid 529 through 785 or resid 788 thro \ ugh 865 or resid 871 through 872 or (resid 873 and (name N or name CA or name C \ or name O or name CB )) or resid 874 through 881 or (resid 882 and (name N or na \ me CA or name C or name O or name CB )) or resid 883 through 884 or resid 893 th \ rough 897 or (resid 898 through 899 and (name N or name CA or name C or name O o \ r name CB )) or resid 900 through 905 or (resid 906 and (name N or name CA or na \ me C or name O or name CB )) or resid 907 through 1089 or resid 1094 through 110 \ 5 or (resid 1109 and (name N or name CA or name C or name O or name CB )) or res \ id 1110 through 1123 or resid 1125 through 1140)) selection = (chain 'P' and (resid 27 through 96 or (resid 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 through 141 or (resid 142 and (name N or n \ ame CA or name C or name O or name CB )) or resid 166 through 209 or resid 216 t \ hrough 475 or resid 487 through 707 or resid 710 through 881 or (resid 882 and ( \ name N or name CA or name C or name O or name CB )) or resid 883 through 897 or \ (resid 898 through 899 and (name N or name CA or name C or name O or name CB )) \ or resid 900 through 905 or (resid 906 and (name N or name CA or name C or name \ O or name CB )) or resid 907 through 916 or (resid 917 and (name N or name CA or \ name C or name O or name CB )) or resid 918 through 935 or resid 945 through 10 \ 69 or resid 1073 through 1089 or resid 1094 through 1105 or (resid 1109 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1110 through 1120 or ( \ resid 1121 and (name N or name CA or name C or name O or name CB )) or resid 112 \ 2 through 1140)) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'L' } 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: 2.950 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: 0.040 Extract box with map and model: 1.120 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 65.090 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.130 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 28421 Z= 0.296 Angle : 1.018 14.702 38662 Z= 0.572 Chirality : 0.062 1.003 4377 Planarity : 0.007 0.082 4987 Dihedral : 15.189 88.797 10075 Min Nonbonded Distance : 1.176 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.85 % Favored : 93.74 % Rotamer: Outliers : 0.58 % Allowed : 8.77 % Favored : 90.65 % Cbeta Deviations : 0.06 % 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: -3.94 (0.11), residues: 3485 helix: -3.13 (0.13), residues: 581 sheet: -2.26 (0.17), residues: 716 loop : -2.70 (0.11), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 886 HIS 0.011 0.002 HIS E 110 PHE 0.103 0.003 PHE P 802 TYR 0.030 0.002 TYR P 495 ARG 0.006 0.001 ARG D 328 Details of bonding type rmsd hydrogen bonds : bond 0.25839 ( 853) hydrogen bonds : angle 9.96555 ( 2304) SS BOND : bond 0.00725 ( 42) SS BOND : angle 3.55366 ( 84) covalent geometry : bond 0.00603 (28379) covalent geometry : angle 1.00595 (38578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 358 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7182 (m-30) cc_final: 0.6871 (m-30) REVERT: A 920 GLN cc_start: 0.5704 (mm-40) cc_final: 0.5198 (mm-40) REVERT: A 923 ILE cc_start: 0.6136 (mt) cc_final: 0.5546 (mt) REVERT: A 1086 LYS cc_start: 0.2746 (pttm) cc_final: 0.0894 (mmtm) REVERT: A 1142 GLN cc_start: 0.6746 (mm110) cc_final: 0.5744 (pt0) REVERT: D 52 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7709 (tm-30) REVERT: D 886 TRP cc_start: 0.6823 (p90) cc_final: 0.6270 (p90) REVERT: D 923 ILE cc_start: 0.5337 (mp) cc_final: 0.4866 (mp) REVERT: D 1086 LYS cc_start: 0.6253 (mppt) cc_final: 0.5892 (mtmt) REVERT: P 800 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: P 802 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.6933 (t80) REVERT: H 103 ARG cc_start: 0.0562 (ttm170) cc_final: 0.0189 (mmm-85) REVERT: H 109 SER cc_start: 0.2590 (OUTLIER) cc_final: 0.1678 (t) REVERT: B 40 GLN cc_start: 0.2511 (tt0) cc_final: 0.1383 (mp10) outliers start: 18 outliers final: 4 residues processed: 373 average time/residue: 0.3818 time to fit residues: 228.4278 Evaluate side-chains 187 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain P residue 590 CYS Chi-restraints excluded: chain P residue 800 PHE Chi-restraints excluded: chain P residue 801 ASN Chi-restraints excluded: chain P residue 802 PHE Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 30.0000 chunk 270 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 279 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 170 optimal weight: 0.5980 chunk 208 optimal weight: 5.9990 chunk 324 optimal weight: 20.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 920 GLN A 954 GLN A 969 ASN A 978 ASN A1010 GLN A1011 GLN A1023 ASN A1048 HIS D 66 HIS D 81 ASN D 188 ASN D 211 ASN D 919 ASN D 935 GLN D 954 GLN D 978 ASN D1023 ASN D1054 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 125 ASN P 360 ASN P 370 ASN P 394 ASN P 774 GLN ** P 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 935 GLN P1023 ASN P1054 GLN P1101 HIS P1108 ASN L 1 GLN L 40 ASN L 88 GLN L 105 ASN ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS C 59 GLN C 88 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN F 105 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.245945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.217468 restraints weight = 45209.359| |-----------------------------------------------------------------------------| r_work (start): 0.4831 rms_B_bonded: 2.59 r_work: 0.4467 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 28421 Z= 0.162 Angle : 0.675 11.232 38662 Z= 0.358 Chirality : 0.047 0.210 4377 Planarity : 0.005 0.070 4987 Dihedral : 6.068 59.344 3823 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 2.69 % Allowed : 12.59 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.81 (0.13), residues: 3485 helix: -0.48 (0.20), residues: 586 sheet: -1.91 (0.18), residues: 725 loop : -2.35 (0.12), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P1102 HIS 0.009 0.001 HIS E 33 PHE 0.025 0.002 PHE P 802 TYR 0.021 0.001 TYR A 170 ARG 0.005 0.000 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.05809 ( 853) hydrogen bonds : angle 6.65400 ( 2304) SS BOND : bond 0.00454 ( 42) SS BOND : angle 2.40193 ( 84) covalent geometry : bond 0.00369 (28379) covalent geometry : angle 0.66617 (38578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 198 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 920 GLN cc_start: 0.6596 (mm110) cc_final: 0.6198 (mm110) REVERT: A 923 ILE cc_start: 0.6326 (mt) cc_final: 0.5600 (mt) REVERT: A 1086 LYS cc_start: 0.4222 (pttm) cc_final: 0.1882 (mmtt) REVERT: A 1142 GLN cc_start: 0.6980 (mm110) cc_final: 0.5762 (pt0) REVERT: D 52 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7336 (tm-30) REVERT: D 266 TYR cc_start: 0.5893 (m-10) cc_final: 0.5214 (m-80) REVERT: D 886 TRP cc_start: 0.7009 (p90) cc_final: 0.6714 (p90) REVERT: D 920 GLN cc_start: 0.5717 (tp40) cc_final: 0.4618 (pt0) REVERT: D 923 ILE cc_start: 0.5649 (OUTLIER) cc_final: 0.5269 (mp) REVERT: D 990 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6831 (tt0) REVERT: D 1086 LYS cc_start: 0.6757 (mppt) cc_final: 0.6498 (mtmt) REVERT: P 102 ARG cc_start: 0.6848 (mtt90) cc_final: 0.6638 (ptm-80) REVERT: P 282 ASN cc_start: 0.7750 (t0) cc_final: 0.7496 (m110) REVERT: P 789 TYR cc_start: 0.3903 (m-80) cc_final: 0.3506 (m-80) REVERT: P 872 GLN cc_start: 0.7701 (tp-100) cc_final: 0.7093 (tt0) REVERT: P 935 GLN cc_start: 0.8010 (tt0) cc_final: 0.7737 (tt0) REVERT: H 40 GLN cc_start: 0.2646 (tt0) cc_final: 0.1290 (mp10) REVERT: H 103 ARG cc_start: 0.0626 (ttm170) cc_final: -0.0047 (tpp80) REVERT: H 112 MET cc_start: 0.1894 (OUTLIER) cc_final: 0.1600 (mmm) REVERT: B 40 GLN cc_start: 0.2837 (tt0) cc_final: 0.1960 (mp10) REVERT: E 40 GLN cc_start: 0.2324 (tt0) cc_final: 0.0927 (mp10) REVERT: E 46 LEU cc_start: 0.1896 (OUTLIER) cc_final: 0.1649 (mt) outliers start: 83 outliers final: 31 residues processed: 262 average time/residue: 0.3384 time to fit residues: 149.0512 Evaluate side-chains 197 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 188 ASN Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 902 MET Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain P residue 131 CYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain P residue 538 CYS Chi-restraints excluded: chain P residue 590 CYS Chi-restraints excluded: chain P residue 718 PHE Chi-restraints excluded: chain P residue 763 LEU Chi-restraints excluded: chain P residue 802 PHE Chi-restraints excluded: chain P residue 874 THR Chi-restraints excluded: chain P residue 1108 ASN Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 125 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 304 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 333 optimal weight: 30.0000 chunk 196 optimal weight: 3.9990 chunk 280 optimal weight: 0.5980 chunk 325 optimal weight: 6.9990 chunk 354 optimal weight: 30.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1048 HIS D 66 HIS D 188 ASN D 314 GLN D 675 GLN D 755 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 965 GLN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.245240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.213420 restraints weight = 44814.901| |-----------------------------------------------------------------------------| r_work (start): 0.4773 rms_B_bonded: 3.15 r_work: 0.4383 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28421 Z= 0.137 Angle : 0.604 11.608 38662 Z= 0.319 Chirality : 0.045 0.210 4377 Planarity : 0.005 0.067 4987 Dihedral : 5.592 59.942 3818 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.52 % Allowed : 14.50 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.31 (0.13), residues: 3485 helix: 0.43 (0.22), residues: 594 sheet: -1.75 (0.18), residues: 751 loop : -2.12 (0.12), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 100 HIS 0.008 0.001 HIS D 66 PHE 0.022 0.001 PHE D 168 TYR 0.026 0.001 TYR D1067 ARG 0.005 0.000 ARG A 567 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 853) hydrogen bonds : angle 6.15339 ( 2304) SS BOND : bond 0.00389 ( 42) SS BOND : angle 1.92230 ( 84) covalent geometry : bond 0.00315 (28379) covalent geometry : angle 0.59847 (38578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 177 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.6950 (tt0) cc_final: 0.6528 (mt0) REVERT: A 920 GLN cc_start: 0.6747 (mm110) cc_final: 0.6296 (mm110) REVERT: A 923 ILE cc_start: 0.6389 (mt) cc_final: 0.5663 (mt) REVERT: A 1142 GLN cc_start: 0.7133 (mm110) cc_final: 0.5808 (pt0) REVERT: D 266 TYR cc_start: 0.6050 (m-10) cc_final: 0.5522 (m-10) REVERT: D 358 ILE cc_start: 0.2083 (OUTLIER) cc_final: 0.1838 (mt) REVERT: D 886 TRP cc_start: 0.7185 (p90) cc_final: 0.6728 (p90) REVERT: D 916 LEU cc_start: -0.0335 (OUTLIER) cc_final: -0.0605 (tt) REVERT: D 920 GLN cc_start: 0.6181 (tp40) cc_final: 0.4536 (pt0) REVERT: D 923 ILE cc_start: 0.5781 (OUTLIER) cc_final: 0.5197 (mp) REVERT: D 996 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8604 (mm) REVERT: D 1125 ASN cc_start: 0.4138 (t0) cc_final: 0.3437 (m-40) REVERT: P 789 TYR cc_start: 0.4248 (m-80) cc_final: 0.3843 (m-80) REVERT: P 802 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6524 (t80) REVERT: P 872 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7533 (tm-30) REVERT: P 902 MET cc_start: 0.7881 (mmm) cc_final: 0.7597 (mmm) REVERT: H 40 GLN cc_start: 0.1729 (tt0) cc_final: 0.0911 (mp10) REVERT: H 112 MET cc_start: 0.1579 (OUTLIER) cc_final: 0.1378 (mmm) REVERT: B 40 GLN cc_start: 0.2336 (tt0) cc_final: 0.1696 (mp10) REVERT: B 103 ARG cc_start: -0.0316 (ttt90) cc_final: -0.0578 (mmm-85) REVERT: E 40 GLN cc_start: 0.1352 (tt0) cc_final: 0.0900 (mt0) REVERT: E 46 LEU cc_start: 0.1705 (OUTLIER) cc_final: 0.1184 (mt) outliers start: 78 outliers final: 43 residues processed: 234 average time/residue: 0.3397 time to fit residues: 134.2460 Evaluate side-chains 202 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 902 MET Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain P residue 131 CYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 538 CYS Chi-restraints excluded: chain P residue 582 LEU Chi-restraints excluded: chain P residue 590 CYS Chi-restraints excluded: chain P residue 615 VAL Chi-restraints excluded: chain P residue 718 PHE Chi-restraints excluded: chain P residue 738 CYS Chi-restraints excluded: chain P residue 747 THR Chi-restraints excluded: chain P residue 802 PHE Chi-restraints excluded: chain P residue 858 LEU Chi-restraints excluded: chain P residue 959 LEU Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain E residue 46 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 216 optimal weight: 0.0970 chunk 324 optimal weight: 9.9990 chunk 75 optimal weight: 0.0470 chunk 152 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 282 optimal weight: 0.8980 chunk 253 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 235 optimal weight: 9.9990 chunk 51 optimal weight: 0.0370 chunk 87 optimal weight: 0.8980 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 969 ASN D 66 HIS ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 755 GLN D1083 HIS ** P 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 919 ASN P1108 ASN P1113 GLN ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN F 88 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.241099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.207481 restraints weight = 46492.635| |-----------------------------------------------------------------------------| r_work (start): 0.4790 rms_B_bonded: 4.32 r_work: 0.4368 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 28421 Z= 0.105 Angle : 0.549 10.412 38662 Z= 0.288 Chirality : 0.044 0.237 4377 Planarity : 0.004 0.066 4987 Dihedral : 5.148 55.781 3817 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.98 % Allowed : 15.21 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.98 (0.14), residues: 3485 helix: 0.92 (0.22), residues: 595 sheet: -1.54 (0.17), residues: 796 loop : -1.97 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 100 HIS 0.010 0.001 HIS P1088 PHE 0.020 0.001 PHE D 168 TYR 0.024 0.001 TYR D 170 ARG 0.004 0.000 ARG E 103 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 853) hydrogen bonds : angle 5.76177 ( 2304) SS BOND : bond 0.00372 ( 42) SS BOND : angle 1.73223 ( 84) covalent geometry : bond 0.00238 (28379) covalent geometry : angle 0.54389 (38578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 185 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.6095 (OUTLIER) cc_final: 0.5887 (p) REVERT: A 239 GLN cc_start: 0.7030 (tt0) cc_final: 0.6445 (mt0) REVERT: A 920 GLN cc_start: 0.6712 (mm110) cc_final: 0.4088 (pt0) REVERT: A 923 ILE cc_start: 0.6315 (mt) cc_final: 0.5581 (mt) REVERT: A 983 ARG cc_start: 0.7555 (ttp80) cc_final: 0.7298 (tmt170) REVERT: A 1142 GLN cc_start: 0.7071 (mm110) cc_final: 0.6373 (mt0) REVERT: D 170 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: D 266 TYR cc_start: 0.6090 (m-10) cc_final: 0.5674 (m-10) REVERT: D 358 ILE cc_start: 0.2410 (OUTLIER) cc_final: 0.2172 (mt) REVERT: D 886 TRP cc_start: 0.7117 (p90) cc_final: 0.6739 (p90) REVERT: D 916 LEU cc_start: 0.0325 (OUTLIER) cc_final: -0.0319 (tt) REVERT: D 920 GLN cc_start: 0.5943 (tp40) cc_final: 0.4158 (pt0) REVERT: D 923 ILE cc_start: 0.5700 (OUTLIER) cc_final: 0.5080 (mp) REVERT: D 990 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: D 996 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8453 (mm) REVERT: D 1086 LYS cc_start: 0.6766 (mppt) cc_final: 0.6446 (mtmm) REVERT: D 1125 ASN cc_start: 0.4396 (t0) cc_final: 0.3755 (m-40) REVERT: P 361 CYS cc_start: 0.6382 (OUTLIER) cc_final: 0.6049 (t) REVERT: P 789 TYR cc_start: 0.3880 (m-80) cc_final: 0.3488 (m-80) REVERT: P 802 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.6502 (t80) REVERT: P 872 GLN cc_start: 0.8065 (tp-100) cc_final: 0.7766 (tm-30) REVERT: P 902 MET cc_start: 0.7961 (mmm) cc_final: 0.7705 (mmm) REVERT: H 40 GLN cc_start: 0.1113 (tt0) cc_final: 0.0597 (mp10) REVERT: H 103 ARG cc_start: -0.0294 (ttm170) cc_final: -0.0961 (mmm-85) REVERT: B 40 GLN cc_start: 0.1848 (tt0) cc_final: 0.1480 (mp10) REVERT: E 40 GLN cc_start: 0.0843 (tt0) cc_final: 0.0601 (mt0) REVERT: E 46 LEU cc_start: 0.1395 (OUTLIER) cc_final: 0.0859 (mt) REVERT: E 112 MET cc_start: 0.0530 (mmt) cc_final: 0.0249 (mmt) outliers start: 92 outliers final: 50 residues processed: 258 average time/residue: 0.3461 time to fit residues: 151.4060 Evaluate side-chains 218 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 158 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 902 MET Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain P residue 131 CYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 538 CYS Chi-restraints excluded: chain P residue 582 LEU Chi-restraints excluded: chain P residue 615 VAL Chi-restraints excluded: chain P residue 738 CYS Chi-restraints excluded: chain P residue 747 THR Chi-restraints excluded: chain P residue 802 PHE Chi-restraints excluded: chain P residue 858 LEU Chi-restraints excluded: chain P residue 874 THR Chi-restraints excluded: chain P residue 959 LEU Chi-restraints excluded: chain P residue 1083 HIS Chi-restraints excluded: chain P residue 1137 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain E residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 297 optimal weight: 8.9990 chunk 219 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 298 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 263 optimal weight: 0.4980 chunk 129 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 969 ASN D 66 HIS D 655 HIS ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 755 GLN ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1054 GLN ** P 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 801 ASN ** P 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN C 57 ASN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.233877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.198783 restraints weight = 44148.534| |-----------------------------------------------------------------------------| r_work (start): 0.4715 rms_B_bonded: 4.01 r_work: 0.4208 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 28421 Z= 0.264 Angle : 0.735 18.334 38662 Z= 0.384 Chirality : 0.050 0.302 4377 Planarity : 0.006 0.099 4987 Dihedral : 5.820 52.001 3816 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.62 % Allowed : 16.05 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.13 (0.13), residues: 3485 helix: 0.71 (0.22), residues: 591 sheet: -1.48 (0.17), residues: 830 loop : -2.11 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D1102 HIS 0.019 0.002 HIS P1088 PHE 0.040 0.002 PHE A1075 TYR 0.026 0.002 TYR A 269 ARG 0.006 0.001 ARG D 577 Details of bonding type rmsd hydrogen bonds : bond 0.05301 ( 853) hydrogen bonds : angle 6.18154 ( 2304) SS BOND : bond 0.00579 ( 42) SS BOND : angle 2.28146 ( 84) covalent geometry : bond 0.00630 (28379) covalent geometry : angle 0.72778 (38578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 161 time to evaluate : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7084 (tt0) cc_final: 0.6522 (mt0) REVERT: A 914 ASN cc_start: 0.4207 (OUTLIER) cc_final: 0.1066 (t0) REVERT: A 920 GLN cc_start: 0.7169 (mm110) cc_final: 0.6243 (mm110) REVERT: A 923 ILE cc_start: 0.6604 (mt) cc_final: 0.6042 (mt) REVERT: A 985 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.7058 (p0) REVERT: A 1126 CYS cc_start: 0.2920 (OUTLIER) cc_final: 0.2588 (m) REVERT: A 1142 GLN cc_start: 0.7286 (mm110) cc_final: 0.6524 (mt0) REVERT: D 266 TYR cc_start: 0.6980 (m-10) cc_final: 0.6504 (m-10) REVERT: D 358 ILE cc_start: 0.2222 (OUTLIER) cc_final: 0.1977 (mt) REVERT: D 574 ASP cc_start: 0.7845 (t70) cc_final: 0.7438 (t0) REVERT: D 886 TRP cc_start: 0.7293 (p90) cc_final: 0.6866 (p90) REVERT: D 920 GLN cc_start: 0.7035 (tp40) cc_final: 0.6054 (mm-40) REVERT: D 922 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6913 (mt) REVERT: D 923 ILE cc_start: 0.5960 (OUTLIER) cc_final: 0.5645 (mp) REVERT: D 996 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8538 (mm) REVERT: D 1017 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8174 (tt0) REVERT: D 1086 LYS cc_start: 0.7260 (mppt) cc_final: 0.6964 (mtmm) REVERT: P 318 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8056 (p90) REVERT: P 789 TYR cc_start: 0.5760 (m-80) cc_final: 0.4901 (m-80) REVERT: P 902 MET cc_start: 0.8458 (mmm) cc_final: 0.8197 (mmt) REVERT: H 40 GLN cc_start: 0.1583 (tt0) cc_final: 0.0849 (mp10) REVERT: H 103 ARG cc_start: -0.0524 (ttm170) cc_final: -0.0840 (mmm-85) REVERT: B 103 ARG cc_start: -0.0870 (ttt90) cc_final: -0.1151 (mmm-85) REVERT: E 40 GLN cc_start: 0.1244 (tt0) cc_final: 0.0639 (mp10) REVERT: E 46 LEU cc_start: 0.1502 (OUTLIER) cc_final: 0.0759 (mt) outliers start: 112 outliers final: 66 residues processed: 256 average time/residue: 0.3363 time to fit residues: 147.4069 Evaluate side-chains 223 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 148 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 131 CYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 287 ASP Chi-restraints excluded: chain P residue 318 PHE Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 538 CYS Chi-restraints excluded: chain P residue 551 VAL Chi-restraints excluded: chain P residue 582 LEU Chi-restraints excluded: chain P residue 615 VAL Chi-restraints excluded: chain P residue 718 PHE Chi-restraints excluded: chain P residue 732 THR Chi-restraints excluded: chain P residue 738 CYS Chi-restraints excluded: chain P residue 743 CYS Chi-restraints excluded: chain P residue 747 THR Chi-restraints excluded: chain P residue 861 LEU Chi-restraints excluded: chain P residue 959 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain E residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 173 optimal weight: 0.9990 chunk 285 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 144 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 163 optimal weight: 0.2980 chunk 200 optimal weight: 9.9990 chunk 315 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN D 66 HIS D 314 GLN ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 ASN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.238315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.204555 restraints weight = 44663.696| |-----------------------------------------------------------------------------| r_work (start): 0.4735 rms_B_bonded: 3.62 r_work: 0.4279 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28421 Z= 0.115 Angle : 0.574 12.859 38662 Z= 0.300 Chirality : 0.044 0.192 4377 Planarity : 0.005 0.071 4987 Dihedral : 5.106 28.551 3813 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.78 % Allowed : 17.44 % Favored : 79.77 % 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: -1.87 (0.14), residues: 3485 helix: 1.08 (0.23), residues: 591 sheet: -1.43 (0.17), residues: 850 loop : -1.94 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1102 HIS 0.007 0.001 HIS B 33 PHE 0.018 0.001 PHE P1121 TYR 0.020 0.001 TYR D1067 ARG 0.003 0.000 ARG P1000 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 853) hydrogen bonds : angle 5.79896 ( 2304) SS BOND : bond 0.00689 ( 42) SS BOND : angle 1.81813 ( 84) covalent geometry : bond 0.00260 (28379) covalent geometry : angle 0.56870 (38578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 161 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.3174 (OUTLIER) cc_final: 0.2876 (m-80) REVERT: A 914 ASN cc_start: 0.3002 (OUTLIER) cc_final: 0.1257 (t0) REVERT: A 920 GLN cc_start: 0.6842 (mm110) cc_final: 0.6157 (mm110) REVERT: A 923 ILE cc_start: 0.6439 (mt) cc_final: 0.5806 (mt) REVERT: A 1142 GLN cc_start: 0.7278 (mm110) cc_final: 0.6483 (mt0) REVERT: D 81 ASN cc_start: 0.5231 (OUTLIER) cc_final: 0.4991 (p0) REVERT: D 266 TYR cc_start: 0.6321 (m-10) cc_final: 0.5869 (m-10) REVERT: D 358 ILE cc_start: 0.1982 (OUTLIER) cc_final: 0.1720 (mt) REVERT: D 886 TRP cc_start: 0.7303 (p90) cc_final: 0.6780 (p90) REVERT: D 920 GLN cc_start: 0.6113 (tp40) cc_final: 0.5122 (mm-40) REVERT: D 923 ILE cc_start: 0.5651 (OUTLIER) cc_final: 0.5392 (mp) REVERT: D 996 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8565 (mm) REVERT: D 1125 ASN cc_start: 0.4086 (t0) cc_final: 0.3515 (m-40) REVERT: P 756 TYR cc_start: 0.7994 (m-80) cc_final: 0.7783 (m-80) REVERT: P 789 TYR cc_start: 0.5479 (m-80) cc_final: 0.4653 (m-80) REVERT: P 872 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7838 (tm-30) REVERT: P 902 MET cc_start: 0.8225 (mmm) cc_final: 0.8011 (mmt) REVERT: H 40 GLN cc_start: 0.1855 (tt0) cc_final: 0.0924 (mp10) REVERT: B 40 GLN cc_start: 0.2401 (tt0) cc_final: 0.1856 (mp10) REVERT: E 40 GLN cc_start: 0.1594 (tt0) cc_final: 0.0790 (mp10) REVERT: F 96 PHE cc_start: 0.1767 (m-10) cc_final: 0.1542 (m-10) outliers start: 86 outliers final: 60 residues processed: 237 average time/residue: 0.3370 time to fit residues: 137.1257 Evaluate side-chains 217 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 151 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 287 ASP Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 538 CYS Chi-restraints excluded: chain P residue 551 VAL Chi-restraints excluded: chain P residue 582 LEU Chi-restraints excluded: chain P residue 615 VAL Chi-restraints excluded: chain P residue 725 GLU Chi-restraints excluded: chain P residue 738 CYS Chi-restraints excluded: chain P residue 743 CYS Chi-restraints excluded: chain P residue 747 THR Chi-restraints excluded: chain P residue 861 LEU Chi-restraints excluded: chain P residue 959 LEU Chi-restraints excluded: chain P residue 1032 CYS Chi-restraints excluded: chain P residue 1115 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 44 optimal weight: 3.9990 chunk 306 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 chunk 345 optimal weight: 30.0000 chunk 265 optimal weight: 0.9990 chunk 133 optimal weight: 30.0000 chunk 131 optimal weight: 5.9990 chunk 338 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN D 66 HIS ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1058 HIS ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 ASN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.232642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.171857 restraints weight = 44154.970| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 2.85 r_work: 0.4239 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 28421 Z= 0.261 Angle : 0.742 16.651 38662 Z= 0.386 Chirality : 0.050 0.247 4377 Planarity : 0.006 0.064 4987 Dihedral : 5.748 30.428 3813 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.60 % Favored : 92.37 % Rotamer: Outliers : 3.50 % Allowed : 17.51 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.14), residues: 3485 helix: 0.51 (0.22), residues: 616 sheet: -1.53 (0.18), residues: 806 loop : -2.03 (0.12), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1102 HIS 0.010 0.002 HIS P1088 PHE 0.042 0.003 PHE A1075 TYR 0.026 0.002 TYR D 265 ARG 0.010 0.001 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.05312 ( 853) hydrogen bonds : angle 6.15121 ( 2304) SS BOND : bond 0.00492 ( 42) SS BOND : angle 2.21882 ( 84) covalent geometry : bond 0.00626 (28379) covalent geometry : angle 0.73511 (38578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 158 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.3541 (OUTLIER) cc_final: 0.3172 (m-80) REVERT: A 675 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7225 (pp30) REVERT: A 920 GLN cc_start: 0.6979 (mm110) cc_final: 0.6661 (mm110) REVERT: A 923 ILE cc_start: 0.6700 (mt) cc_final: 0.6159 (mt) REVERT: D 266 TYR cc_start: 0.6852 (m-10) cc_final: 0.6239 (m-80) REVERT: D 358 ILE cc_start: 0.2735 (OUTLIER) cc_final: 0.2532 (mt) REVERT: D 574 ASP cc_start: 0.7680 (t70) cc_final: 0.7240 (t0) REVERT: D 886 TRP cc_start: 0.7161 (p90) cc_final: 0.6740 (p90) REVERT: D 920 GLN cc_start: 0.6804 (tp40) cc_final: 0.6260 (mm-40) REVERT: D 994 ASP cc_start: 0.7417 (p0) cc_final: 0.7146 (p0) REVERT: D 996 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8425 (mm) REVERT: D 1102 TRP cc_start: 0.4875 (m100) cc_final: 0.4426 (m-90) REVERT: P 318 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.7989 (p90) REVERT: P 718 PHE cc_start: 0.4338 (OUTLIER) cc_final: 0.3847 (m-10) REVERT: P 756 TYR cc_start: 0.8301 (m-80) cc_final: 0.8065 (m-80) REVERT: P 789 TYR cc_start: 0.6205 (m-80) cc_final: 0.5264 (m-80) REVERT: P 872 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7851 (tm-30) outliers start: 108 outliers final: 83 residues processed: 251 average time/residue: 0.3310 time to fit residues: 142.6271 Evaluate side-chains 238 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 149 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 928 ASN Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 66 HIS Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 287 ASP Chi-restraints excluded: chain P residue 318 PHE Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 538 CYS Chi-restraints excluded: chain P residue 551 VAL Chi-restraints excluded: chain P residue 582 LEU Chi-restraints excluded: chain P residue 615 VAL Chi-restraints excluded: chain P residue 718 PHE Chi-restraints excluded: chain P residue 721 SER Chi-restraints excluded: chain P residue 725 GLU Chi-restraints excluded: chain P residue 738 CYS Chi-restraints excluded: chain P residue 743 CYS Chi-restraints excluded: chain P residue 747 THR Chi-restraints excluded: chain P residue 861 LEU Chi-restraints excluded: chain P residue 959 LEU Chi-restraints excluded: chain P residue 1032 CYS Chi-restraints excluded: chain P residue 1115 ILE Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 3 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 339 optimal weight: 50.0000 chunk 215 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN D 66 HIS D 675 GLN ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 ASN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.238194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.206903 restraints weight = 43918.867| |-----------------------------------------------------------------------------| r_work (start): 0.4715 rms_B_bonded: 3.04 r_work: 0.4294 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28421 Z= 0.133 Angle : 0.591 12.317 38662 Z= 0.308 Chirality : 0.045 0.304 4377 Planarity : 0.005 0.063 4987 Dihedral : 5.176 28.949 3813 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.88 % Allowed : 18.12 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3485 helix: 0.79 (0.22), residues: 630 sheet: -1.44 (0.17), residues: 822 loop : -1.90 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1102 HIS 0.007 0.001 HIS B 33 PHE 0.035 0.001 PHE P1121 TYR 0.018 0.001 TYR D1067 ARG 0.003 0.000 ARG P1000 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 853) hydrogen bonds : angle 5.78384 ( 2304) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.81688 ( 84) covalent geometry : bond 0.00312 (28379) covalent geometry : angle 0.58577 (38578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 160 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 914 ASN cc_start: 0.3260 (OUTLIER) cc_final: 0.0712 (t0) REVERT: A 920 GLN cc_start: 0.6917 (mm110) cc_final: 0.6461 (mm-40) REVERT: A 923 ILE cc_start: 0.6433 (mt) cc_final: 0.5853 (mt) REVERT: A 1095 PHE cc_start: 0.5446 (OUTLIER) cc_final: 0.5014 (t80) REVERT: D 266 TYR cc_start: 0.6399 (m-10) cc_final: 0.5830 (m-80) REVERT: D 574 ASP cc_start: 0.7541 (t70) cc_final: 0.7182 (t0) REVERT: D 886 TRP cc_start: 0.7256 (p90) cc_final: 0.6687 (p90) REVERT: D 996 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8449 (mm) REVERT: D 1102 TRP cc_start: 0.4668 (m100) cc_final: 0.4255 (m-10) REVERT: D 1125 ASN cc_start: 0.4232 (t0) cc_final: 0.3662 (m-40) REVERT: P 318 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8046 (p90) REVERT: P 756 TYR cc_start: 0.8109 (m-80) cc_final: 0.7896 (m-80) REVERT: P 789 TYR cc_start: 0.5913 (m-80) cc_final: 0.4907 (m-80) REVERT: H 40 GLN cc_start: 0.2201 (tt0) cc_final: 0.1091 (mp10) REVERT: B 112 MET cc_start: 0.0974 (ptt) cc_final: 0.0059 (mtt) REVERT: E 40 GLN cc_start: 0.2213 (tt0) cc_final: 0.1143 (mp10) outliers start: 89 outliers final: 73 residues processed: 238 average time/residue: 0.3258 time to fit residues: 133.8775 Evaluate side-chains 228 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 151 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1095 PHE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 287 ASP Chi-restraints excluded: chain P residue 318 PHE Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 538 CYS Chi-restraints excluded: chain P residue 551 VAL Chi-restraints excluded: chain P residue 552 LEU Chi-restraints excluded: chain P residue 582 LEU Chi-restraints excluded: chain P residue 615 VAL Chi-restraints excluded: chain P residue 617 CYS Chi-restraints excluded: chain P residue 721 SER Chi-restraints excluded: chain P residue 725 GLU Chi-restraints excluded: chain P residue 738 CYS Chi-restraints excluded: chain P residue 743 CYS Chi-restraints excluded: chain P residue 747 THR Chi-restraints excluded: chain P residue 861 LEU Chi-restraints excluded: chain P residue 959 LEU Chi-restraints excluded: chain P residue 1032 CYS Chi-restraints excluded: chain P residue 1115 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain B residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 351 optimal weight: 7.9990 chunk 348 optimal weight: 40.0000 chunk 215 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 chunk 37 optimal weight: 30.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS D 134 GLN ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1088 HIS ** P 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.226789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.191027 restraints weight = 42449.849| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 3.68 r_work: 0.3947 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 28421 Z= 0.232 Angle : 0.698 14.327 38662 Z= 0.364 Chirality : 0.048 0.336 4377 Planarity : 0.005 0.067 4987 Dihedral : 5.507 29.329 3813 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.11 % Allowed : 18.09 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3485 helix: 0.56 (0.21), residues: 631 sheet: -1.53 (0.17), residues: 831 loop : -1.91 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP P1102 HIS 0.009 0.002 HIS P1088 PHE 0.054 0.002 PHE P1121 TYR 0.023 0.002 TYR A 904 ARG 0.004 0.000 ARG P 577 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 853) hydrogen bonds : angle 5.96527 ( 2304) SS BOND : bond 0.00440 ( 42) SS BOND : angle 2.16110 ( 84) covalent geometry : bond 0.00555 (28379) covalent geometry : angle 0.69162 (38578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 152 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7058 (mmm) cc_final: 0.6858 (ttp) REVERT: A 920 GLN cc_start: 0.7249 (mm110) cc_final: 0.6765 (mm110) REVERT: A 923 ILE cc_start: 0.6766 (mt) cc_final: 0.6212 (mt) REVERT: A 1095 PHE cc_start: 0.5841 (OUTLIER) cc_final: 0.5255 (t80) REVERT: D 574 ASP cc_start: 0.7752 (t70) cc_final: 0.7378 (t0) REVERT: D 873 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: D 886 TRP cc_start: 0.7415 (p90) cc_final: 0.7069 (p90) REVERT: D 996 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8443 (mm) REVERT: D 1102 TRP cc_start: 0.4973 (m100) cc_final: 0.4334 (m-90) REVERT: P 318 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8072 (p90) REVERT: P 789 TYR cc_start: 0.6297 (m-80) cc_final: 0.5416 (m-80) REVERT: B 112 MET cc_start: 0.0710 (ptt) cc_final: -0.0022 (mtt) outliers start: 96 outliers final: 80 residues processed: 237 average time/residue: 0.3407 time to fit residues: 137.3046 Evaluate side-chains 231 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 147 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1095 PHE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 928 ASN Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 66 HIS Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 287 ASP Chi-restraints excluded: chain P residue 291 CYS Chi-restraints excluded: chain P residue 318 PHE Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 538 CYS Chi-restraints excluded: chain P residue 551 VAL Chi-restraints excluded: chain P residue 552 LEU Chi-restraints excluded: chain P residue 582 LEU Chi-restraints excluded: chain P residue 615 VAL Chi-restraints excluded: chain P residue 617 CYS Chi-restraints excluded: chain P residue 721 SER Chi-restraints excluded: chain P residue 725 GLU Chi-restraints excluded: chain P residue 738 CYS Chi-restraints excluded: chain P residue 743 CYS Chi-restraints excluded: chain P residue 747 THR Chi-restraints excluded: chain P residue 791 THR Chi-restraints excluded: chain P residue 861 LEU Chi-restraints excluded: chain P residue 959 LEU Chi-restraints excluded: chain P residue 1032 CYS Chi-restraints excluded: chain P residue 1115 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain B residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 320 optimal weight: 20.0000 chunk 274 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 42 optimal weight: 0.0020 chunk 286 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 920 GLN D 66 HIS D 121 ASN ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 901 GLN P1108 ASN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN E 53 HIS ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.231576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.196120 restraints weight = 42678.460| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 3.48 r_work: 0.4054 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28421 Z= 0.116 Angle : 0.571 9.315 38662 Z= 0.299 Chirality : 0.045 0.224 4377 Planarity : 0.004 0.063 4987 Dihedral : 4.990 28.637 3813 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.59 % Allowed : 18.64 % Favored : 78.77 % 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: -1.72 (0.14), residues: 3485 helix: 0.96 (0.22), residues: 632 sheet: -1.36 (0.17), residues: 815 loop : -1.78 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D1102 HIS 0.008 0.001 HIS D1083 PHE 0.051 0.001 PHE P1121 TYR 0.017 0.001 TYR D1067 ARG 0.003 0.000 ARG P 815 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 853) hydrogen bonds : angle 5.60064 ( 2304) SS BOND : bond 0.00311 ( 42) SS BOND : angle 1.67273 ( 84) covalent geometry : bond 0.00271 (28379) covalent geometry : angle 0.56664 (38578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 164 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 914 ASN cc_start: 0.3316 (OUTLIER) cc_final: 0.0764 (t0) REVERT: A 920 GLN cc_start: 0.6966 (mm-40) cc_final: 0.6194 (mm110) REVERT: A 923 ILE cc_start: 0.6400 (mt) cc_final: 0.5844 (mt) REVERT: A 1095 PHE cc_start: 0.5385 (OUTLIER) cc_final: 0.5096 (t80) REVERT: D 266 TYR cc_start: 0.6398 (m-10) cc_final: 0.5842 (m-80) REVERT: D 574 ASP cc_start: 0.7370 (t70) cc_final: 0.7036 (t70) REVERT: D 920 GLN cc_start: 0.5349 (mm-40) cc_final: 0.3914 (pt0) REVERT: D 996 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8546 (mt) REVERT: D 1083 HIS cc_start: 0.6207 (OUTLIER) cc_final: 0.5418 (p-80) REVERT: D 1102 TRP cc_start: 0.4618 (m100) cc_final: 0.4286 (m-90) REVERT: P 318 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.7937 (p90) REVERT: P 789 TYR cc_start: 0.5854 (m-80) cc_final: 0.4838 (m-80) REVERT: H 40 GLN cc_start: 0.1191 (tt0) cc_final: 0.0632 (mp10) REVERT: B 112 MET cc_start: 0.0369 (ptt) cc_final: -0.0359 (mtt) REVERT: E 40 GLN cc_start: 0.1150 (tt0) cc_final: 0.0603 (mp10) outliers start: 80 outliers final: 67 residues processed: 232 average time/residue: 0.3395 time to fit residues: 134.1850 Evaluate side-chains 226 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 154 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1095 PHE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1083 HIS Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 287 ASP Chi-restraints excluded: chain P residue 291 CYS Chi-restraints excluded: chain P residue 318 PHE Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 538 CYS Chi-restraints excluded: chain P residue 551 VAL Chi-restraints excluded: chain P residue 552 LEU Chi-restraints excluded: chain P residue 582 LEU Chi-restraints excluded: chain P residue 615 VAL Chi-restraints excluded: chain P residue 617 CYS Chi-restraints excluded: chain P residue 721 SER Chi-restraints excluded: chain P residue 725 GLU Chi-restraints excluded: chain P residue 738 CYS Chi-restraints excluded: chain P residue 743 CYS Chi-restraints excluded: chain P residue 747 THR Chi-restraints excluded: chain P residue 791 THR Chi-restraints excluded: chain P residue 861 LEU Chi-restraints excluded: chain P residue 959 LEU Chi-restraints excluded: chain P residue 1032 CYS Chi-restraints excluded: chain P residue 1115 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain B residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 148 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 112 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 125 optimal weight: 30.0000 chunk 205 optimal weight: 0.5980 chunk 182 optimal weight: 2.9990 chunk 268 optimal weight: 0.5980 chunk 278 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.234174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.198992 restraints weight = 42134.744| |-----------------------------------------------------------------------------| r_work (start): 0.4500 rms_B_bonded: 3.36 r_work: 0.4068 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.165 28421 Z= 0.149 Angle : 0.699 59.198 38662 Z= 0.392 Chirality : 0.047 0.944 4377 Planarity : 0.005 0.072 4987 Dihedral : 4.997 28.579 3813 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 2.43 % Allowed : 19.00 % Favored : 78.58 % Cbeta Deviations : 0.03 % 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: -1.71 (0.14), residues: 3485 helix: 0.97 (0.22), residues: 632 sheet: -1.35 (0.18), residues: 813 loop : -1.78 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1102 HIS 0.007 0.001 HIS D1083 PHE 0.049 0.001 PHE P1121 TYR 0.017 0.001 TYR P1047 ARG 0.002 0.000 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 853) hydrogen bonds : angle 5.60389 ( 2304) SS BOND : bond 0.00301 ( 42) SS BOND : angle 1.64670 ( 84) covalent geometry : bond 0.00325 (28379) covalent geometry : angle 0.69505 (38578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13849.03 seconds wall clock time: 240 minutes 48.82 seconds (14448.82 seconds total)