Starting phenix.real_space_refine on Sun Feb 18 17:37:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0z_27113/02_2024/8d0z_27113.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0z_27113/02_2024/8d0z_27113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0z_27113/02_2024/8d0z_27113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0z_27113/02_2024/8d0z_27113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0z_27113/02_2024/8d0z_27113.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0z_27113/02_2024/8d0z_27113.pdb" } resolution = 3.7 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= 0.002 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 106 5.16 5 C 14351 2.51 5 N 3751 2.21 5 O 4358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 98": "OD1" <-> "OD2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22566 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 6425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 824, 6425 Classifications: {'peptide': 824} Link IDs: {'PTRANS': 43, 'TRANS': 780} Chain breaks: 8 Chain: "A" Number of atoms: 7939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7939 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 54, 'TRANS': 960} Chain breaks: 7 Chain: "B" Number of atoms: 6395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6395 Classifications: {'peptide': 820} Link IDs: {'PTRANS': 45, 'TRANS': 774} Chain breaks: 8 Chain: "H" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "L" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 763 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 12.24, per 1000 atoms: 0.54 Number of scatterers: 22566 At special positions: 0 Unit cell: (143.165, 140.03, 214.225, 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 106 16.00 O 4358 8.00 N 3751 7.00 C 14351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 705 " - pdb=" SG CYS A 883 " distance=2.09 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 883 " - pdb=" SG CYS B 705 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.77 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS B 883 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=1.71 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.69 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 717 " " NAG B1301 " - " ASN B 717 " " NAG B1302 " - " ASN B 801 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B 331 " " NAG C1301 " - " ASN C 717 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C1134 " Time building additional restraints: 9.43 Conformation dependent library (CDL) restraints added in 4.6 seconds 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5384 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 45 sheets defined 25.6% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 802 through 806 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 851 through 856 Processing helix chain 'C' and resid 866 through 882 Processing helix chain 'C' and resid 884 through 890 removed outlier: 3.548A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.502A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.048A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.646A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.106A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.810A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 888 No H-bonds generated for 'chain 'B' and resid 886 through 888' Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.506A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.728A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 96 through 100A Processing helix chain 'L' and resid 49 through 53 removed outlier: 4.222A pdb=" N ASN L 53 " --> pdb=" O ARG L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.761A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.116A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.515A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.895A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.387A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.284A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.620A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.390A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.441A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.441A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.829A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.416A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.441A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.725A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.804A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.422A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.247A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AC4, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.489A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.612A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.636A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.763A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.058A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.653A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.146A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.407A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.833A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.607A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.496A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.626A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.494A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.494A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.337A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.721A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.111A pdb=" N TYR H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.545A pdb=" N CYS H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.635A pdb=" N HIS L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AE9, first strand: chain 'L' and resid 19 through 24 1075 hydrogen bonds defined for protein. 2913 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: 11.34 Time building geometry restraints manager: 10.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 4648 1.32 - 1.46: 8308 1.46 - 1.61: 9945 1.61 - 1.75: 31 1.75 - 1.90: 124 Bond restraints: 23056 Sorted by residual: bond pdb=" CB PHE A 888 " pdb=" CG PHE A 888 " ideal model delta sigma weight residual 1.502 1.300 0.202 2.30e-02 1.89e+03 7.73e+01 bond pdb=" CB HIS A1064 " pdb=" CG HIS A1064 " ideal model delta sigma weight residual 1.497 1.382 0.115 1.40e-02 5.10e+03 6.79e+01 bond pdb=" CB PHE C 55 " pdb=" CG PHE C 55 " ideal model delta sigma weight residual 1.502 1.335 0.167 2.30e-02 1.89e+03 5.27e+01 bond pdb=" CB PHE B 888 " pdb=" CG PHE B 888 " ideal model delta sigma weight residual 1.502 1.353 0.149 2.30e-02 1.89e+03 4.18e+01 bond pdb=" CB ILE C 850 " pdb=" CG1 ILE C 850 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 23051 not shown) Histogram of bond angle deviations from ideal: 96.47 - 104.03: 397 104.03 - 111.59: 9527 111.59 - 119.14: 9364 119.14 - 126.70: 11883 126.70 - 134.26: 191 Bond angle restraints: 31362 Sorted by residual: angle pdb=" N ASP L 26 " pdb=" CA ASP L 26 " pdb=" C ASP L 26 " ideal model delta sigma weight residual 112.38 98.06 14.32 1.22e+00 6.72e-01 1.38e+02 angle pdb=" C THR A 599 " pdb=" N PRO A 600 " pdb=" CA PRO A 600 " ideal model delta sigma weight residual 119.56 128.76 -9.20 1.02e+00 9.61e-01 8.14e+01 angle pdb=" N GLN A 613 " pdb=" CA GLN A 613 " pdb=" C GLN A 613 " ideal model delta sigma weight residual 111.28 120.73 -9.45 1.09e+00 8.42e-01 7.52e+01 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 111.41 98.47 12.94 1.50e+00 4.44e-01 7.44e+01 angle pdb=" C PHE C 329 " pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 119.78 128.61 -8.83 1.03e+00 9.43e-01 7.35e+01 ... (remaining 31357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 13435 17.71 - 35.43: 359 35.43 - 53.14: 101 53.14 - 70.85: 30 70.85 - 88.57: 14 Dihedral angle restraints: 13939 sinusoidal: 5592 harmonic: 8347 Sorted by residual: dihedral pdb=" CB CYS A 705 " pdb=" SG CYS A 705 " pdb=" SG CYS B 883 " pdb=" CB CYS B 883 " ideal model delta sinusoidal sigma weight residual 93.00 146.44 -53.44 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" C ASN L 27 " pdb=" N ASN L 27 " pdb=" CA ASN L 27 " pdb=" CB ASN L 27 " ideal model delta harmonic sigma weight residual -122.60 -110.97 -11.63 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -119.41 33.41 1 1.00e+01 1.00e-02 1.59e+01 ... (remaining 13936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2684 0.106 - 0.212: 779 0.212 - 0.318: 116 0.318 - 0.425: 27 0.425 - 0.531: 9 Chirality restraints: 3615 Sorted by residual: chirality pdb=" CB VAL A 826 " pdb=" CA VAL A 826 " pdb=" CG1 VAL A 826 " pdb=" CG2 VAL A 826 " both_signs ideal model delta sigma weight residual False -2.63 -3.16 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CB ILE C 850 " pdb=" CA ILE C 850 " pdb=" CG1 ILE C 850 " pdb=" CG2 ILE C 850 " both_signs ideal model delta sigma weight residual False 2.64 3.15 -0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" C2 NAG B1304 " pdb=" C1 NAG B1304 " pdb=" C3 NAG B1304 " pdb=" N2 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.49 -2.97 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 3612 not shown) Planarity restraints: 4072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 717 " -0.066 2.00e-02 2.50e+03 6.97e-02 6.08e+01 pdb=" CG ASN C 717 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 717 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 717 " 0.109 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " -0.043 2.00e-02 2.50e+03 4.60e-02 2.64e+01 pdb=" CG ASN B 717 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " 0.073 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 904 " -0.066 2.00e-02 2.50e+03 3.61e-02 2.61e+01 pdb=" CG TYR B 904 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 904 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 904 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR B 904 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR B 904 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 904 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 904 " -0.057 2.00e-02 2.50e+03 ... (remaining 4069 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 926 2.67 - 3.23: 21380 3.23 - 3.79: 36890 3.79 - 4.34: 49490 4.34 - 4.90: 80169 Nonbonded interactions: 188855 Sorted by model distance: nonbonded pdb=" ND2 ASN L 27 " pdb=" OE1 GLN L 31 " model vdw 2.116 2.520 nonbonded pdb=" O VAL L 28 " pdb=" N GLN L 31 " model vdw 2.320 2.520 nonbonded pdb=" N PRO L 7 " pdb=" O PRO L 7 " model vdw 2.329 2.496 nonbonded pdb=" N ASP L 26 " pdb=" N ASN L 27 " model vdw 2.357 2.560 nonbonded pdb=" C VAL L 28 " pdb=" N SER L 30 " model vdw 2.361 3.350 ... (remaining 188850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 28 through 1144 or resid 1302 through 1304)) selection = (chain 'C' and (resid 28 through 143 or resid 154 through 331 or resid 531 throu \ gh 827 or resid 854 through 1144 or resid 1301 through 1303)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 20.810 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 66.130 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.021 0.202 23056 Z= 1.385 Angle : 1.788 14.319 31362 Z= 1.221 Chirality : 0.103 0.531 3615 Planarity : 0.008 0.055 4061 Dihedral : 9.883 88.565 8447 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.08 % Allowed : 0.67 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 2822 helix: 0.73 (0.18), residues: 621 sheet: 1.28 (0.19), residues: 657 loop : 0.16 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.010 TRP H 36 HIS 0.011 0.002 HIS B1083 PHE 0.046 0.006 PHE A 888 TYR 0.066 0.008 TYR B 904 ARG 0.008 0.001 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 582 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 TRP cc_start: 0.6830 (t60) cc_final: 0.6527 (t60) REVERT: C 98 SER cc_start: 0.6900 (m) cc_final: 0.6470 (t) REVERT: C 128 ILE cc_start: 0.7390 (mt) cc_final: 0.6916 (tt) REVERT: C 229 LEU cc_start: 0.7140 (mt) cc_final: 0.6785 (mt) REVERT: C 589 PRO cc_start: 0.7976 (Cg_exo) cc_final: 0.7735 (Cg_endo) REVERT: C 756 TYR cc_start: 0.5727 (m-80) cc_final: 0.5461 (m-80) REVERT: C 869 MET cc_start: 0.8576 (mtt) cc_final: 0.8368 (mtt) REVERT: C 1029 MET cc_start: 0.8808 (tpp) cc_final: 0.8441 (tpp) REVERT: A 234 ASN cc_start: 0.5550 (m-40) cc_final: 0.4981 (t0) REVERT: A 453 TYR cc_start: 0.6929 (p90) cc_final: 0.6718 (p90) REVERT: A 495 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6385 (p90) REVERT: A 756 TYR cc_start: 0.4976 (m-80) cc_final: 0.4731 (m-80) REVERT: A 761 THR cc_start: 0.8098 (m) cc_final: 0.7802 (t) REVERT: A 762 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7428 (mm-40) REVERT: B 129 LYS cc_start: 0.8021 (mttt) cc_final: 0.7572 (tttt) REVERT: B 227 VAL cc_start: 0.8603 (p) cc_final: 0.8371 (t) REVERT: B 241 LEU cc_start: 0.7665 (mt) cc_final: 0.7115 (mt) REVERT: B 823 PHE cc_start: 0.7154 (m-80) cc_final: 0.6951 (m-80) REVERT: H 34 MET cc_start: 0.7258 (mmm) cc_final: 0.6811 (tpp) REVERT: H 95 ASP cc_start: 0.5856 (t0) cc_final: 0.4872 (t0) outliers start: 2 outliers final: 1 residues processed: 584 average time/residue: 0.3979 time to fit residues: 342.0471 Evaluate side-chains 245 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 243 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 271 GLN C 762 GLN C1054 GLN C1113 GLN C1135 ASN A 49 HIS A 121 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 755 GLN A 762 GLN A 804 GLN A 914 ASN A 935 GLN A1048 HIS B 81 ASN B 115 GLN B 188 ASN B 914 ASN B 949 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23056 Z= 0.246 Angle : 0.691 8.222 31362 Z= 0.381 Chirality : 0.047 0.200 3615 Planarity : 0.005 0.041 4061 Dihedral : 5.624 31.130 3294 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.94 % Rotamer: Outliers : 2.10 % Allowed : 7.61 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 2822 helix: 2.33 (0.20), residues: 615 sheet: 1.03 (0.19), residues: 683 loop : -0.29 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 64 HIS 0.006 0.001 HIS B1083 PHE 0.042 0.002 PHE A 888 TYR 0.029 0.002 TYR A 505 ARG 0.009 0.001 ARG H 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 326 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6684 (m) cc_final: 0.6267 (t) REVERT: C 869 MET cc_start: 0.8563 (mtt) cc_final: 0.8330 (mtt) REVERT: C 1029 MET cc_start: 0.8582 (tpp) cc_final: 0.8288 (tpp) REVERT: C 1138 TYR cc_start: 0.6826 (t80) cc_final: 0.6598 (t80) REVERT: A 228 ASP cc_start: 0.6835 (m-30) cc_final: 0.6088 (p0) REVERT: A 234 ASN cc_start: 0.5292 (m-40) cc_final: 0.4976 (t0) REVERT: A 451 TYR cc_start: 0.4796 (m-10) cc_final: 0.4286 (m-10) REVERT: A 471 GLU cc_start: 0.6448 (tp30) cc_final: 0.6078 (tp30) REVERT: A 650 LEU cc_start: 0.8772 (tp) cc_final: 0.8531 (tt) REVERT: A 752 LEU cc_start: 0.7509 (mt) cc_final: 0.7084 (tp) REVERT: A 761 THR cc_start: 0.8269 (m) cc_final: 0.8001 (t) REVERT: A 762 GLN cc_start: 0.7825 (mm110) cc_final: 0.7611 (mm-40) REVERT: B 129 LYS cc_start: 0.7891 (mttt) cc_final: 0.7395 (tttt) REVERT: B 218 GLN cc_start: 0.7225 (mt0) cc_final: 0.6557 (mp10) REVERT: B 651 ILE cc_start: 0.8520 (mm) cc_final: 0.8238 (mt) REVERT: B 855 PHE cc_start: 0.6731 (m-80) cc_final: 0.6494 (m-80) REVERT: B 957 GLN cc_start: 0.7268 (mt0) cc_final: 0.6995 (mm-40) REVERT: B 983 ARG cc_start: 0.6777 (mpt180) cc_final: 0.6576 (mmt-90) REVERT: B 1092 GLU cc_start: 0.6859 (pp20) cc_final: 0.6526 (pp20) REVERT: H 50 ILE cc_start: 0.8342 (tt) cc_final: 0.8131 (tt) REVERT: H 83 ARG cc_start: 0.5589 (ttm-80) cc_final: 0.5377 (ttp-110) REVERT: H 108 LEU cc_start: 0.6097 (tt) cc_final: 0.5867 (tp) outliers start: 53 outliers final: 32 residues processed: 362 average time/residue: 0.3324 time to fit residues: 191.0041 Evaluate side-chains 250 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 216 optimal weight: 0.2980 chunk 176 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 260 optimal weight: 1.9990 chunk 281 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 87 ASN C1113 GLN A 121 ASN A 321 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 532 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B 969 ASN B1048 HIS ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 23056 Z= 0.258 Angle : 0.633 12.399 31362 Z= 0.344 Chirality : 0.046 0.210 3615 Planarity : 0.004 0.037 4061 Dihedral : 5.353 35.245 3292 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 3.21 % Allowed : 8.87 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 2822 helix: 2.52 (0.20), residues: 609 sheet: 0.87 (0.18), residues: 690 loop : -0.50 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 64 HIS 0.007 0.001 HIS B1083 PHE 0.033 0.002 PHE A 888 TYR 0.026 0.002 TYR C1067 ARG 0.004 0.001 ARG H 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 254 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6618 (m) cc_final: 0.6177 (t) REVERT: C 238 PHE cc_start: 0.6342 (OUTLIER) cc_final: 0.5416 (t80) REVERT: C 614 ASP cc_start: 0.7043 (t0) cc_final: 0.6829 (t0) REVERT: A 64 TRP cc_start: 0.5370 (t-100) cc_final: 0.5062 (t60) REVERT: A 228 ASP cc_start: 0.6956 (m-30) cc_final: 0.5984 (p0) REVERT: A 234 ASN cc_start: 0.5204 (m-40) cc_final: 0.4870 (t0) REVERT: A 471 GLU cc_start: 0.6512 (tp30) cc_final: 0.6309 (tp30) REVERT: A 650 LEU cc_start: 0.8645 (tp) cc_final: 0.8422 (tt) REVERT: B 129 LYS cc_start: 0.7927 (mttt) cc_final: 0.7484 (mttm) REVERT: B 218 GLN cc_start: 0.7219 (mt0) cc_final: 0.6483 (mp10) REVERT: B 651 ILE cc_start: 0.8555 (mm) cc_final: 0.8255 (mt) REVERT: B 957 GLN cc_start: 0.7235 (mt0) cc_final: 0.6991 (mm-40) REVERT: B 983 ARG cc_start: 0.6900 (mpt180) cc_final: 0.6700 (mmt-90) REVERT: B 994 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: H 78 LEU cc_start: 0.6638 (tp) cc_final: 0.6422 (mt) REVERT: H 86 ASP cc_start: 0.6805 (m-30) cc_final: 0.6562 (m-30) REVERT: L 3 GLU cc_start: 0.4194 (mm-30) cc_final: 0.3850 (mm-30) outliers start: 81 outliers final: 57 residues processed: 316 average time/residue: 0.3209 time to fit residues: 164.2224 Evaluate side-chains 262 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 203 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 257 optimal weight: 2.9990 chunk 195 optimal weight: 0.1980 chunk 135 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 261 optimal weight: 0.6980 chunk 276 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN B 188 ASN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 23056 Z= 0.207 Angle : 0.577 9.883 31362 Z= 0.311 Chirality : 0.045 0.199 3615 Planarity : 0.004 0.071 4061 Dihedral : 5.112 33.841 3292 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.91 % Favored : 97.06 % Rotamer: Outliers : 3.01 % Allowed : 10.46 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 2822 helix: 2.62 (0.20), residues: 617 sheet: 0.79 (0.19), residues: 684 loop : -0.60 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 64 HIS 0.007 0.001 HIS B1083 PHE 0.023 0.002 PHE B 168 TYR 0.023 0.002 TYR C1067 ARG 0.006 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 246 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6558 (m) cc_final: 0.6209 (t) REVERT: C 238 PHE cc_start: 0.6172 (OUTLIER) cc_final: 0.5284 (t80) REVERT: C 592 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.7060 (p90) REVERT: C 614 ASP cc_start: 0.7021 (t0) cc_final: 0.6719 (t0) REVERT: A 202 LYS cc_start: 0.7913 (mttt) cc_final: 0.7639 (mtmm) REVERT: A 228 ASP cc_start: 0.6986 (m-30) cc_final: 0.5913 (p0) REVERT: A 365 TYR cc_start: 0.8239 (m-80) cc_final: 0.8005 (m-80) REVERT: B 129 LYS cc_start: 0.8046 (mttt) cc_final: 0.7810 (mttt) REVERT: B 218 GLN cc_start: 0.7020 (mt0) cc_final: 0.6368 (mp10) REVERT: B 651 ILE cc_start: 0.8567 (mm) cc_final: 0.8239 (mt) REVERT: B 983 ARG cc_start: 0.6841 (mpt180) cc_final: 0.6472 (mmt-90) REVERT: B 994 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: H 78 LEU cc_start: 0.6765 (tp) cc_final: 0.6557 (mt) REVERT: L 36 TYR cc_start: 0.7652 (m-80) cc_final: 0.7432 (m-10) outliers start: 76 outliers final: 52 residues processed: 301 average time/residue: 0.3156 time to fit residues: 153.3612 Evaluate side-chains 267 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 212 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 230 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1088 HIS A 784 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 23056 Z= 0.511 Angle : 0.750 11.394 31362 Z= 0.402 Chirality : 0.050 0.207 3615 Planarity : 0.005 0.044 4061 Dihedral : 5.804 34.477 3292 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 4.52 % Allowed : 10.62 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 2822 helix: 2.08 (0.20), residues: 610 sheet: 0.55 (0.19), residues: 700 loop : -1.07 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 886 HIS 0.010 0.002 HIS A1058 PHE 0.030 0.003 PHE A 133 TYR 0.030 0.003 TYR C1067 ARG 0.007 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 215 time to evaluate : 2.817 Fit side-chains revert: symmetry clash REVERT: C 98 SER cc_start: 0.6328 (m) cc_final: 0.6007 (t) REVERT: C 238 PHE cc_start: 0.6315 (OUTLIER) cc_final: 0.5316 (t80) REVERT: C 592 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.7211 (p90) REVERT: C 614 ASP cc_start: 0.7167 (t0) cc_final: 0.6744 (t0) REVERT: A 500 THR cc_start: 0.7405 (OUTLIER) cc_final: 0.7043 (t) REVERT: B 218 GLN cc_start: 0.7250 (mt0) cc_final: 0.6561 (mp10) REVERT: B 983 ARG cc_start: 0.6965 (mpt180) cc_final: 0.6662 (mmt-90) REVERT: B 1019 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7871 (ttm110) REVERT: H 82 ASN cc_start: 0.8132 (t0) cc_final: 0.7736 (m-40) outliers start: 114 outliers final: 87 residues processed: 310 average time/residue: 0.3104 time to fit residues: 156.5018 Evaluate side-chains 278 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 187 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 93 optimal weight: 0.6980 chunk 248 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 276 optimal weight: 7.9990 chunk 229 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23056 Z= 0.206 Angle : 0.595 12.300 31362 Z= 0.316 Chirality : 0.045 0.210 3615 Planarity : 0.004 0.041 4061 Dihedral : 5.317 37.128 3291 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 3.21 % Allowed : 12.56 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 2822 helix: 2.51 (0.20), residues: 615 sheet: 0.55 (0.19), residues: 692 loop : -0.96 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 91 HIS 0.004 0.001 HIS B 207 PHE 0.020 0.002 PHE B 970 TYR 0.022 0.001 TYR C1067 ARG 0.006 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 223 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6423 (m) cc_final: 0.6103 (t) REVERT: C 157 PHE cc_start: 0.4342 (t80) cc_final: 0.3717 (m-80) REVERT: C 173 GLN cc_start: 0.7013 (mm-40) cc_final: 0.6714 (pm20) REVERT: C 238 PHE cc_start: 0.6263 (OUTLIER) cc_final: 0.5217 (t80) REVERT: C 614 ASP cc_start: 0.7051 (t0) cc_final: 0.6546 (t0) REVERT: A 869 MET cc_start: 0.7965 (mtm) cc_final: 0.7719 (mtm) REVERT: B 133 PHE cc_start: 0.6855 (m-80) cc_final: 0.6102 (m-80) REVERT: B 218 GLN cc_start: 0.7225 (mt0) cc_final: 0.6434 (mp10) REVERT: B 983 ARG cc_start: 0.6997 (mpt180) cc_final: 0.6574 (mmt-90) REVERT: H 78 LEU cc_start: 0.6662 (tp) cc_final: 0.6291 (mt) REVERT: H 82 ASN cc_start: 0.8138 (t0) cc_final: 0.7905 (m-40) REVERT: L 45 VAL cc_start: 0.7983 (m) cc_final: 0.7748 (p) outliers start: 81 outliers final: 59 residues processed: 281 average time/residue: 0.3018 time to fit residues: 139.4943 Evaluate side-chains 264 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 204 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 266 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 202 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 chunk 232 optimal weight: 0.0050 chunk 154 optimal weight: 0.7980 chunk 275 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 969 ASN B1002 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 23056 Z= 0.155 Angle : 0.549 13.823 31362 Z= 0.292 Chirality : 0.044 0.176 3615 Planarity : 0.004 0.095 4061 Dihedral : 4.872 34.863 3291 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 2.54 % Allowed : 13.59 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 2822 helix: 2.85 (0.20), residues: 610 sheet: 0.55 (0.19), residues: 697 loop : -0.86 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 91 HIS 0.002 0.000 HIS A1064 PHE 0.018 0.001 PHE B 592 TYR 0.020 0.001 TYR C1067 ARG 0.004 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 237 time to evaluate : 2.671 Fit side-chains revert: symmetry clash REVERT: C 98 SER cc_start: 0.6426 (m) cc_final: 0.6088 (t) REVERT: C 153 MET cc_start: 0.2027 (ttt) cc_final: 0.1715 (mtt) REVERT: C 157 PHE cc_start: 0.4364 (t80) cc_final: 0.3877 (m-10) REVERT: C 187 LYS cc_start: 0.6455 (tptt) cc_final: 0.5417 (pttt) REVERT: C 238 PHE cc_start: 0.6305 (OUTLIER) cc_final: 0.5251 (t80) REVERT: C 984 LEU cc_start: 0.6781 (mm) cc_final: 0.6469 (mp) REVERT: A 500 THR cc_start: 0.7206 (OUTLIER) cc_final: 0.6976 (t) REVERT: A 869 MET cc_start: 0.7956 (mtm) cc_final: 0.7715 (mtm) REVERT: B 52 GLN cc_start: 0.7778 (tp40) cc_final: 0.7476 (tp40) REVERT: B 218 GLN cc_start: 0.7279 (mt0) cc_final: 0.6992 (mt0) REVERT: B 651 ILE cc_start: 0.8549 (mm) cc_final: 0.8241 (mt) REVERT: B 983 ARG cc_start: 0.7033 (mpt180) cc_final: 0.6806 (mmt-90) REVERT: H 34 MET cc_start: 0.6251 (mpp) cc_final: 0.5741 (mpp) REVERT: H 78 LEU cc_start: 0.6648 (tp) cc_final: 0.6437 (mt) REVERT: L 45 VAL cc_start: 0.7953 (m) cc_final: 0.7729 (p) outliers start: 64 outliers final: 53 residues processed: 286 average time/residue: 0.2992 time to fit residues: 141.3307 Evaluate side-chains 266 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 211 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 170 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1142 GLN A 580 GLN A 804 GLN A 935 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 23056 Z= 0.419 Angle : 0.705 14.441 31362 Z= 0.374 Chirality : 0.049 0.238 3615 Planarity : 0.005 0.047 4061 Dihedral : 5.562 36.786 3291 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 3.33 % Allowed : 13.87 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 2822 helix: 2.30 (0.20), residues: 609 sheet: 0.40 (0.19), residues: 701 loop : -1.11 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 64 HIS 0.010 0.002 HIS B 207 PHE 0.025 0.002 PHE C 186 TYR 0.030 0.002 TYR B 269 ARG 0.007 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 206 time to evaluate : 2.762 Fit side-chains REVERT: C 238 PHE cc_start: 0.6353 (OUTLIER) cc_final: 0.5293 (t80) REVERT: C 614 ASP cc_start: 0.7128 (t0) cc_final: 0.6693 (t0) REVERT: A 353 TRP cc_start: 0.4982 (m-90) cc_final: 0.4774 (m-90) REVERT: A 500 THR cc_start: 0.7418 (OUTLIER) cc_final: 0.7150 (t) REVERT: A 754 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7832 (mm) REVERT: A 869 MET cc_start: 0.8061 (mtm) cc_final: 0.7809 (mtm) REVERT: B 133 PHE cc_start: 0.7014 (m-80) cc_final: 0.6390 (m-80) REVERT: B 218 GLN cc_start: 0.7276 (mt0) cc_final: 0.6976 (mt0) REVERT: B 983 ARG cc_start: 0.6869 (mpt180) cc_final: 0.6543 (mmt-90) REVERT: B 1019 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7812 (ttm110) REVERT: L 45 VAL cc_start: 0.8138 (m) cc_final: 0.7905 (p) outliers start: 84 outliers final: 71 residues processed: 270 average time/residue: 0.3045 time to fit residues: 135.2142 Evaluate side-chains 260 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 185 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 250 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 240 optimal weight: 0.7980 chunk 256 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 111 optimal weight: 0.1980 chunk 201 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 232 optimal weight: 0.0030 chunk 242 optimal weight: 0.9980 chunk 255 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 23056 Z= 0.158 Angle : 0.569 14.065 31362 Z= 0.301 Chirality : 0.045 0.232 3615 Planarity : 0.004 0.045 4061 Dihedral : 4.975 33.589 3291 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.65 % Favored : 96.31 % Rotamer: Outliers : 2.10 % Allowed : 14.94 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 2822 helix: 2.75 (0.20), residues: 614 sheet: 0.42 (0.19), residues: 689 loop : -0.95 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 64 HIS 0.004 0.001 HIS B1083 PHE 0.018 0.001 PHE C 186 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 219 time to evaluate : 2.463 Fit side-chains revert: symmetry clash REVERT: C 106 PHE cc_start: 0.6077 (m-80) cc_final: 0.5865 (m-80) REVERT: C 153 MET cc_start: 0.1920 (ttt) cc_final: 0.1375 (mtt) REVERT: C 157 PHE cc_start: 0.4701 (t80) cc_final: 0.4072 (p90) REVERT: C 238 PHE cc_start: 0.6295 (OUTLIER) cc_final: 0.5297 (t80) REVERT: C 539 VAL cc_start: 0.8428 (t) cc_final: 0.8186 (m) REVERT: A 157 PHE cc_start: 0.5038 (OUTLIER) cc_final: 0.4526 (m-80) REVERT: A 353 TRP cc_start: 0.4762 (m-90) cc_final: 0.4544 (m-90) REVERT: B 52 GLN cc_start: 0.7737 (tp40) cc_final: 0.7442 (tp40) REVERT: B 133 PHE cc_start: 0.6927 (m-80) cc_final: 0.6370 (m-80) REVERT: B 218 GLN cc_start: 0.7160 (mt0) cc_final: 0.6586 (mt0) REVERT: B 612 TYR cc_start: 0.8523 (m-80) cc_final: 0.7861 (m-80) REVERT: B 651 ILE cc_start: 0.8619 (mm) cc_final: 0.8281 (mt) REVERT: B 983 ARG cc_start: 0.7035 (mpt180) cc_final: 0.6641 (mmt-90) outliers start: 53 outliers final: 46 residues processed: 255 average time/residue: 0.3240 time to fit residues: 135.8888 Evaluate side-chains 256 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 208 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 86 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 168 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 262 optimal weight: 0.9980 chunk 226 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23056 Z= 0.177 Angle : 0.560 13.672 31362 Z= 0.296 Chirality : 0.044 0.195 3615 Planarity : 0.004 0.047 4061 Dihedral : 4.848 33.369 3291 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 1.90 % Allowed : 15.29 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 2822 helix: 2.85 (0.20), residues: 616 sheet: 0.42 (0.19), residues: 687 loop : -0.96 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 64 HIS 0.004 0.001 HIS B1083 PHE 0.028 0.001 PHE A 543 TYR 0.027 0.001 TYR A 160 ARG 0.003 0.000 ARG H 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 211 time to evaluate : 2.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.1915 (ttt) cc_final: 0.1387 (mtt) REVERT: C 157 PHE cc_start: 0.4731 (t80) cc_final: 0.4043 (p90) REVERT: C 238 PHE cc_start: 0.6327 (OUTLIER) cc_final: 0.5259 (t80) REVERT: C 539 VAL cc_start: 0.8433 (t) cc_final: 0.8200 (m) REVERT: A 157 PHE cc_start: 0.4935 (OUTLIER) cc_final: 0.4572 (m-80) REVERT: A 353 TRP cc_start: 0.4777 (m-90) cc_final: 0.4553 (m-90) REVERT: B 52 GLN cc_start: 0.7696 (tp40) cc_final: 0.7418 (tp40) REVERT: B 133 PHE cc_start: 0.6818 (m-80) cc_final: 0.6323 (m-80) REVERT: B 612 TYR cc_start: 0.8540 (m-80) cc_final: 0.7892 (m-80) REVERT: B 651 ILE cc_start: 0.8606 (mm) cc_final: 0.8267 (mt) REVERT: H 34 MET cc_start: 0.5976 (mpp) cc_final: 0.5270 (tpp) REVERT: H 78 LEU cc_start: 0.6853 (tp) cc_final: 0.6333 (mt) REVERT: L 104 LEU cc_start: 0.8223 (tp) cc_final: 0.8009 (tp) outliers start: 48 outliers final: 44 residues processed: 244 average time/residue: 0.3017 time to fit residues: 121.7444 Evaluate side-chains 252 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 206 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 86 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 180 optimal weight: 0.0070 chunk 241 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 209 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.105999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.086478 restraints weight = 56426.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.086662 restraints weight = 49633.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.087088 restraints weight = 45383.658| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23056 Z= 0.211 Angle : 0.567 13.595 31362 Z= 0.300 Chirality : 0.045 0.197 3615 Planarity : 0.004 0.047 4061 Dihedral : 4.840 32.803 3291 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 2.26 % Allowed : 14.82 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 2822 helix: 2.79 (0.20), residues: 612 sheet: 0.41 (0.19), residues: 687 loop : -0.99 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 64 HIS 0.004 0.001 HIS B1083 PHE 0.018 0.001 PHE B 592 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG H 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4485.58 seconds wall clock time: 82 minutes 52.67 seconds (4972.67 seconds total)