Starting phenix.real_space_refine on Wed Sep 25 16:02:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtq_14145/09_2024/7qtq_14145_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtq_14145/09_2024/7qtq_14145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtq_14145/09_2024/7qtq_14145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtq_14145/09_2024/7qtq_14145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtq_14145/09_2024/7qtq_14145_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtq_14145/09_2024/7qtq_14145_trim.cif" } resolution = 3.3 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= -0.014 sd= 1.031 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: 6 Type Number sf(0) Gaussians I 8 10.91 5 S 202 5.16 5 C 17708 2.51 5 N 4934 2.21 5 O 5281 1.98 5 H 26827 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 54960 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 24843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1635, 24843 Classifications: {'peptide': 1635} Link IDs: {'PCIS': 1, 'PTRANS': 112, 'TRANS': 1521} Chain breaks: 30 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1, 'DHA:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2486 Unusual residues: {'T44': 1} Classifications: {'peptide': 154, 'undetermined': 1} Link IDs: {'PTRANS': 11, 'TRANS': 142, None: 1} Not linked: pdbres="T44 A2573 " pdbres="ALA A2574 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'T44:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 24843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1634, 24843 Classifications: {'peptide': 1634} Link IDs: {'PCIS': 1, 'PTRANS': 112, 'TRANS': 1520} Chain breaks: 30 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DHA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2486 Unusual residues: {'T44': 1} Classifications: {'peptide': 154, 'undetermined': 1} Link IDs: {'PTRANS': 11, 'TRANS': 142, None: 1} Not linked: pdbres="T44 B2573 " pdbres="ALA B2574 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'T44:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 19.08, per 1000 atoms: 0.35 Number of scatterers: 54960 At special positions: 0 Unit cell: (207.9, 165.825, 122.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) I 8 52.95 S 202 16.00 O 5281 8.00 N 4934 7.00 C 17708 6.00 H 26827 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=78, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 52 " distance=2.02 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 92 " distance=2.02 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 120 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 138 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 297 " distance=1.99 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 319 " distance=1.67 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 408 " - pdb=" SG CYS A 607 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 686 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 702 " distance=2.02 Simple disulfide: pdb=" SG CYS A 704 " - pdb=" SG CYS A 725 " distance=2.03 Simple disulfide: pdb=" SG CYS A 729 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS A 773 " - pdb=" SG CYS A 898 " distance=2.04 Simple disulfide: pdb=" SG CYS A 900 " - pdb=" SG CYS A 921 " distance=2.04 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A1031 " distance=1.99 Simple disulfide: pdb=" SG CYS A1042 " - pdb=" SG CYS A1049 " distance=2.03 Simple disulfide: pdb=" SG CYS A1051 " - pdb=" SG CYS A1073 " distance=2.03 Simple disulfide: pdb=" SG CYS A1077 " - pdb=" SG CYS A1108 " distance=2.02 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1145 " distance=2.03 Simple disulfide: pdb=" SG CYS A1245 " - pdb=" SG CYS A1281 " distance=2.03 Simple disulfide: pdb=" SG CYS A1441 " - pdb=" SG CYS A1461 " distance=2.00 Simple disulfide: pdb=" SG CYS A1894 " - pdb=" SG CYS A1920 " distance=2.04 Simple disulfide: pdb=" SG CYS A1898 " - pdb=" SG CYS A1905 " distance=2.03 Simple disulfide: pdb=" SG CYS A1929 " - pdb=" SG CYS A1940 " distance=2.03 Simple disulfide: pdb=" SG CYS A1997 " - pdb=" SG CYS A2025 " distance=2.02 Simple disulfide: pdb=" SG CYS A2001 " - pdb=" SG CYS A2007 " distance=2.04 Simple disulfide: pdb=" SG CYS A2006 " - pdb=" SG CYS A2077 " distance=2.03 Simple disulfide: pdb=" SG CYS A2130 " - pdb=" SG CYS A2154 " distance=2.03 Simple disulfide: pdb=" SG CYS A2134 " - pdb=" SG CYS A2140 " distance=2.03 Simple disulfide: pdb=" SG CYS A2163 " - pdb=" SG CYS A2172 " distance=2.03 Simple disulfide: pdb=" SG CYS A2264 " - pdb=" SG CYS A2281 " distance=2.02 Simple disulfide: pdb=" SG CYS A2442 " - pdb=" SG CYS A2453 " distance=2.03 Simple disulfide: pdb=" SG CYS A2591 " - pdb=" SG CYS A2715 " distance=2.04 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 70 " distance=2.02 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 120 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 138 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 235 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 319 " distance=2.02 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 408 " - pdb=" SG CYS B 607 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 686 " distance=2.02 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 702 " distance=2.02 Simple disulfide: pdb=" SG CYS B 704 " - pdb=" SG CYS B 725 " distance=2.03 Simple disulfide: pdb=" SG CYS B 729 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 773 " - pdb=" SG CYS B 898 " distance=2.03 Simple disulfide: pdb=" SG CYS B 900 " - pdb=" SG CYS B 921 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B1031 " distance=2.02 Simple disulfide: pdb=" SG CYS B1042 " - pdb=" SG CYS B1049 " distance=2.03 Simple disulfide: pdb=" SG CYS B1051 " - pdb=" SG CYS B1073 " distance=2.02 Simple disulfide: pdb=" SG CYS B1077 " - pdb=" SG CYS B1108 " distance=2.02 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1145 " distance=2.03 Simple disulfide: pdb=" SG CYS B1245 " - pdb=" SG CYS B1281 " distance=2.03 Simple disulfide: pdb=" SG CYS B1441 " - pdb=" SG CYS B1461 " distance=2.02 Simple disulfide: pdb=" SG CYS B1894 " - pdb=" SG CYS B1920 " distance=2.03 Simple disulfide: pdb=" SG CYS B1898 " - pdb=" SG CYS B1905 " distance=2.03 Simple disulfide: pdb=" SG CYS B1929 " - pdb=" SG CYS B1940 " distance=2.03 Simple disulfide: pdb=" SG CYS B1997 " - pdb=" SG CYS B2025 " distance=2.02 Simple disulfide: pdb=" SG CYS B2001 " - pdb=" SG CYS B2007 " distance=2.03 Simple disulfide: pdb=" SG CYS B2006 " - pdb=" SG CYS B2077 " distance=2.03 Simple disulfide: pdb=" SG CYS B2130 " - pdb=" SG CYS B2154 " distance=2.03 Simple disulfide: pdb=" SG CYS B2134 " - pdb=" SG CYS B2140 " distance=2.03 Simple disulfide: pdb=" SG CYS B2163 " - pdb=" SG CYS B2172 " distance=2.03 Simple disulfide: pdb=" SG CYS B2264 " - pdb=" SG CYS B2281 " distance=2.02 Simple disulfide: pdb=" SG CYS B2442 " - pdb=" SG CYS B2453 " distance=2.03 Simple disulfide: pdb=" SG CYS B2591 " - pdb=" SG CYS B2715 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied ALPHA1-4 " NAG C 2 " - " MAN C 3 " " NAG E 2 " - " MAN E 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2801 " - " ASN A2250 " " NAG A2802 " - " ASN A2295 " " NAG A2803 " - " ASN A2122 " " NAG A2804 " - " ASN A 947 " " NAG A2805 " - " ASN A 198 " " NAG A2806 " - " ASN A 495 " " NAG B2801 " - " ASN B 198 " " NAG B2802 " - " ASN B 495 " " NAG B2803 " - " ASN B2250 " " NAG B2804 " - " ASN B2295 " " NAG B2805 " - " ASN B2122 " " NAG B2806 " - " ASN B 947 " " NAG C 1 " - " ASN A2014 " " NAG D 1 " - " ASN A 483 " " NAG E 1 " - " ASN B2014 " " NAG F 1 " - " ASN B 483 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.79 Conformation dependent library (CDL) restraints added in 3.2 seconds 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6626 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 36 sheets defined 33.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.758A pdb=" N LEU A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 4.053A pdb=" N GLN A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 173 removed outlier: 3.553A pdb=" N ILE A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 215 through 219 Processing helix chain 'A' and resid 220 through 226 Processing helix chain 'A' and resid 274 through 293 removed outlier: 3.530A pdb=" N ARG A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 removed outlier: 3.649A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 377 removed outlier: 3.743A pdb=" N GLU A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 removed outlier: 3.713A pdb=" N LEU A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 422 through 427' Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.924A pdb=" N LEU A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 472 removed outlier: 4.396A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 471 " --> pdb=" O GLN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.968A pdb=" N GLN A 481 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 502 removed outlier: 3.615A pdb=" N GLN A 502 " --> pdb=" O HIS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 572 Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.980A pdb=" N LEU A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 603 removed outlier: 3.547A pdb=" N MET A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 673 Processing helix chain 'A' and resid 727 through 743 Processing helix chain 'A' and resid 923 through 947 removed outlier: 4.128A pdb=" N VAL A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 3.592A pdb=" N ALA A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 988 removed outlier: 3.646A pdb=" N LEU A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS A 985 " --> pdb=" O THR A 981 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE A 986 " --> pdb=" O PHE A 982 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1008 Processing helix chain 'A' and resid 1075 through 1087 removed outlier: 3.661A pdb=" N LEU A1080 " --> pdb=" O SER A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1153 Processing helix chain 'A' and resid 1318 through 1327 Processing helix chain 'A' and resid 1853 through 1857 removed outlier: 3.760A pdb=" N PHE A1857 " --> pdb=" O THR A1853 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1853 through 1857' Processing helix chain 'A' and resid 1861 through 1863 No H-bonds generated for 'chain 'A' and resid 1861 through 1863' Processing helix chain 'A' and resid 1887 through 1901 removed outlier: 3.617A pdb=" N GLU A1901 " --> pdb=" O ARG A1897 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1940 removed outlier: 4.113A pdb=" N GLY A1939 " --> pdb=" O SER A1936 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2004 Processing helix chain 'A' and resid 2090 through 2094 Processing helix chain 'A' and resid 2098 through 2100 No H-bonds generated for 'chain 'A' and resid 2098 through 2100' Processing helix chain 'A' and resid 2122 through 2137 removed outlier: 4.037A pdb=" N HIS A2137 " --> pdb=" O GLU A2133 " (cutoff:3.500A) Processing helix chain 'A' and resid 2238 through 2242 Processing helix chain 'A' and resid 2319 through 2325 Processing helix chain 'A' and resid 2338 through 2343 Processing helix chain 'A' and resid 2353 through 2358 Processing helix chain 'A' and resid 2359 through 2370 removed outlier: 3.840A pdb=" N LEU A2363 " --> pdb=" O GLN A2359 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A2364 " --> pdb=" O VAL A2360 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A2370 " --> pdb=" O VAL A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2387 through 2394 removed outlier: 3.954A pdb=" N ILE A2391 " --> pdb=" O GLY A2387 " (cutoff:3.500A) Processing helix chain 'A' and resid 2395 through 2397 No H-bonds generated for 'chain 'A' and resid 2395 through 2397' Processing helix chain 'A' and resid 2425 through 2441 Processing helix chain 'A' and resid 2446 through 2455 removed outlier: 3.607A pdb=" N SER A2452 " --> pdb=" O GLN A2448 " (cutoff:3.500A) Processing helix chain 'A' and resid 2458 through 2471 removed outlier: 3.708A pdb=" N GLN A2466 " --> pdb=" O LEU A2462 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A2471 " --> pdb=" O THR A2467 " (cutoff:3.500A) Processing helix chain 'A' and resid 2491 through 2496 Processing helix chain 'A' and resid 2515 through 2520 removed outlier: 3.787A pdb=" N ALA A2520 " --> pdb=" O LEU A2516 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2531 Processing helix chain 'A' and resid 2535 through 2548 removed outlier: 4.058A pdb=" N DHA A2540 " --> pdb=" O LYS A2536 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A2543 " --> pdb=" O PHE A2539 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A2544 " --> pdb=" O DHA A2540 " (cutoff:3.500A) Processing helix chain 'A' and resid 2554 through 2564 removed outlier: 3.593A pdb=" N ALA A2558 " --> pdb=" O ALA A2554 " (cutoff:3.500A) Processing helix chain 'A' and resid 2575 through 2589 removed outlier: 3.936A pdb=" N GLN A2582 " --> pdb=" O ARG A2578 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A2583 " --> pdb=" O ALA A2579 " (cutoff:3.500A) Processing helix chain 'A' and resid 2591 through 2603 removed outlier: 4.031A pdb=" N ALA A2597 " --> pdb=" O VAL A2593 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A2603 " --> pdb=" O HIS A2599 " (cutoff:3.500A) Processing helix chain 'A' and resid 2633 through 2637 Processing helix chain 'A' and resid 2645 through 2666 Processing helix chain 'A' and resid 2711 through 2727 removed outlier: 3.915A pdb=" N ILE A2722 " --> pdb=" O TRP A2718 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN A2723 " --> pdb=" O SER A2719 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A2727 " --> pdb=" O GLN A2723 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 45 removed outlier: 3.851A pdb=" N LEU B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 removed outlier: 3.602A pdb=" N LEU B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 206 through 214 removed outlier: 3.616A pdb=" N SER B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 274 through 293 removed outlier: 3.649A pdb=" N PHE B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 311 Processing helix chain 'B' and resid 363 through 377 removed outlier: 3.705A pdb=" N GLU B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 removed outlier: 3.851A pdb=" N LEU B 426 " --> pdb=" O PHE B 422 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 422 through 427' Processing helix chain 'B' and resid 435 through 445 Processing helix chain 'B' and resid 449 through 459 removed outlier: 3.577A pdb=" N LEU B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 471 removed outlier: 4.390A pdb=" N GLN B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN B 468 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE B 471 " --> pdb=" O GLN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 removed outlier: 4.036A pdb=" N GLN B 481 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 502 removed outlier: 3.503A pdb=" N GLN B 502 " --> pdb=" O HIS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 572 Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.969A pdb=" N LEU B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU B 578 " --> pdb=" O PRO B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 604 Processing helix chain 'B' and resid 659 through 673 removed outlier: 3.547A pdb=" N GLY B 673 " --> pdb=" O GLN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 743 Processing helix chain 'B' and resid 925 through 949 removed outlier: 3.774A pdb=" N VAL B 932 " --> pdb=" O VAL B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 961 removed outlier: 3.504A pdb=" N SER B 956 " --> pdb=" O PRO B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 988 removed outlier: 4.594A pdb=" N SER B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 984 through 988' Processing helix chain 'B' and resid 990 through 1010 removed outlier: 3.625A pdb=" N LEU B1009 " --> pdb=" O TYR B1005 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B1010 " --> pdb=" O GLN B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1088 Processing helix chain 'B' and resid 1147 through 1154 Processing helix chain 'B' and resid 1318 through 1328 removed outlier: 3.819A pdb=" N GLU B1324 " --> pdb=" O PHE B1320 " (cutoff:3.500A) Processing helix chain 'B' and resid 1853 through 1857 removed outlier: 3.747A pdb=" N PHE B1857 " --> pdb=" O THR B1853 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1853 through 1857' Processing helix chain 'B' and resid 1861 through 1863 No H-bonds generated for 'chain 'B' and resid 1861 through 1863' Processing helix chain 'B' and resid 1887 through 1900 Processing helix chain 'B' and resid 1936 through 1940 removed outlier: 4.263A pdb=" N GLY B1939 " --> pdb=" O SER B1936 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2004 removed outlier: 3.598A pdb=" N PHE B1995 " --> pdb=" O SER B1991 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS B2001 " --> pdb=" O CYS B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2090 through 2094 Processing helix chain 'B' and resid 2098 through 2100 No H-bonds generated for 'chain 'B' and resid 2098 through 2100' Processing helix chain 'B' and resid 2122 through 2137 removed outlier: 3.636A pdb=" N ARG B2129 " --> pdb=" O ALA B2125 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS B2137 " --> pdb=" O GLU B2133 " (cutoff:3.500A) Processing helix chain 'B' and resid 2319 through 2325 Processing helix chain 'B' and resid 2338 through 2343 Processing helix chain 'B' and resid 2353 through 2358 Processing helix chain 'B' and resid 2361 through 2369 removed outlier: 3.658A pdb=" N VAL B2366 " --> pdb=" O ALA B2362 " (cutoff:3.500A) Processing helix chain 'B' and resid 2376 through 2379 Processing helix chain 'B' and resid 2387 through 2393 removed outlier: 3.968A pdb=" N ILE B2391 " --> pdb=" O GLY B2387 " (cutoff:3.500A) Processing helix chain 'B' and resid 2394 through 2397 Processing helix chain 'B' and resid 2425 through 2441 removed outlier: 3.616A pdb=" N GLN B2431 " --> pdb=" O GLU B2427 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B2434 " --> pdb=" O ARG B2430 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B2436 " --> pdb=" O GLN B2432 " (cutoff:3.500A) Processing helix chain 'B' and resid 2446 through 2455 removed outlier: 3.597A pdb=" N CYS B2453 " --> pdb=" O GLU B2449 " (cutoff:3.500A) Processing helix chain 'B' and resid 2458 through 2470 removed outlier: 3.525A pdb=" N ALA B2465 " --> pdb=" O ILE B2461 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN B2466 " --> pdb=" O LEU B2462 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B2467 " --> pdb=" O ASN B2463 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B2468 " --> pdb=" O ASP B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2491 through 2496 Processing helix chain 'B' and resid 2515 through 2520 removed outlier: 3.740A pdb=" N ALA B2520 " --> pdb=" O LEU B2516 " (cutoff:3.500A) Processing helix chain 'B' and resid 2520 through 2530 Processing helix chain 'B' and resid 2535 through 2546 removed outlier: 3.802A pdb=" N DHA B2540 " --> pdb=" O LYS B2536 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B2543 " --> pdb=" O PHE B2539 " (cutoff:3.500A) Processing helix chain 'B' and resid 2554 through 2564 removed outlier: 3.560A pdb=" N ALA B2558 " --> pdb=" O ALA B2554 " (cutoff:3.500A) Processing helix chain 'B' and resid 2575 through 2589 removed outlier: 3.930A pdb=" N GLN B2582 " --> pdb=" O ARG B2578 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B2583 " --> pdb=" O ALA B2579 " (cutoff:3.500A) Processing helix chain 'B' and resid 2591 through 2603 removed outlier: 3.888A pdb=" N ALA B2597 " --> pdb=" O VAL B2593 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B2601 " --> pdb=" O ALA B2597 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B2603 " --> pdb=" O HIS B2599 " (cutoff:3.500A) Processing helix chain 'B' and resid 2627 through 2632 removed outlier: 3.575A pdb=" N PHE B2632 " --> pdb=" O VAL B2628 " (cutoff:3.500A) Processing helix chain 'B' and resid 2633 through 2637 Processing helix chain 'B' and resid 2645 through 2666 removed outlier: 4.033A pdb=" N GLN B2657 " --> pdb=" O LEU B2653 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B2663 " --> pdb=" O PHE B2659 " (cutoff:3.500A) Processing helix chain 'B' and resid 2711 through 2720 removed outlier: 3.501A pdb=" N PHE B2717 " --> pdb=" O ALA B2713 " (cutoff:3.500A) Processing helix chain 'B' and resid 2720 through 2727 removed outlier: 3.886A pdb=" N ALA B2727 " --> pdb=" O GLN B2723 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 194 Processing sheet with id=AA2, first strand: chain 'A' and resid 197 through 198 removed outlier: 3.914A pdb=" N MET A 203 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA4, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AA5, first strand: chain 'A' and resid 695 through 697 Processing sheet with id=AA6, first strand: chain 'A' and resid 771 through 772 removed outlier: 4.737A pdb=" N CYS A 900 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 908 " --> pdb=" O CYS A 900 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1117 through 1120 Processing sheet with id=AA8, first strand: chain 'A' and resid 1254 through 1255 Processing sheet with id=AA9, first strand: chain 'A' and resid 1366 through 1371 removed outlier: 3.690A pdb=" N THR A1292 " --> pdb=" O TRP A1368 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A1289 " --> pdb=" O GLY A1440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1865 through 1867 Processing sheet with id=AB2, first strand: chain 'A' and resid 1907 through 1910 removed outlier: 3.768A pdb=" N TYR A1923 " --> pdb=" O LEU A1907 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1971 through 1975 removed outlier: 6.464A pdb=" N PHE A1971 " --> pdb=" O SER A2037 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER A2037 " --> pdb=" O PHE A1971 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1979 through 1981 removed outlier: 6.548A pdb=" N THR A2027 " --> pdb=" O ARG A1980 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2095 through 2096 Processing sheet with id=AB6, first strand: chain 'A' and resid 2102 through 2103 Processing sheet with id=AB7, first strand: chain 'A' and resid 2200 through 2203 Processing sheet with id=AB8, first strand: chain 'A' and resid 2212 through 2217 removed outlier: 4.111A pdb=" N GLY A2230 " --> pdb=" O LEU A2284 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU A2284 " --> pdb=" O GLY A2230 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER A2297 " --> pdb=" O ILE A2329 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL A2331 " --> pdb=" O SER A2297 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU A2299 " --> pdb=" O VAL A2331 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA A2333 " --> pdb=" O LEU A2299 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE A2301 " --> pdb=" O ALA A2333 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ALA A2296 " --> pdb=" O ARG A2379 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR A2381 " --> pdb=" O ALA A2296 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A2298 " --> pdb=" O THR A2381 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ALA A2383 " --> pdb=" O VAL A2298 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL A2300 " --> pdb=" O ALA A2383 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG A2409 " --> pdb=" O ARG A2378 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A2380 " --> pdb=" O ARG A2409 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL A2411 " --> pdb=" O VAL A2380 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A2382 " --> pdb=" O VAL A2411 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N MET A2413 " --> pdb=" O LEU A2382 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA A2384 " --> pdb=" O MET A2413 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA A2410 " --> pdb=" O LEU A2507 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY A2509 " --> pdb=" O ALA A2410 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A2412 " --> pdb=" O GLY A2509 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N SER A2511 " --> pdb=" O LEU A2412 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU A2506 " --> pdb=" O PHE A2609 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N TYR A2611 " --> pdb=" O LEU A2506 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A2508 " --> pdb=" O TYR A2611 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ALA A2613 " --> pdb=" O ILE A2508 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N SER A2510 " --> pdb=" O ALA A2613 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N SER A2696 " --> pdb=" O VAL A2608 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N MET A2610 " --> pdb=" O SER A2696 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.682A pdb=" N SER B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 192 through 194 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AC3, first strand: chain 'B' and resid 328 through 330 Processing sheet with id=AC4, first strand: chain 'B' and resid 629 through 631 Processing sheet with id=AC5, first strand: chain 'B' and resid 695 through 697 Processing sheet with id=AC6, first strand: chain 'B' and resid 771 through 772 removed outlier: 4.694A pdb=" N CYS B 900 " --> pdb=" O LEU B 908 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1040 through 1041 removed outlier: 4.869A pdb=" N CYS B1051 " --> pdb=" O VAL B1059 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1117 through 1120 Processing sheet with id=AC9, first strand: chain 'B' and resid 1254 through 1255 Processing sheet with id=AD1, first strand: chain 'B' and resid 1366 through 1371 removed outlier: 3.723A pdb=" N THR B1292 " --> pdb=" O TRP B1368 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR B1289 " --> pdb=" O GLY B1440 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1865 through 1867 removed outlier: 3.615A pdb=" N LEU B1944 " --> pdb=" O ILE B1866 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1909 through 1910 Processing sheet with id=AD4, first strand: chain 'B' and resid 1971 through 1975 removed outlier: 6.454A pdb=" N PHE B1971 " --> pdb=" O SER B2037 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER B2037 " --> pdb=" O PHE B1971 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS B1973 " --> pdb=" O THR B2035 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N CYS B2036 " --> pdb=" O VAL B2113 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N VAL B2113 " --> pdb=" O CYS B2036 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE B2183 " --> pdb=" O LEU B2097 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1979 through 1981 removed outlier: 6.732A pdb=" N THR B2027 " --> pdb=" O ARG B1980 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 2102 through 2103 Processing sheet with id=AD7, first strand: chain 'B' and resid 2200 through 2203 removed outlier: 7.181A pdb=" N GLN B2208 " --> pdb=" O TRP B2255 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 2212 through 2217 removed outlier: 4.175A pdb=" N GLY B2230 " --> pdb=" O LEU B2284 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU B2284 " --> pdb=" O GLY B2230 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL B2300 " --> pdb=" O ALA B2383 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B2382 " --> pdb=" O ARG B2409 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 2507 through 2511 removed outlier: 7.136A pdb=" N ILE B2508 " --> pdb=" O TYR B2611 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ALA B2613 " --> pdb=" O ILE B2508 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER B2510 " --> pdb=" O ALA B2613 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N MET B2610 " --> pdb=" O SER B2696 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2355 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: 21.69 Time building geometry restraints manager: 13.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.68: 55360 1.68 - 2.52: 242 2.52 - 3.36: 1 3.36 - 4.20: 0 4.20 - 5.05: 1 Warning: very large bond lengths. Bond restraints: 55604 Sorted by residual: bond pdb=" CH2 TRP B1879 " pdb=" HH2 TRP B1879 " ideal model delta sigma weight residual 0.930 5.047 -4.117 2.00e-02 2.50e+03 4.24e+04 bond pdb=" CH2 TRP B2354 " pdb=" HH2 TRP B2354 " ideal model delta sigma weight residual 0.930 2.911 -1.981 2.00e-02 2.50e+03 9.81e+03 bond pdb=" CB DHA B2540 " pdb=" HB2 DHA B2540 " ideal model delta sigma weight residual 0.930 1.090 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" CB DHA B2540 " pdb=" HB1 DHA B2540 " ideal model delta sigma weight residual 0.930 1.090 -0.160 2.00e-02 2.50e+03 6.36e+01 bond pdb=" CB DHA A2540 " pdb=" HB2 DHA A2540 " ideal model delta sigma weight residual 0.930 1.089 -0.159 2.00e-02 2.50e+03 6.36e+01 ... (remaining 55599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.48: 100037 13.48 - 26.96: 0 26.96 - 40.44: 1 40.44 - 53.92: 0 53.92 - 67.40: 1 Bond angle restraints: 100039 Sorted by residual: angle pdb=" CZ2 TRP B1879 " pdb=" CH2 TRP B1879 " pdb=" HH2 TRP B1879 " ideal model delta sigma weight residual 119.25 51.85 67.40 3.00e+00 1.11e-01 5.05e+02 angle pdb=" CZ3 TRP B1879 " pdb=" CH2 TRP B1879 " pdb=" HH2 TRP B1879 " ideal model delta sigma weight residual 119.25 158.31 -39.06 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C ASN A2250 " pdb=" CA ASN A2250 " pdb=" CB ASN A2250 " ideal model delta sigma weight residual 111.89 101.64 10.25 1.42e+00 4.96e-01 5.21e+01 angle pdb=" O PHE B 494 " pdb=" C PHE B 494 " pdb=" N ASN B 495 " ideal model delta sigma weight residual 122.09 114.84 7.25 1.09e+00 8.42e-01 4.43e+01 angle pdb=" CA HIS A 313 " pdb=" CB HIS A 313 " pdb=" CG HIS A 313 " ideal model delta sigma weight residual 113.80 120.25 -6.45 1.00e+00 1.00e+00 4.16e+01 ... (remaining 100034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.90: 24824 22.90 - 45.80: 1723 45.80 - 68.70: 374 68.70 - 91.60: 56 91.60 - 114.50: 7 Dihedral angle restraints: 26984 sinusoidal: 14901 harmonic: 12083 Sorted by residual: dihedral pdb=" C DHA A2540 " pdb=" N DHA A2540 " pdb=" CA DHA A2540 " pdb=" CB DHA A2540 " ideal model delta harmonic sigma weight residual -122.60 -179.89 57.29 0 2.50e+00 1.60e-01 5.25e+02 dihedral pdb=" CE3 TRP B1879 " pdb=" CZ3 TRP B1879 " pdb=" CH2 TRP B1879 " pdb=" HH2 TRP B1879 " ideal model delta harmonic sigma weight residual -180.00 -65.50 -114.50 0 5.00e+00 4.00e-02 5.24e+02 dihedral pdb=" N DHA A2540 " pdb=" C DHA A2540 " pdb=" CA DHA A2540 " pdb=" CB DHA A2540 " ideal model delta harmonic sigma weight residual 122.80 179.89 -57.09 0 2.50e+00 1.60e-01 5.21e+02 ... (remaining 26981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.280: 4242 0.280 - 0.561: 9 0.561 - 0.841: 3 0.841 - 1.121: 0 1.121 - 1.402: 1 Chirality restraints: 4255 Sorted by residual: chirality pdb=" C1 MAN C 3 " pdb=" O4 NAG C 2 " pdb=" C2 MAN C 3 " pdb=" O5 MAN C 3 " both_signs ideal model delta sigma weight residual False 2.40 2.08 0.32 2.00e-02 2.50e+03 2.50e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.01e+01 chirality pdb=" C1 MAN E 3 " pdb=" O4 NAG E 2 " pdb=" C2 MAN E 3 " pdb=" O5 MAN E 3 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.71e+01 ... (remaining 4252 not shown) Planarity restraints: 8393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1879 " -0.365 2.00e-02 2.50e+03 2.88e-01 3.33e+03 pdb=" CG TRP B1879 " -0.141 2.00e-02 2.50e+03 pdb=" CD1 TRP B1879 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B1879 " -0.031 2.00e-02 2.50e+03 pdb=" NE1 TRP B1879 " 0.192 2.00e-02 2.50e+03 pdb=" CE2 TRP B1879 " 0.167 2.00e-02 2.50e+03 pdb=" CE3 TRP B1879 " -0.100 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1879 " 0.305 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1879 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP B1879 " 0.233 2.00e-02 2.50e+03 pdb=" HD1 TRP B1879 " -0.014 2.00e-02 2.50e+03 pdb=" HE1 TRP B1879 " 0.306 2.00e-02 2.50e+03 pdb=" HE3 TRP B1879 " -0.244 2.00e-02 2.50e+03 pdb=" HZ2 TRP B1879 " 0.444 2.00e-02 2.50e+03 pdb=" HZ3 TRP B1879 " -0.011 2.00e-02 2.50e+03 pdb=" HH2 TRP B1879 " -0.776 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 565 " 0.129 2.00e-02 2.50e+03 1.37e-01 2.83e+02 pdb=" CD GLN A 565 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN A 565 " -0.122 2.00e-02 2.50e+03 pdb=" NE2 GLN A 565 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 565 " -0.200 2.00e-02 2.50e+03 pdb="HE22 GLN A 565 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 562 " -0.102 2.00e-02 2.50e+03 1.07e-01 1.72e+02 pdb=" CG ASN A 562 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 562 " 0.095 2.00e-02 2.50e+03 pdb=" ND2 ASN A 562 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 562 " 0.154 2.00e-02 2.50e+03 pdb="HD22 ASN A 562 " -0.160 2.00e-02 2.50e+03 ... (remaining 8390 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.29: 11658 2.29 - 2.96: 138117 2.96 - 3.62: 174428 3.62 - 4.29: 262205 4.29 - 4.96: 411605 Nonbonded interactions: 998013 Sorted by model distance: nonbonded pdb=" O TYR A1966 " pdb="HH12 ARG B 169 " model vdw 1.620 2.450 nonbonded pdb=" O GLN A 761 " pdb="HE22 GLN A 772 " model vdw 1.621 2.450 nonbonded pdb=" OD2 ASP B 76 " pdb=" HE ARG B 78 " model vdw 1.631 2.450 nonbonded pdb=" OE1 GLN B 99 " pdb=" HH TYR B 126 " model vdw 1.634 2.450 nonbonded pdb=" OD2 ASP A2505 " pdb="HD22 ASN A2607 " model vdw 1.637 2.450 ... (remaining 998008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 973 or resid 983 through 2250 or (resid 2251 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2 or name NE1 or name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2 o \ r name H or name HA or name HB2 or name HB3 or name HD1 or name HE1 or name HE3 \ or name HZ2 or name HZ3)) or resid 2252 through 2572 or resid 2573 through 2727 \ or resid 2801 through 2806)) selection = (chain 'B' and (resid 31 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name H or name HA )) or resid 197 through 314 or (resid 315 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2 or name CE1 or name CE2 or name CZ or name OH or name H or name HA or nam \ e HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2)) or resid 316 \ through 505 or (resid 549 and (name N or name CA or name C or name O or name HA \ 2 or name HA3)) or resid 550 through 637 or resid 646 through 2572 or resid 2573 \ through 2727 or resid 2801 through 2806)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.380 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: 0.700 Extract box with map and model: 1.600 Check model and map are aligned: 0.310 Set scattering table: 0.370 Process input model: 91.620 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.170 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:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.008 0.107 28777 Z= 0.506 Angle : 0.830 10.746 38988 Z= 0.466 Chirality : 0.058 1.402 4255 Planarity : 0.006 0.073 5112 Dihedral : 15.289 104.119 10920 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 0.20 % Allowed : 0.70 % Favored : 99.11 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.14), residues: 3443 helix: -0.99 (0.15), residues: 1039 sheet: -2.26 (0.24), residues: 406 loop : -1.62 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B2251 HIS 0.022 0.001 HIS A 313 PHE 0.049 0.002 PHE A 602 TYR 0.016 0.002 TYR B2059 ARG 0.029 0.001 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 393 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 387 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.6222 (tpp-160) cc_final: 0.5295 (tpm170) REVERT: A 313 HIS cc_start: 0.6530 (OUTLIER) cc_final: 0.6121 (p-80) REVERT: A 459 PHE cc_start: 0.8113 (m-10) cc_final: 0.6831 (t80) REVERT: A 498 HIS cc_start: 0.7597 (t70) cc_final: 0.7256 (t-90) REVERT: A 581 GLN cc_start: 0.8223 (tt0) cc_final: 0.7904 (tp40) REVERT: A 2513 ASP cc_start: 0.7787 (m-30) cc_final: 0.7543 (m-30) REVERT: B 459 PHE cc_start: 0.8111 (m-10) cc_final: 0.6488 (t80) REVERT: B 551 PHE cc_start: 0.8061 (m-10) cc_final: 0.7861 (m-10) REVERT: B 559 GLU cc_start: 0.8069 (tp30) cc_final: 0.7862 (tp30) REVERT: B 899 TRP cc_start: 0.7359 (p90) cc_final: 0.7109 (p90) outliers start: 6 outliers final: 2 residues processed: 392 average time/residue: 0.8482 time to fit residues: 504.4936 Evaluate side-chains 317 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 314 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 2353 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 169 optimal weight: 0.1980 chunk 207 optimal weight: 7.9990 chunk 323 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 558 GLN B 130 GLN B 562 ASN B 699 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28777 Z= 0.242 Angle : 0.621 8.825 38988 Z= 0.317 Chirality : 0.042 0.337 4255 Planarity : 0.006 0.131 5112 Dihedral : 7.600 91.659 4336 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.40 % Allowed : 5.86 % Favored : 93.74 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 3443 helix: -0.53 (0.15), residues: 1067 sheet: -2.11 (0.25), residues: 407 loop : -1.55 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B1879 HIS 0.005 0.001 HIS A1043 PHE 0.017 0.001 PHE A 579 TYR 0.015 0.001 TYR B 945 ARG 0.008 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 336 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 PHE cc_start: 0.8089 (m-10) cc_final: 0.6820 (t80) REVERT: A 468 GLN cc_start: 0.8036 (mt0) cc_final: 0.7225 (mm110) REVERT: A 498 HIS cc_start: 0.7649 (t70) cc_final: 0.7241 (t-90) REVERT: A 1080 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8757 (mp) REVERT: B 459 PHE cc_start: 0.8053 (m-10) cc_final: 0.6419 (t80) REVERT: B 991 ASP cc_start: 0.8474 (p0) cc_final: 0.8098 (p0) REVERT: B 1005 TYR cc_start: 0.8112 (m-10) cc_final: 0.7794 (m-10) REVERT: B 1891 ASN cc_start: 0.5844 (m110) cc_final: 0.5640 (m110) REVERT: B 2002 ASP cc_start: 0.7724 (m-30) cc_final: 0.7464 (m-30) outliers start: 12 outliers final: 9 residues processed: 345 average time/residue: 0.9011 time to fit residues: 465.8233 Evaluate side-chains 318 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 308 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 2210 LEU Chi-restraints excluded: chain A residue 2353 ASN Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 699 ASN Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 937 ARG Chi-restraints excluded: chain B residue 2353 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 269 optimal weight: 0.3980 chunk 220 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 323 optimal weight: 0.9990 chunk 349 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28777 Z= 0.250 Angle : 0.591 8.768 38988 Z= 0.299 Chirality : 0.041 0.339 4255 Planarity : 0.006 0.132 5112 Dihedral : 7.067 80.399 4334 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.63 % Allowed : 7.09 % Favored : 92.28 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.14), residues: 3443 helix: -0.25 (0.15), residues: 1067 sheet: -2.02 (0.25), residues: 399 loop : -1.49 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 899 HIS 0.004 0.001 HIS A 313 PHE 0.012 0.001 PHE B 698 TYR 0.013 0.001 TYR B2157 ARG 0.007 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 329 time to evaluate : 3.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.6178 (tpp-160) cc_final: 0.5169 (tpm170) REVERT: A 459 PHE cc_start: 0.8051 (m-10) cc_final: 0.6810 (t80) REVERT: A 468 GLN cc_start: 0.8006 (mt0) cc_final: 0.7231 (mm110) REVERT: A 498 HIS cc_start: 0.7654 (t70) cc_final: 0.7255 (t-90) REVERT: A 1080 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8627 (mp) REVERT: A 2240 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7189 (tp30) REVERT: B 294 ARG cc_start: 0.7635 (mmm160) cc_final: 0.7233 (mmm160) REVERT: B 459 PHE cc_start: 0.8010 (m-10) cc_final: 0.6460 (t80) REVERT: B 991 ASP cc_start: 0.8510 (p0) cc_final: 0.8105 (p0) REVERT: B 1891 ASN cc_start: 0.5814 (m110) cc_final: 0.5601 (m110) REVERT: B 2002 ASP cc_start: 0.7610 (m-30) cc_final: 0.7389 (m-30) outliers start: 19 outliers final: 15 residues processed: 342 average time/residue: 0.9150 time to fit residues: 473.1252 Evaluate side-chains 319 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 302 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 921 CYS Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1370 LEU Chi-restraints excluded: chain A residue 2210 LEU Chi-restraints excluded: chain A residue 2240 GLU Chi-restraints excluded: chain A residue 2353 ASN Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 700 SER Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 937 ARG Chi-restraints excluded: chain B residue 2347 SER Chi-restraints excluded: chain B residue 2353 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 325 optimal weight: 0.9990 chunk 344 optimal weight: 0.9980 chunk 169 optimal weight: 0.1980 chunk 308 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN B 699 ASN B2304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 28777 Z= 0.236 Angle : 0.567 11.719 38988 Z= 0.284 Chirality : 0.040 0.299 4255 Planarity : 0.006 0.133 5112 Dihedral : 6.635 66.641 4334 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.80 % Allowed : 8.58 % Favored : 90.62 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3443 helix: 0.03 (0.16), residues: 1075 sheet: -2.00 (0.26), residues: 389 loop : -1.43 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B2562 HIS 0.006 0.001 HIS B 320 PHE 0.010 0.001 PHE A 579 TYR 0.012 0.001 TYR B2157 ARG 0.006 0.000 ARG B1283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 341 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 317 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.6289 (tpp-160) cc_final: 0.5246 (tpm170) REVERT: A 459 PHE cc_start: 0.8028 (m-10) cc_final: 0.6788 (t80) REVERT: A 468 GLN cc_start: 0.7986 (mt0) cc_final: 0.7237 (mm110) REVERT: A 556 ASN cc_start: 0.7744 (t0) cc_final: 0.7492 (t0) REVERT: A 1080 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8747 (mp) REVERT: A 2240 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7199 (tp30) REVERT: B 459 PHE cc_start: 0.7999 (m-10) cc_final: 0.6437 (t80) REVERT: B 991 ASP cc_start: 0.8475 (p0) cc_final: 0.8127 (p0) REVERT: B 1961 ARG cc_start: 0.7349 (mmm160) cc_final: 0.7048 (mmm160) outliers start: 24 outliers final: 19 residues processed: 332 average time/residue: 0.9321 time to fit residues: 465.6741 Evaluate side-chains 326 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 305 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 2210 LEU Chi-restraints excluded: chain A residue 2240 GLU Chi-restraints excluded: chain A residue 2292 MET Chi-restraints excluded: chain A residue 2353 ASN Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 699 ASN Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2347 SER Chi-restraints excluded: chain B residue 2353 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 293 optimal weight: 0.7980 chunk 237 optimal weight: 0.0020 chunk 0 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 HIS B 699 ASN B1876 GLN B2304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 28777 Z= 0.212 Angle : 0.552 10.453 38988 Z= 0.276 Chirality : 0.040 0.288 4255 Planarity : 0.005 0.133 5112 Dihedral : 6.277 59.985 4334 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.83 % Allowed : 9.18 % Favored : 89.99 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3443 helix: 0.20 (0.16), residues: 1082 sheet: -1.94 (0.26), residues: 389 loop : -1.38 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B2562 HIS 0.006 0.001 HIS B 320 PHE 0.011 0.001 PHE B 698 TYR 0.011 0.001 TYR B2157 ARG 0.007 0.000 ARG B1283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 326 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 PHE cc_start: 0.8015 (m-10) cc_final: 0.6811 (t80) REVERT: A 468 GLN cc_start: 0.7984 (mt0) cc_final: 0.7244 (mm110) REVERT: A 1080 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8795 (mp) REVERT: A 1283 ARG cc_start: 0.7462 (mmt90) cc_final: 0.7099 (mmp80) REVERT: A 2064 TYR cc_start: 0.8798 (m-80) cc_final: 0.8554 (m-80) REVERT: A 2240 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7168 (tp30) REVERT: B 167 ARG cc_start: 0.8182 (tpt170) cc_final: 0.7911 (tpp80) REVERT: B 459 PHE cc_start: 0.7985 (m-10) cc_final: 0.6472 (t80) REVERT: B 553 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.6272 (t80) REVERT: B 991 ASP cc_start: 0.8462 (p0) cc_final: 0.8132 (p0) REVERT: B 1961 ARG cc_start: 0.7326 (mmm160) cc_final: 0.7049 (mmm160) outliers start: 25 outliers final: 19 residues processed: 340 average time/residue: 0.8833 time to fit residues: 450.3377 Evaluate side-chains 327 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 305 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1370 LEU Chi-restraints excluded: chain A residue 2210 LEU Chi-restraints excluded: chain A residue 2240 GLU Chi-restraints excluded: chain A residue 2353 ASN Chi-restraints excluded: chain A residue 2568 HIS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 1370 LEU Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2347 SER Chi-restraints excluded: chain B residue 2353 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 2.9990 chunk 309 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 202 optimal weight: 0.7980 chunk 84 optimal weight: 0.0050 chunk 344 optimal weight: 0.9980 chunk 285 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 HIS A 699 ASN B 699 ASN B2304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28777 Z= 0.208 Angle : 0.543 9.755 38988 Z= 0.271 Chirality : 0.039 0.278 4255 Planarity : 0.005 0.133 5112 Dihedral : 5.986 60.014 4334 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.96 % Allowed : 9.97 % Favored : 89.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3443 helix: 0.39 (0.16), residues: 1090 sheet: -1.86 (0.27), residues: 389 loop : -1.32 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2562 HIS 0.006 0.001 HIS B 320 PHE 0.022 0.001 PHE A 566 TYR 0.012 0.001 TYR B2157 ARG 0.006 0.000 ARG B1283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 346 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 317 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.6302 (tpp-160) cc_final: 0.5445 (tpm170) REVERT: A 182 GLN cc_start: 0.9025 (mp10) cc_final: 0.8714 (mp10) REVERT: A 459 PHE cc_start: 0.7975 (m-10) cc_final: 0.6800 (t80) REVERT: A 468 GLN cc_start: 0.7919 (mt0) cc_final: 0.7250 (mm110) REVERT: A 1080 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8839 (mp) REVERT: A 2064 TYR cc_start: 0.8753 (m-80) cc_final: 0.8508 (m-80) REVERT: A 2240 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7175 (tp30) REVERT: B 167 ARG cc_start: 0.8175 (tpt170) cc_final: 0.7903 (tpp80) REVERT: B 459 PHE cc_start: 0.7993 (m-10) cc_final: 0.6467 (t80) REVERT: B 553 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.6284 (t80) REVERT: B 625 TYR cc_start: 0.4353 (p90) cc_final: 0.3800 (p90) REVERT: B 991 ASP cc_start: 0.8444 (p0) cc_final: 0.8155 (p0) REVERT: B 1961 ARG cc_start: 0.7284 (mmm160) cc_final: 0.7004 (mmm160) outliers start: 29 outliers final: 23 residues processed: 334 average time/residue: 0.8942 time to fit residues: 446.6526 Evaluate side-chains 320 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 294 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1370 LEU Chi-restraints excluded: chain A residue 2210 LEU Chi-restraints excluded: chain A residue 2240 GLU Chi-restraints excluded: chain A residue 2292 MET Chi-restraints excluded: chain A residue 2353 ASN Chi-restraints excluded: chain A residue 2568 HIS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 699 ASN Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 1370 LEU Chi-restraints excluded: chain B residue 1972 GLN Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2347 SER Chi-restraints excluded: chain B residue 2353 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 251 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 192 optimal weight: 0.0970 chunk 343 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN B2304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28777 Z= 0.244 Angle : 0.548 9.500 38988 Z= 0.274 Chirality : 0.040 0.277 4255 Planarity : 0.005 0.133 5112 Dihedral : 5.923 59.015 4334 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.99 % Allowed : 10.34 % Favored : 88.67 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3443 helix: 0.46 (0.16), residues: 1090 sheet: -1.86 (0.27), residues: 389 loop : -1.30 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2562 HIS 0.006 0.001 HIS B 320 PHE 0.020 0.001 PHE A 698 TYR 0.012 0.001 TYR B2157 ARG 0.007 0.000 ARG B1283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 304 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.6160 (tpp-160) cc_final: 0.5471 (tpm170) REVERT: A 182 GLN cc_start: 0.9025 (mp10) cc_final: 0.8721 (mp10) REVERT: A 459 PHE cc_start: 0.7975 (m-10) cc_final: 0.6815 (t80) REVERT: A 468 GLN cc_start: 0.7924 (mt0) cc_final: 0.7253 (mm110) REVERT: A 1080 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8838 (mp) REVERT: A 2026 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8687 (pp) REVERT: A 2240 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7182 (tp30) REVERT: B 459 PHE cc_start: 0.7963 (m-10) cc_final: 0.6443 (t80) REVERT: B 496 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7509 (m-10) REVERT: B 553 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6334 (t80) REVERT: B 625 TYR cc_start: 0.4424 (p90) cc_final: 0.3824 (p90) REVERT: B 698 PHE cc_start: 0.7319 (t80) cc_final: 0.7107 (t80) REVERT: B 991 ASP cc_start: 0.8444 (p0) cc_final: 0.8166 (p0) outliers start: 30 outliers final: 20 residues processed: 324 average time/residue: 0.8850 time to fit residues: 430.8969 Evaluate side-chains 323 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 298 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1370 LEU Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2210 LEU Chi-restraints excluded: chain A residue 2240 GLU Chi-restraints excluded: chain A residue 2353 ASN Chi-restraints excluded: chain A residue 2568 HIS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 1317 PHE Chi-restraints excluded: chain B residue 1370 LEU Chi-restraints excluded: chain B residue 1972 GLN Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2347 SER Chi-restraints excluded: chain B residue 2353 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 169 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 269 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28777 Z= 0.282 Angle : 0.557 9.176 38988 Z= 0.279 Chirality : 0.040 0.274 4255 Planarity : 0.005 0.133 5112 Dihedral : 5.933 57.092 4334 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.89 % Allowed : 10.64 % Favored : 88.47 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 3443 helix: 0.51 (0.16), residues: 1090 sheet: -1.81 (0.27), residues: 384 loop : -1.32 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2251 HIS 0.006 0.001 HIS B 320 PHE 0.012 0.001 PHE B 494 TYR 0.014 0.001 TYR B2157 ARG 0.006 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 324 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 297 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.6269 (tpp-160) cc_final: 0.5503 (tpm170) REVERT: A 182 GLN cc_start: 0.9032 (mp10) cc_final: 0.8724 (mp10) REVERT: A 459 PHE cc_start: 0.7976 (m-10) cc_final: 0.6815 (t80) REVERT: A 468 GLN cc_start: 0.7924 (mt0) cc_final: 0.7260 (mm110) REVERT: A 1080 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8843 (mp) REVERT: A 2026 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8706 (pp) REVERT: A 2064 TYR cc_start: 0.8876 (m-80) cc_final: 0.8584 (m-80) REVERT: A 2240 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7180 (tp30) REVERT: B 459 PHE cc_start: 0.7928 (m-10) cc_final: 0.6420 (t80) REVERT: B 496 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7483 (m-10) REVERT: B 553 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6335 (t80) REVERT: B 625 TYR cc_start: 0.4582 (p90) cc_final: 0.3878 (p90) REVERT: B 698 PHE cc_start: 0.7457 (t80) cc_final: 0.7225 (t80) REVERT: B 991 ASP cc_start: 0.8451 (p0) cc_final: 0.8177 (p0) outliers start: 27 outliers final: 18 residues processed: 315 average time/residue: 0.9046 time to fit residues: 426.7647 Evaluate side-chains 310 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 287 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1370 LEU Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2210 LEU Chi-restraints excluded: chain A residue 2240 GLU Chi-restraints excluded: chain A residue 2353 ASN Chi-restraints excluded: chain A residue 2568 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 1077 CYS Chi-restraints excluded: chain B residue 1317 PHE Chi-restraints excluded: chain B residue 1370 LEU Chi-restraints excluded: chain B residue 2273 THR Chi-restraints excluded: chain B residue 2353 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.6095 > 50: distance: 78 - 187: 14.193 distance: 81 - 184: 7.997 distance: 99 - 179: 14.885 distance: 128 - 136: 9.588 distance: 136 - 137: 13.877 distance: 136 - 143: 9.937 distance: 137 - 138: 5.450 distance: 137 - 140: 6.622 distance: 137 - 144: 6.960 distance: 138 - 139: 9.973 distance: 138 - 150: 8.200 distance: 140 - 141: 13.114 distance: 140 - 142: 3.193 distance: 140 - 145: 12.647 distance: 141 - 146: 9.337 distance: 142 - 147: 4.435 distance: 142 - 148: 3.555 distance: 150 - 151: 12.573 distance: 150 - 154: 14.198 distance: 151 - 152: 14.906 distance: 151 - 155: 12.807 distance: 151 - 156: 5.654 distance: 152 - 153: 9.417 distance: 152 - 157: 16.002 distance: 157 - 158: 9.136 distance: 157 - 167: 6.488 distance: 158 - 159: 4.789 distance: 158 - 168: 5.548 distance: 159 - 160: 16.778 distance: 159 - 174: 22.600 distance: 161 - 162: 3.517 distance: 161 - 169: 6.749 distance: 161 - 170: 5.006 distance: 162 - 163: 6.548 distance: 162 - 164: 5.817 distance: 163 - 165: 4.201 distance: 164 - 166: 6.073 distance: 174 - 175: 6.823 distance: 174 - 180: 13.861 distance: 175 - 176: 7.146 distance: 175 - 178: 6.804 distance: 175 - 181: 3.782 distance: 176 - 177: 4.680 distance: 176 - 184: 13.569 distance: 178 - 179: 8.197 distance: 178 - 182: 7.120 distance: 178 - 183: 4.292 distance: 184 - 185: 11.585 distance: 184 - 198: 13.345 distance: 185 - 186: 8.316 distance: 185 - 188: 11.758 distance: 185 - 199: 12.304 distance: 186 - 187: 9.470 distance: 186 - 208: 4.440 distance: 188 - 189: 7.515 distance: 188 - 200: 3.968 distance: 188 - 201: 3.502 distance: 189 - 190: 10.154 distance: 189 - 191: 6.770 distance: 190 - 192: 5.368 distance: 190 - 202: 3.565 distance: 191 - 193: 4.656 distance: 191 - 194: 3.601 distance: 192 - 193: 4.141 distance: 193 - 195: 5.222 distance: 194 - 196: 4.230 distance: 196 - 197: 4.520 distance: 209 - 215: 6.975 distance: 211 - 313: 6.175 distance: 212 - 213: 5.703 distance: 212 - 216: 7.226 distance: 212 - 217: 3.661 distance: 220 - 234: 8.690 distance: 222 - 223: 4.628 distance: 222 - 224: 3.052 distance: 223 - 228: 3.229 distance: 235 - 236: 4.145 distance: 236 - 237: 4.872 distance: 236 - 246: 13.319 distance: 239 - 241: 4.132 distance: 246 - 247: 13.253 distance: 246 - 250: 12.443 distance: 247 - 248: 8.196 distance: 247 - 251: 8.034 distance: 247 - 252: 7.921 distance: 248 - 249: 12.585 distance: 253 - 254: 3.156 distance: 253 - 262: 21.372 distance: 254 - 255: 4.229 distance: 254 - 257: 6.059 distance: 254 - 263: 3.011 distance: 255 - 256: 7.057 distance: 255 - 275: 4.177 distance: 257 - 258: 4.829 distance: 257 - 264: 9.554 distance: 257 - 265: 7.792 distance: 258 - 259: 5.609 distance: 258 - 267: 4.250 distance: 259 - 268: 4.585 distance: 259 - 269: 3.784 distance: 260 - 261: 5.430 distance: 260 - 270: 5.291 distance: 260 - 271: 3.233 distance: 261 - 274: 3.292