Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:18:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drv_8908/12_2022/6drv_8908.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drv_8908/12_2022/6drv_8908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drv_8908/12_2022/6drv_8908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drv_8908/12_2022/6drv_8908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drv_8908/12_2022/6drv_8908.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drv_8908/12_2022/6drv_8908.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 829": "OD1" <-> "OD2" Residue "A PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 829": "OD1" <-> "OD2" Residue "B PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 829": "OD1" <-> "OD2" Residue "C PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 829": "OD1" <-> "OD2" Residue "D PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 32888 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8222 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 958} Chain: "B" Number of atoms: 8222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8222 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 958} Chain: "C" Number of atoms: 8222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8222 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 958} Chain: "D" Number of atoms: 8222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8222 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 958} Time building chain proxies: 17.86, per 1000 atoms: 0.54 Number of scatterers: 32888 At special positions: 0 Unit cell: (191.737, 150.969, 98.735, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 160 16.00 O 6116 8.00 N 5816 7.00 C 20796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 537 " distance=2.04 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 537 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 537 " distance=2.04 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS D 537 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.44 Conformation dependent library (CDL) restraints added in 4.9 seconds 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7624 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 52 sheets defined 19.0% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 4.623A pdb=" N ALA A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 19 Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 66 through 71 Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.890A pdb=" N GLU A 76 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.521A pdb=" N LEU A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 397 through 407 removed outlier: 3.558A pdb=" N THR A 401 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 427 removed outlier: 4.520A pdb=" N LEU A 427 " --> pdb=" O MET A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 433 through 449 Processing helix chain 'A' and resid 466 through 480 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.087A pdb=" N SER A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.934A pdb=" N TYR A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.700A pdb=" N CYS A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 806 through 815 Processing helix chain 'A' and resid 924 through 927 Processing helix chain 'A' and resid 964 through 971 Processing helix chain 'A' and resid 973 through 977 Processing helix chain 'A' and resid 1005 through 1009 Processing helix chain 'B' and resid 3 through 15 removed outlier: 4.622A pdb=" N ALA B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 15 " --> pdb=" O VAL B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 19 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 66 through 71 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.890A pdb=" N GLU B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.520A pdb=" N LEU B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 397 through 407 removed outlier: 3.558A pdb=" N THR B 401 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 4.521A pdb=" N LEU B 427 " --> pdb=" O MET B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 433 through 449 Processing helix chain 'B' and resid 466 through 480 Processing helix chain 'B' and resid 520 through 527 removed outlier: 4.087A pdb=" N SER B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 3.934A pdb=" N TYR B 553 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 604 removed outlier: 3.700A pdb=" N CYS B 603 " --> pdb=" O ARG B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 806 through 815 Processing helix chain 'B' and resid 924 through 927 Processing helix chain 'B' and resid 964 through 971 Processing helix chain 'B' and resid 973 through 977 Processing helix chain 'B' and resid 1005 through 1009 Processing helix chain 'C' and resid 3 through 15 removed outlier: 4.624A pdb=" N ALA C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 15 " --> pdb=" O VAL C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 19 Processing helix chain 'C' and resid 39 through 45 Processing helix chain 'C' and resid 66 through 71 Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.889A pdb=" N GLU C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 Processing helix chain 'C' and resid 131 through 137 removed outlier: 3.520A pdb=" N LEU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 369 through 383 Processing helix chain 'C' and resid 397 through 407 removed outlier: 3.557A pdb=" N THR C 401 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 427 removed outlier: 4.521A pdb=" N LEU C 427 " --> pdb=" O MET C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 432 No H-bonds generated for 'chain 'C' and resid 430 through 432' Processing helix chain 'C' and resid 433 through 449 Processing helix chain 'C' and resid 466 through 480 Processing helix chain 'C' and resid 520 through 527 removed outlier: 4.086A pdb=" N SER C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 removed outlier: 3.935A pdb=" N TYR C 553 " --> pdb=" O GLY C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 604 removed outlier: 3.699A pdb=" N CYS C 603 " --> pdb=" O ARG C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 625 Processing helix chain 'C' and resid 790 through 795 Processing helix chain 'C' and resid 806 through 815 Processing helix chain 'C' and resid 924 through 927 Processing helix chain 'C' and resid 964 through 971 Processing helix chain 'C' and resid 973 through 977 Processing helix chain 'C' and resid 1005 through 1009 Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.624A pdb=" N ALA D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 15 " --> pdb=" O VAL D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 19 Processing helix chain 'D' and resid 39 through 45 Processing helix chain 'D' and resid 66 through 71 Proline residue: D 71 - end of helix Processing helix chain 'D' and resid 72 through 77 removed outlier: 3.890A pdb=" N GLU D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 Processing helix chain 'D' and resid 131 through 137 removed outlier: 3.520A pdb=" N LEU D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 199 Processing helix chain 'D' and resid 369 through 383 Processing helix chain 'D' and resid 397 through 407 removed outlier: 3.557A pdb=" N THR D 401 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 4.521A pdb=" N LEU D 427 " --> pdb=" O MET D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 433 through 449 Processing helix chain 'D' and resid 466 through 480 Processing helix chain 'D' and resid 520 through 527 removed outlier: 4.087A pdb=" N SER D 526 " --> pdb=" O LYS D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 removed outlier: 3.935A pdb=" N TYR D 553 " --> pdb=" O GLY D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 604 removed outlier: 3.699A pdb=" N CYS D 603 " --> pdb=" O ARG D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 625 Processing helix chain 'D' and resid 790 through 795 Processing helix chain 'D' and resid 806 through 815 Processing helix chain 'D' and resid 924 through 927 Processing helix chain 'D' and resid 964 through 971 Processing helix chain 'D' and resid 973 through 977 Processing helix chain 'D' and resid 1005 through 1009 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 87 removed outlier: 8.573A pdb=" N GLU A 58 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR A 127 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE A 151 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR A 162 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 153 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 232 removed outlier: 6.622A pdb=" N GLN A 246 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE A 226 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU A 244 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A 228 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU A 242 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A 230 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 240 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE A 232 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 238 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 274 removed outlier: 5.634A pdb=" N GLN A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN A 263 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR A 318 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU A 323 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 339 Processing sheet with id=AA7, first strand: chain 'A' and resid 485 through 486 removed outlier: 8.108A pdb=" N GLN A 486 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP A 457 " --> pdb=" O GLN A 486 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 410 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER A 458 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP A 412 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG A 353 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG A 389 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 355 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 534 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE A 567 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 536 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TRP A 569 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N GLU A 538 " --> pdb=" O TRP A 569 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 579 Processing sheet with id=AA9, first strand: chain 'A' and resid 628 through 633 Processing sheet with id=AB1, first strand: chain 'A' and resid 662 through 670 removed outlier: 6.182A pdb=" N LEU A 659 " --> pdb=" O PRO A 663 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY A 693 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU A 725 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU A 695 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 717 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN A 703 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 715 " --> pdb=" O GLN A 703 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 740 through 743 removed outlier: 5.920A pdb=" N ASN A 760 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU A 766 " --> pdb=" O ASN A 760 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 777 through 784 removed outlier: 6.324A pdb=" N GLN A 888 " --> pdb=" O LEU A 778 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN A 886 " --> pdb=" O PRO A 780 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG A 782 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY A 884 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN A 784 " --> pdb=" O ARG A 882 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARG A 882 " --> pdb=" O GLN A 784 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 883 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A 990 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ASP A 955 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP A 955 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN A1018 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N GLN A 957 " --> pdb=" O HIS A1016 " (cutoff:3.500A) removed outlier: 13.465A pdb=" N HIS A1016 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 20.535A pdb=" N ASN A 959 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 23.695A pdb=" N ARG A1014 " --> pdb=" O ASN A 959 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS A 845 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 834 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR A 830 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 836 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA A 828 " --> pdb=" O LEU A 836 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 838 " --> pdb=" O CYS A 826 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS A 826 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA A 840 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 777 through 784 removed outlier: 6.324A pdb=" N GLN A 888 " --> pdb=" O LEU A 778 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN A 886 " --> pdb=" O PRO A 780 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG A 782 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY A 884 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN A 784 " --> pdb=" O ARG A 882 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARG A 882 " --> pdb=" O GLN A 784 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 883 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A 990 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ASP A 955 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TRP A 952 " --> pdb=" O ASN A 946 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN A 946 " --> pdb=" O TRP A 952 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLY A 954 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU A 944 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 958 " --> pdb=" O CYS A 940 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N CYS A 940 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR A 942 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU A 901 " --> pdb=" O THR A 942 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 87 removed outlier: 8.574A pdb=" N GLU B 58 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR B 127 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE B 151 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR B 162 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 153 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 147 through 148 Processing sheet with id=AB8, first strand: chain 'B' and resid 222 through 232 removed outlier: 6.623A pdb=" N GLN B 246 " --> pdb=" O SER B 224 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 226 " --> pdb=" O GLU B 244 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU B 244 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 228 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU B 242 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR B 230 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 240 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B 232 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG B 238 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 266 through 274 removed outlier: 5.633A pdb=" N GLN B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN B 263 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR B 318 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU B 323 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 336 through 339 Processing sheet with id=AC2, first strand: chain 'B' and resid 485 through 486 removed outlier: 8.108A pdb=" N GLN B 486 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP B 457 " --> pdb=" O GLN B 486 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 410 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER B 458 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP B 412 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG B 353 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG B 389 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 355 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B 534 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE B 567 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 536 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TRP B 569 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N GLU B 538 " --> pdb=" O TRP B 569 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 576 through 579 Processing sheet with id=AC4, first strand: chain 'B' and resid 628 through 633 Processing sheet with id=AC5, first strand: chain 'B' and resid 662 through 670 removed outlier: 6.182A pdb=" N LEU B 659 " --> pdb=" O PRO B 663 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY B 693 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU B 725 " --> pdb=" O GLY B 693 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU B 695 " --> pdb=" O LEU B 723 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 717 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN B 703 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 715 " --> pdb=" O GLN B 703 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 740 through 743 removed outlier: 5.918A pdb=" N ASN B 760 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU B 766 " --> pdb=" O ASN B 760 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 777 through 784 removed outlier: 6.324A pdb=" N GLN B 888 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN B 886 " --> pdb=" O PRO B 780 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG B 782 " --> pdb=" O GLY B 884 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY B 884 " --> pdb=" O ARG B 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN B 784 " --> pdb=" O ARG B 882 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARG B 882 " --> pdb=" O GLN B 784 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 883 " --> pdb=" O GLY B 989 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE B 990 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ASP B 955 " --> pdb=" O PHE B 990 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP B 955 " --> pdb=" O GLN B1018 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN B1018 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N GLN B 957 " --> pdb=" O HIS B1016 " (cutoff:3.500A) removed outlier: 13.464A pdb=" N HIS B1016 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 20.535A pdb=" N ASN B 959 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 23.696A pdb=" N ARG B1014 " --> pdb=" O ASN B 959 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS B 845 " --> pdb=" O THR B 849 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA B 834 " --> pdb=" O THR B 830 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR B 830 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU B 836 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA B 828 " --> pdb=" O LEU B 836 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR B 838 " --> pdb=" O CYS B 826 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS B 826 " --> pdb=" O THR B 838 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA B 840 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 777 through 784 removed outlier: 6.324A pdb=" N GLN B 888 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN B 886 " --> pdb=" O PRO B 780 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG B 782 " --> pdb=" O GLY B 884 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY B 884 " --> pdb=" O ARG B 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN B 784 " --> pdb=" O ARG B 882 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARG B 882 " --> pdb=" O GLN B 784 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 883 " --> pdb=" O GLY B 989 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE B 990 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ASP B 955 " --> pdb=" O PHE B 990 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TRP B 952 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN B 946 " --> pdb=" O TRP B 952 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLY B 954 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU B 944 " --> pdb=" O GLY B 954 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE B 958 " --> pdb=" O CYS B 940 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N CYS B 940 " --> pdb=" O PHE B 958 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR B 942 " --> pdb=" O LEU B 901 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 901 " --> pdb=" O THR B 942 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AD1, first strand: chain 'C' and resid 83 through 87 removed outlier: 8.573A pdb=" N GLU C 58 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR C 127 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE C 151 " --> pdb=" O TYR C 162 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR C 162 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU C 153 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AD3, first strand: chain 'C' and resid 222 through 232 removed outlier: 6.623A pdb=" N GLN C 246 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE C 226 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU C 244 " --> pdb=" O PHE C 226 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL C 228 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU C 242 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C 230 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 240 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE C 232 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG C 238 " --> pdb=" O PHE C 232 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 266 through 274 removed outlier: 5.633A pdb=" N GLN C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN C 263 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR C 318 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU C 323 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 336 through 339 Processing sheet with id=AD6, first strand: chain 'C' and resid 485 through 486 removed outlier: 8.108A pdb=" N GLN C 486 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP C 457 " --> pdb=" O GLN C 486 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 410 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N SER C 458 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP C 412 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG C 353 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG C 389 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL C 355 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU C 534 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE C 567 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 536 " --> pdb=" O PHE C 567 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TRP C 569 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N GLU C 538 " --> pdb=" O TRP C 569 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 576 through 579 Processing sheet with id=AD8, first strand: chain 'C' and resid 628 through 633 Processing sheet with id=AD9, first strand: chain 'C' and resid 662 through 670 removed outlier: 6.182A pdb=" N LEU C 659 " --> pdb=" O PRO C 663 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY C 693 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU C 725 " --> pdb=" O GLY C 693 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU C 695 " --> pdb=" O LEU C 723 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 717 " --> pdb=" O VAL C 701 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN C 703 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE C 715 " --> pdb=" O GLN C 703 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 740 through 743 removed outlier: 5.919A pdb=" N ASN C 760 " --> pdb=" O LEU C 766 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU C 766 " --> pdb=" O ASN C 760 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 777 through 784 removed outlier: 6.324A pdb=" N GLN C 888 " --> pdb=" O LEU C 778 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN C 886 " --> pdb=" O PRO C 780 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG C 782 " --> pdb=" O GLY C 884 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY C 884 " --> pdb=" O ARG C 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN C 784 " --> pdb=" O ARG C 882 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG C 882 " --> pdb=" O GLN C 784 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 883 " --> pdb=" O GLY C 989 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE C 990 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 12.043A pdb=" N ASP C 955 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP C 955 " --> pdb=" O GLN C1018 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN C1018 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N GLN C 957 " --> pdb=" O HIS C1016 " (cutoff:3.500A) removed outlier: 13.464A pdb=" N HIS C1016 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 20.534A pdb=" N ASN C 959 " --> pdb=" O ARG C1014 " (cutoff:3.500A) removed outlier: 23.696A pdb=" N ARG C1014 " --> pdb=" O ASN C 959 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS C 845 " --> pdb=" O THR C 849 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA C 834 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR C 830 " --> pdb=" O ALA C 834 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 836 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA C 828 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR C 838 " --> pdb=" O CYS C 826 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS C 826 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA C 840 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 777 through 784 removed outlier: 6.324A pdb=" N GLN C 888 " --> pdb=" O LEU C 778 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN C 886 " --> pdb=" O PRO C 780 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG C 782 " --> pdb=" O GLY C 884 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY C 884 " --> pdb=" O ARG C 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN C 784 " --> pdb=" O ARG C 882 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG C 882 " --> pdb=" O GLN C 784 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 883 " --> pdb=" O GLY C 989 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE C 990 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 12.043A pdb=" N ASP C 955 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TRP C 952 " --> pdb=" O ASN C 946 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN C 946 " --> pdb=" O TRP C 952 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLY C 954 " --> pdb=" O GLU C 944 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU C 944 " --> pdb=" O GLY C 954 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE C 958 " --> pdb=" O CYS C 940 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N CYS C 940 " --> pdb=" O PHE C 958 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR C 942 " --> pdb=" O LEU C 901 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU C 901 " --> pdb=" O THR C 942 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AE5, first strand: chain 'D' and resid 83 through 87 removed outlier: 8.573A pdb=" N GLU D 58 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR D 127 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE D 151 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR D 162 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU D 153 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 147 through 148 Processing sheet with id=AE7, first strand: chain 'D' and resid 222 through 232 removed outlier: 6.622A pdb=" N GLN D 246 " --> pdb=" O SER D 224 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE D 226 " --> pdb=" O GLU D 244 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU D 244 " --> pdb=" O PHE D 226 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 228 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU D 242 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR D 230 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 240 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE D 232 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG D 238 " --> pdb=" O PHE D 232 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 266 through 274 removed outlier: 5.633A pdb=" N GLN D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN D 263 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR D 318 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU D 323 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 336 through 339 Processing sheet with id=AF1, first strand: chain 'D' and resid 485 through 486 removed outlier: 8.108A pdb=" N GLN D 486 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP D 457 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 410 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER D 458 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP D 412 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ARG D 353 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG D 389 " --> pdb=" O ARG D 353 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL D 355 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU D 534 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE D 567 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU D 536 " --> pdb=" O PHE D 567 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TRP D 569 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLU D 538 " --> pdb=" O TRP D 569 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 576 through 579 Processing sheet with id=AF3, first strand: chain 'D' and resid 628 through 633 Processing sheet with id=AF4, first strand: chain 'D' and resid 662 through 670 removed outlier: 6.182A pdb=" N LEU D 659 " --> pdb=" O PRO D 663 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY D 693 " --> pdb=" O GLU D 725 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU D 725 " --> pdb=" O GLY D 693 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU D 695 " --> pdb=" O LEU D 723 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 717 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN D 703 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE D 715 " --> pdb=" O GLN D 703 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 740 through 743 removed outlier: 5.918A pdb=" N ASN D 760 " --> pdb=" O LEU D 766 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU D 766 " --> pdb=" O ASN D 760 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 777 through 784 removed outlier: 6.325A pdb=" N GLN D 888 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN D 886 " --> pdb=" O PRO D 780 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG D 782 " --> pdb=" O GLY D 884 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY D 884 " --> pdb=" O ARG D 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN D 784 " --> pdb=" O ARG D 882 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG D 882 " --> pdb=" O GLN D 784 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE D 883 " --> pdb=" O GLY D 989 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE D 990 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 12.043A pdb=" N ASP D 955 " --> pdb=" O PHE D 990 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP D 955 " --> pdb=" O GLN D1018 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN D1018 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N GLN D 957 " --> pdb=" O HIS D1016 " (cutoff:3.500A) removed outlier: 13.465A pdb=" N HIS D1016 " --> pdb=" O GLN D 957 " (cutoff:3.500A) removed outlier: 20.534A pdb=" N ASN D 959 " --> pdb=" O ARG D1014 " (cutoff:3.500A) removed outlier: 23.696A pdb=" N ARG D1014 " --> pdb=" O ASN D 959 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS D 845 " --> pdb=" O THR D 849 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA D 834 " --> pdb=" O THR D 830 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR D 830 " --> pdb=" O ALA D 834 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU D 836 " --> pdb=" O ALA D 828 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA D 828 " --> pdb=" O LEU D 836 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR D 838 " --> pdb=" O CYS D 826 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS D 826 " --> pdb=" O THR D 838 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA D 840 " --> pdb=" O LEU D 824 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 777 through 784 removed outlier: 6.325A pdb=" N GLN D 888 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN D 886 " --> pdb=" O PRO D 780 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG D 782 " --> pdb=" O GLY D 884 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY D 884 " --> pdb=" O ARG D 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN D 784 " --> pdb=" O ARG D 882 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG D 882 " --> pdb=" O GLN D 784 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE D 883 " --> pdb=" O GLY D 989 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE D 990 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 12.043A pdb=" N ASP D 955 " --> pdb=" O PHE D 990 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TRP D 952 " --> pdb=" O ASN D 946 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN D 946 " --> pdb=" O TRP D 952 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY D 954 " --> pdb=" O GLU D 944 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU D 944 " --> pdb=" O GLY D 954 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE D 958 " --> pdb=" O CYS D 940 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N CYS D 940 " --> pdb=" O PHE D 958 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR D 942 " --> pdb=" O LEU D 901 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU D 901 " --> pdb=" O THR D 942 " (cutoff:3.500A) 1268 hydrogen bonds defined for protein. 3288 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: 15.41 Time building geometry restraints manager: 14.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8490 1.32 - 1.44: 7752 1.44 - 1.56: 17358 1.56 - 1.68: 0 1.68 - 1.81: 256 Bond restraints: 33856 Sorted by residual: bond pdb=" CA TYR C 539 " pdb=" C TYR C 539 " ideal model delta sigma weight residual 1.521 1.469 0.052 1.23e-02 6.61e+03 1.78e+01 bond pdb=" CA TYR B 539 " pdb=" C TYR B 539 " ideal model delta sigma weight residual 1.521 1.470 0.051 1.23e-02 6.61e+03 1.75e+01 bond pdb=" CA TYR D 539 " pdb=" C TYR D 539 " ideal model delta sigma weight residual 1.521 1.470 0.051 1.23e-02 6.61e+03 1.72e+01 bond pdb=" CA TYR A 539 " pdb=" C TYR A 539 " ideal model delta sigma weight residual 1.521 1.471 0.051 1.23e-02 6.61e+03 1.69e+01 bond pdb=" CA TYR C 553 " pdb=" C TYR C 553 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.60e+01 ... (remaining 33851 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.07: 1162 106.07 - 113.02: 17809 113.02 - 119.97: 11747 119.97 - 126.91: 14819 126.91 - 133.86: 655 Bond angle restraints: 46192 Sorted by residual: angle pdb=" C ARG D 532 " pdb=" N PRO D 533 " pdb=" CA PRO D 533 " ideal model delta sigma weight residual 120.31 126.67 -6.36 9.80e-01 1.04e+00 4.21e+01 angle pdb=" C ARG C 532 " pdb=" N PRO C 533 " pdb=" CA PRO C 533 " ideal model delta sigma weight residual 120.31 126.66 -6.35 9.80e-01 1.04e+00 4.20e+01 angle pdb=" C ARG B 532 " pdb=" N PRO B 533 " pdb=" CA PRO B 533 " ideal model delta sigma weight residual 120.31 126.65 -6.34 9.80e-01 1.04e+00 4.19e+01 angle pdb=" C ARG A 532 " pdb=" N PRO A 533 " pdb=" CA PRO A 533 " ideal model delta sigma weight residual 120.31 126.62 -6.31 9.80e-01 1.04e+00 4.15e+01 angle pdb=" C ASP C 803 " pdb=" N PRO C 804 " pdb=" CA PRO C 804 " ideal model delta sigma weight residual 119.84 127.89 -8.05 1.25e+00 6.40e-01 4.14e+01 ... (remaining 46187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 18820 17.81 - 35.63: 748 35.63 - 53.44: 136 53.44 - 71.26: 92 71.26 - 89.07: 60 Dihedral angle restraints: 19856 sinusoidal: 8016 harmonic: 11840 Sorted by residual: dihedral pdb=" CA LEU A 911 " pdb=" C LEU A 911 " pdb=" N THR A 912 " pdb=" CA THR A 912 " ideal model delta harmonic sigma weight residual -180.00 -159.34 -20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU B 911 " pdb=" C LEU B 911 " pdb=" N THR B 912 " pdb=" CA THR B 912 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU D 911 " pdb=" C LEU D 911 " pdb=" N THR D 912 " pdb=" CA THR D 912 " ideal model delta harmonic sigma weight residual -180.00 -159.36 -20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 19853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2250 0.055 - 0.109: 1864 0.109 - 0.164: 638 0.164 - 0.219: 72 0.219 - 0.273: 8 Chirality restraints: 4832 Sorted by residual: chirality pdb=" CA TRP D 554 " pdb=" N TRP D 554 " pdb=" C TRP D 554 " pdb=" CB TRP D 554 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA TRP A 554 " pdb=" N TRP A 554 " pdb=" C TRP A 554 " pdb=" CB TRP A 554 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA TRP B 554 " pdb=" N TRP B 554 " pdb=" C TRP B 554 " pdb=" CB TRP B 554 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 4829 not shown) Planarity restraints: 6100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 501 " -0.114 5.00e-02 4.00e+02 1.72e-01 4.73e+01 pdb=" N PRO C 502 " 0.297 5.00e-02 4.00e+02 pdb=" CA PRO C 502 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO C 502 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 501 " 0.114 5.00e-02 4.00e+02 1.72e-01 4.73e+01 pdb=" N PRO D 502 " -0.297 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 501 " -0.114 5.00e-02 4.00e+02 1.72e-01 4.73e+01 pdb=" N PRO B 502 " 0.297 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.088 5.00e-02 4.00e+02 ... (remaining 6097 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 1189 2.67 - 3.23: 32290 3.23 - 3.79: 57525 3.79 - 4.34: 77794 4.34 - 4.90: 127486 Nonbonded interactions: 296284 Sorted by model distance: nonbonded pdb=" O ASP C 369 " pdb=" OD1 ASP C 369 " model vdw 2.116 3.040 nonbonded pdb=" O ASP A 369 " pdb=" OD1 ASP A 369 " model vdw 2.117 3.040 nonbonded pdb=" O ASP D 369 " pdb=" OD1 ASP D 369 " model vdw 2.117 3.040 nonbonded pdb=" O ASP B 369 " pdb=" OD1 ASP B 369 " model vdw 2.117 3.040 nonbonded pdb=" N GLN D 904 " pdb=" OE1 GLN D 904 " model vdw 2.136 2.520 ... (remaining 296279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 160 5.16 5 C 20796 2.51 5 N 5816 2.21 5 O 6116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.260 Check model and map are aligned: 0.480 Convert atoms to be neutral: 0.270 Process input model: 88.870 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.017 0.063 33856 Z= 1.123 Angle : 1.436 12.589 46192 Z= 0.902 Chirality : 0.076 0.273 4832 Planarity : 0.022 0.172 6100 Dihedral : 12.561 89.069 12220 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 2.13 % Allowed : 6.78 % Favored : 91.10 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.12), residues: 4088 helix: -1.91 (0.18), residues: 532 sheet: -0.31 (0.14), residues: 1352 loop : -1.68 (0.13), residues: 2204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 793 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 801 average time/residue: 1.6122 time to fit residues: 1508.1119 Evaluate side-chains 476 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 468 time to evaluate : 3.856 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 5.2714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 30.0000 chunk 165 optimal weight: 7.9990 chunk 319 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 370 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 246 GLN A 366 GLN A 396 HIS A 419 HIS A 511 GLN A 647 HIS A 654 HIS ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 246 GLN B 366 GLN B 396 HIS B 419 HIS B 647 HIS B 654 HIS B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN ** B 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 ASN B 986 ASN C 94 HIS C 246 GLN C 295 ASN C 396 HIS C 419 HIS C 647 HIS C 654 HIS C 845 HIS C 959 ASN C 986 ASN D 39 ASN D 94 HIS D 246 GLN D 267 GLN D 396 HIS D 419 HIS D 647 HIS D 654 HIS D 762 GLN D 784 GLN D 959 ASN D 986 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 33856 Z= 0.339 Angle : 0.705 8.671 46192 Z= 0.385 Chirality : 0.048 0.201 4832 Planarity : 0.009 0.073 6100 Dihedral : 6.072 77.876 4484 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4088 helix: -0.31 (0.20), residues: 540 sheet: 0.35 (0.14), residues: 1328 loop : -0.87 (0.13), residues: 2220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 531 time to evaluate : 3.971 Fit side-chains outliers start: 69 outliers final: 20 residues processed: 560 average time/residue: 1.5626 time to fit residues: 1036.5552 Evaluate side-chains 461 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 441 time to evaluate : 3.542 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 0.6416 time to fit residues: 11.4788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 308 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 371 optimal weight: 20.0000 chunk 400 optimal weight: 7.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 605 ASN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN A 950 HIS ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 HIS ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 HIS ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 HIS C 950 HIS C 959 ASN D 605 ASN D 647 HIS D 762 GLN D 950 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 33856 Z= 0.375 Angle : 0.728 11.649 46192 Z= 0.390 Chirality : 0.049 0.194 4832 Planarity : 0.006 0.052 6100 Dihedral : 6.122 73.638 4484 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.91 % Favored : 96.99 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 4088 helix: -0.22 (0.20), residues: 544 sheet: 0.51 (0.14), residues: 1336 loop : -0.35 (0.13), residues: 2208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 442 time to evaluate : 4.227 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 32 residues processed: 489 average time/residue: 1.5931 time to fit residues: 918.7689 Evaluate side-chains 452 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 420 time to evaluate : 3.917 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 27 residues processed: 6 average time/residue: 0.5966 time to fit residues: 10.4997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 372 optimal weight: 20.0000 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 353 optimal weight: 0.9990 chunk 106 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 584 ASN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 584 ASN B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 959 ASN B 986 ASN C 762 GLN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 959 ASN D 762 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 33856 Z= 0.242 Angle : 0.625 12.533 46192 Z= 0.332 Chirality : 0.045 0.181 4832 Planarity : 0.004 0.042 6100 Dihedral : 5.774 70.043 4484 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.02 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 4088 helix: -0.03 (0.21), residues: 552 sheet: 0.72 (0.14), residues: 1304 loop : -0.30 (0.13), residues: 2232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 447 time to evaluate : 4.071 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 32 residues processed: 482 average time/residue: 1.5921 time to fit residues: 907.1190 Evaluate side-chains 465 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 433 time to evaluate : 3.908 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 25 residues processed: 7 average time/residue: 0.8277 time to fit residues: 13.2143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 293 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 336 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 10.0000 chunk 353 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 864 GLN B 584 ASN B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 605 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 959 ASN D 584 ASN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 33856 Z= 0.410 Angle : 0.731 12.816 46192 Z= 0.391 Chirality : 0.050 0.196 4832 Planarity : 0.006 0.044 6100 Dihedral : 6.030 63.819 4484 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.79 % Favored : 97.11 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 4088 helix: -0.12 (0.21), residues: 544 sheet: 0.67 (0.14), residues: 1356 loop : -0.25 (0.13), residues: 2188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 430 time to evaluate : 3.895 Fit side-chains outliers start: 86 outliers final: 40 residues processed: 477 average time/residue: 1.5788 time to fit residues: 890.6965 Evaluate side-chains 459 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 419 time to evaluate : 3.815 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 31 residues processed: 9 average time/residue: 0.6450 time to fit residues: 13.5728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.9990 chunk 355 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 231 optimal weight: 0.0170 chunk 97 optimal weight: 7.9990 chunk 394 optimal weight: 2.9990 chunk 327 optimal weight: 20.0000 chunk 182 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 605 ASN A 726 ASN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS B 584 ASN B 605 ASN B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 959 ASN D 584 ASN D 605 ASN D 762 GLN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 33856 Z= 0.171 Angle : 0.582 17.578 46192 Z= 0.304 Chirality : 0.044 0.156 4832 Planarity : 0.004 0.035 6100 Dihedral : 5.434 61.550 4484 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.76 % Favored : 97.14 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 4088 helix: 0.18 (0.21), residues: 564 sheet: 0.78 (0.14), residues: 1304 loop : -0.19 (0.13), residues: 2220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 452 time to evaluate : 4.262 Fit side-chains outliers start: 50 outliers final: 33 residues processed: 487 average time/residue: 1.5726 time to fit residues: 914.6345 Evaluate side-chains 468 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 435 time to evaluate : 3.889 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 30 residues processed: 3 average time/residue: 0.4882 time to fit residues: 7.7778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 chunk 332 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 584 ASN A 605 ASN A 762 GLN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN B 584 ASN B 605 ASN B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN D 605 ASN D 762 GLN ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.121 33856 Z= 0.488 Angle : 0.796 20.844 46192 Z= 0.423 Chirality : 0.052 0.194 4832 Planarity : 0.006 0.049 6100 Dihedral : 6.065 56.307 4484 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.76 % Favored : 97.14 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 4088 helix: -0.24 (0.21), residues: 564 sheet: 0.69 (0.14), residues: 1376 loop : -0.26 (0.13), residues: 2148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 414 time to evaluate : 4.256 Fit side-chains outliers start: 65 outliers final: 38 residues processed: 458 average time/residue: 1.6285 time to fit residues: 879.3951 Evaluate side-chains 451 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 413 time to evaluate : 3.724 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 33 residues processed: 5 average time/residue: 0.3767 time to fit residues: 8.1803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 250 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 194 optimal weight: 0.4980 chunk 36 optimal weight: 8.9990 chunk 309 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 605 ASN A 647 HIS A 762 GLN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 584 ASN B 605 ASN B 647 HIS B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 HIS C 762 GLN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 GLN D 584 ASN D 605 ASN D 647 HIS ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 33856 Z= 0.160 Angle : 0.563 10.940 46192 Z= 0.294 Chirality : 0.044 0.160 4832 Planarity : 0.003 0.034 6100 Dihedral : 5.275 52.488 4484 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 4088 helix: 0.06 (0.21), residues: 588 sheet: 0.81 (0.14), residues: 1336 loop : -0.18 (0.13), residues: 2164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 434 time to evaluate : 3.756 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 35 residues processed: 472 average time/residue: 1.6136 time to fit residues: 905.0094 Evaluate side-chains 453 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 418 time to evaluate : 4.083 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 3 average time/residue: 0.9466 time to fit residues: 9.3575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 9.9990 chunk 376 optimal weight: 2.9990 chunk 343 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 287 optimal weight: 0.0770 chunk 112 optimal weight: 6.9990 chunk 331 optimal weight: 9.9990 chunk 346 optimal weight: 9.9990 chunk 365 optimal weight: 3.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 605 ASN A 762 GLN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 605 ASN B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN C 762 GLN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 GLN D 584 ASN D 605 ASN ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 33856 Z= 0.290 Angle : 0.655 11.454 46192 Z= 0.346 Chirality : 0.047 0.170 4832 Planarity : 0.005 0.038 6100 Dihedral : 5.580 47.850 4484 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.76 % Favored : 97.21 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.13), residues: 4088 helix: 0.03 (0.21), residues: 568 sheet: 0.84 (0.14), residues: 1352 loop : -0.17 (0.13), residues: 2168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 418 time to evaluate : 3.972 Fit side-chains outliers start: 44 outliers final: 34 residues processed: 457 average time/residue: 1.6400 time to fit residues: 889.0132 Evaluate side-chains 451 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 417 time to evaluate : 3.901 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 33 residues processed: 1 average time/residue: 0.4861 time to fit residues: 5.9699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 7.9990 chunk 406 optimal weight: 5.9990 chunk 374 optimal weight: 0.0010 chunk 323 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 overall best weight: 3.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 762 GLN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 647 HIS B 726 ASN B 762 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 GLN ** C 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 33856 Z= 0.279 Angle : 0.649 10.964 46192 Z= 0.343 Chirality : 0.047 0.172 4832 Planarity : 0.005 0.040 6100 Dihedral : 5.580 43.733 4484 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.13), residues: 4088 helix: -0.03 (0.21), residues: 568 sheet: 0.82 (0.14), residues: 1352 loop : -0.19 (0.13), residues: 2168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 411 time to evaluate : 3.936 Fit side-chains outliers start: 34 outliers final: 34 residues processed: 444 average time/residue: 1.6521 time to fit residues: 866.2938 Evaluate side-chains 444 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 410 time to evaluate : 3.985 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 34 residues processed: 1 average time/residue: 2.1161 time to fit residues: 7.8934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 3.9990 chunk 344 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 324 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 332 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 762 GLN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 647 HIS B 726 ASN B 762 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN B 978 HIS C 584 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 GLN ** C 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 HIS D 584 ASN D 647 HIS ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 978 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118945 restraints weight = 29540.077| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.07 r_work: 0.3189 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 33856 Z= 0.307 Angle : 0.671 11.035 46192 Z= 0.355 Chirality : 0.047 0.176 4832 Planarity : 0.005 0.043 6100 Dihedral : 5.644 38.620 4484 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 4088 helix: -0.09 (0.21), residues: 568 sheet: 0.81 (0.14), residues: 1352 loop : -0.20 (0.13), residues: 2168 =============================================================================== Job complete usr+sys time: 14046.11 seconds wall clock time: 246 minutes 47.31 seconds (14807.31 seconds total)