Starting phenix.real_space_refine on Fri Mar 22 09:55:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drv_8908/03_2024/6drv_8908.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drv_8908/03_2024/6drv_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_8908/03_2024/6drv_8908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drv_8908/03_2024/6drv_8908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drv_8908/03_2024/6drv_8908.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drv_8908/03_2024/6drv_8908.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 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. 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 16.09, per 1000 atoms: 0.49 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: 13.05 Conformation dependent library (CDL) restraints added in 5.7 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: 4.41 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: 15.49 Time building geometry restraints manager: 14.12 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 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: 4.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 14.610 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 88.850 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 1.437 12.589 46192 Z= 0.903 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 : 3.99 Ramachandran Plot: Outliers : 2.13 % Allowed : 6.78 % Favored : 91.10 % Rotamer: Outliers : 0.23 % Allowed : 1.03 % Favored : 98.74 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.006 TRP D 554 HIS 0.009 0.001 HIS A 991 PHE 0.020 0.003 PHE B 990 TYR 0.058 0.007 TYR D 124 ARG 0.006 0.001 ARG D 562 *********************** 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 : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: -0.0456 (tpt) cc_final: -0.0901 (ttm) REVERT: A 3 MET cc_start: 0.2106 (mmm) cc_final: 0.1417 (tpt) REVERT: A 31 HIS cc_start: 0.8054 (p90) cc_final: 0.7835 (p-80) REVERT: A 41 GLU cc_start: 0.7160 (tp30) cc_final: 0.6239 (tm-30) REVERT: A 42 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6260 (tt0) REVERT: A 58 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7317 (mp0) REVERT: A 72 GLU cc_start: 0.6993 (mp0) cc_final: 0.6608 (mm-30) REVERT: A 86 VAL cc_start: 0.7926 (t) cc_final: 0.7520 (p) REVERT: A 129 ASN cc_start: 0.7218 (m-40) cc_final: 0.6895 (t0) REVERT: A 137 GLU cc_start: 0.6492 (pt0) cc_final: 0.5925 (pm20) REVERT: A 242 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7099 (tt0) REVERT: A 244 GLU cc_start: 0.7569 (tt0) cc_final: 0.7167 (tp30) REVERT: A 246 GLN cc_start: 0.7013 (tt0) cc_final: 0.6692 (mt0) REVERT: A 252 ARG cc_start: 0.6458 (mmm-85) cc_final: 0.5939 (mmt180) REVERT: A 253 ASP cc_start: 0.6719 (m-30) cc_final: 0.6270 (p0) REVERT: A 254 TYR cc_start: 0.6961 (p90) cc_final: 0.6547 (p90) REVERT: A 293 ARG cc_start: 0.7718 (mtt90) cc_final: 0.7494 (mpt180) REVERT: A 297 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6287 (tp30) REVERT: A 329 CYS cc_start: 0.7554 (t) cc_final: 0.7182 (p) REVERT: A 335 GLU cc_start: 0.8329 (tt0) cc_final: 0.7398 (tm-30) REVERT: A 363 LEU cc_start: 0.7164 (mt) cc_final: 0.6897 (mm) REVERT: A 371 GLN cc_start: 0.7196 (tp40) cc_final: 0.6891 (mp10) REVERT: A 405 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7423 (ttp80) REVERT: A 432 ARG cc_start: 0.7057 (mtm180) cc_final: 0.6795 (mtp85) REVERT: A 439 GLU cc_start: 0.7473 (tt0) cc_final: 0.7169 (mp0) REVERT: A 443 ARG cc_start: 0.7327 (mtp85) cc_final: 0.6988 (mtp-110) REVERT: A 488 GLU cc_start: 0.7101 (pm20) cc_final: 0.6629 (tm-30) REVERT: A 503 MET cc_start: 0.8137 (mtm) cc_final: 0.7869 (mtp) REVERT: A 552 LYS cc_start: 0.8031 (mttt) cc_final: 0.7829 (mtpm) REVERT: A 662 LYS cc_start: 0.6817 (tttt) cc_final: 0.6568 (mtmm) REVERT: A 746 MET cc_start: 0.6878 (mmm) cc_final: 0.6420 (mmm) REVERT: A 749 CYS cc_start: 0.7141 (t) cc_final: 0.6697 (t) REVERT: A 751 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6586 (mp0) REVERT: A 754 ASN cc_start: 0.6715 (p0) cc_final: 0.6190 (p0) REVERT: A 756 ARG cc_start: 0.7223 (ttm110) cc_final: 0.6746 (mtp180) REVERT: A 758 GLN cc_start: 0.8081 (tt0) cc_final: 0.7866 (tt0) REVERT: A 760 ASN cc_start: 0.7882 (t0) cc_final: 0.7447 (t0) REVERT: A 761 ARG cc_start: 0.7637 (ttt180) cc_final: 0.7278 (ttp80) REVERT: A 769 MET cc_start: 0.7270 (ttt) cc_final: 0.6544 (tmt) REVERT: A 774 LYS cc_start: 0.6822 (tttt) cc_final: 0.6341 (tttt) REVERT: A 782 ARG cc_start: 0.7939 (mtm180) cc_final: 0.7566 (mtp180) REVERT: A 784 GLN cc_start: 0.7809 (tp40) cc_final: 0.7520 (tt0) REVERT: A 858 ARG cc_start: 0.8235 (ttt-90) cc_final: 0.7987 (ttt90) REVERT: A 966 GLN cc_start: 0.7748 (tt0) cc_final: 0.7543 (tt0) REVERT: A 970 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6894 (mp0) REVERT: A 978 HIS cc_start: 0.6286 (m-70) cc_final: 0.5927 (p-80) REVERT: A 997 ASP cc_start: 0.7410 (m-30) cc_final: 0.7037 (m-30) REVERT: A 1005 SER cc_start: 0.7409 (m) cc_final: 0.7040 (p) REVERT: A 1014 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7339 (mtm-85) REVERT: B 1 MET cc_start: -0.0514 (tpt) cc_final: -0.0715 (ttp) REVERT: B 3 MET cc_start: 0.2049 (mmm) cc_final: 0.1422 (tpt) REVERT: B 41 GLU cc_start: 0.7101 (tp30) cc_final: 0.6303 (tm-30) REVERT: B 42 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6404 (mm-30) REVERT: B 86 VAL cc_start: 0.7808 (t) cc_final: 0.7366 (p) REVERT: B 203 MET cc_start: 0.7752 (ptt) cc_final: 0.7543 (ptt) REVERT: B 242 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6937 (tt0) REVERT: B 244 GLU cc_start: 0.7481 (tt0) cc_final: 0.7261 (tt0) REVERT: B 246 GLN cc_start: 0.7004 (tt0) cc_final: 0.6711 (mt0) REVERT: B 252 ARG cc_start: 0.6539 (mmm-85) cc_final: 0.5982 (mmt180) REVERT: B 253 ASP cc_start: 0.6608 (m-30) cc_final: 0.6205 (p0) REVERT: B 254 TYR cc_start: 0.6797 (p90) cc_final: 0.6493 (p90) REVERT: B 293 ARG cc_start: 0.7749 (mtt90) cc_final: 0.7498 (mpt180) REVERT: B 297 GLU cc_start: 0.6745 (mm-30) cc_final: 0.5815 (mp0) REVERT: B 329 CYS cc_start: 0.7478 (t) cc_final: 0.7150 (p) REVERT: B 335 GLU cc_start: 0.8311 (tt0) cc_final: 0.8011 (tt0) REVERT: B 371 GLN cc_start: 0.7066 (tp40) cc_final: 0.6537 (mp10) REVERT: B 432 ARG cc_start: 0.7041 (mtm180) cc_final: 0.6826 (mtp85) REVERT: B 439 GLU cc_start: 0.7571 (tt0) cc_final: 0.7249 (mp0) REVERT: B 443 ARG cc_start: 0.7301 (mtp85) cc_final: 0.6916 (mtp-110) REVERT: B 488 GLU cc_start: 0.7045 (pm20) cc_final: 0.6554 (tm-30) REVERT: B 503 MET cc_start: 0.8172 (mtm) cc_final: 0.7896 (mtp) REVERT: B 552 LYS cc_start: 0.8069 (mttt) cc_final: 0.7855 (mtpm) REVERT: B 682 GLU cc_start: 0.6767 (tt0) cc_final: 0.6531 (tm-30) REVERT: B 746 MET cc_start: 0.6836 (mmm) cc_final: 0.6563 (mmp) REVERT: B 751 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6549 (mp0) REVERT: B 756 ARG cc_start: 0.7091 (ttm110) cc_final: 0.6565 (mtp180) REVERT: B 761 ARG cc_start: 0.7574 (ttt180) cc_final: 0.7217 (ttp80) REVERT: B 762 GLN cc_start: 0.6867 (mm-40) cc_final: 0.6623 (tm-30) REVERT: B 769 MET cc_start: 0.7324 (ttt) cc_final: 0.6751 (tmt) REVERT: B 771 ILE cc_start: 0.8344 (mt) cc_final: 0.8143 (mt) REVERT: B 774 LYS cc_start: 0.6354 (tttt) cc_final: 0.5912 (tttt) REVERT: B 775 LYS cc_start: 0.7840 (mttt) cc_final: 0.7503 (mttp) REVERT: B 782 ARG cc_start: 0.8062 (mtm180) cc_final: 0.7647 (mtp180) REVERT: B 784 GLN cc_start: 0.7682 (tp40) cc_final: 0.7451 (tt0) REVERT: B 805 ASN cc_start: 0.7321 (m-40) cc_final: 0.6975 (m-40) REVERT: B 812 LYS cc_start: 0.7671 (mttt) cc_final: 0.7467 (mttm) REVERT: B 838 THR cc_start: 0.8230 (m) cc_final: 0.7680 (p) REVERT: B 966 GLN cc_start: 0.7633 (tt0) cc_final: 0.7420 (tt0) REVERT: B 970 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6795 (mp0) REVERT: B 978 HIS cc_start: 0.6075 (m-70) cc_final: 0.5533 (p-80) REVERT: B 1005 SER cc_start: 0.7490 (m) cc_final: 0.7166 (p) REVERT: B 1014 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7126 (mtm-85) REVERT: C 1 MET cc_start: -0.0401 (tpt) cc_final: -0.1106 (ttm) REVERT: C 3 MET cc_start: 0.1991 (mmm) cc_final: 0.1398 (tpt) REVERT: C 41 GLU cc_start: 0.6690 (tp30) cc_final: 0.5878 (tm-30) REVERT: C 42 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6443 (mm-30) REVERT: C 50 GLN cc_start: 0.7315 (mm-40) cc_final: 0.7061 (mm110) REVERT: C 86 VAL cc_start: 0.7655 (t) cc_final: 0.7276 (p) REVERT: C 102 THR cc_start: 0.7428 (p) cc_final: 0.7035 (t) REVERT: C 242 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6859 (tt0) REVERT: C 244 GLU cc_start: 0.7352 (tt0) cc_final: 0.7083 (tp30) REVERT: C 246 GLN cc_start: 0.6894 (tt0) cc_final: 0.6614 (mt0) REVERT: C 253 ASP cc_start: 0.6439 (m-30) cc_final: 0.6028 (p0) REVERT: C 254 TYR cc_start: 0.6408 (p90) cc_final: 0.6179 (p90) REVERT: C 297 GLU cc_start: 0.6475 (mm-30) cc_final: 0.5548 (mp0) REVERT: C 335 GLU cc_start: 0.8049 (tt0) cc_final: 0.7790 (tt0) REVERT: C 371 GLN cc_start: 0.6960 (tp40) cc_final: 0.6527 (mp10) REVERT: C 432 ARG cc_start: 0.7043 (mtm180) cc_final: 0.6780 (mtp85) REVERT: C 439 GLU cc_start: 0.7483 (tt0) cc_final: 0.7126 (mp0) REVERT: C 488 GLU cc_start: 0.6926 (pm20) cc_final: 0.6563 (tm-30) REVERT: C 631 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7293 (ttp80) REVERT: C 656 MET cc_start: 0.7939 (mtm) cc_final: 0.7702 (mtt) REVERT: C 660 ASP cc_start: 0.6822 (m-30) cc_final: 0.6458 (m-30) REVERT: C 668 GLU cc_start: 0.7659 (tt0) cc_final: 0.7338 (tt0) REVERT: C 762 GLN cc_start: 0.7048 (mm-40) cc_final: 0.6759 (mm110) REVERT: C 769 MET cc_start: 0.6981 (ttt) cc_final: 0.6771 (tmm) REVERT: C 775 LYS cc_start: 0.7578 (mttt) cc_final: 0.7275 (mttp) REVERT: C 782 ARG cc_start: 0.7611 (mtm180) cc_final: 0.7401 (mtp-110) REVERT: C 812 LYS cc_start: 0.7752 (mttt) cc_final: 0.7522 (mttm) REVERT: C 894 GLU cc_start: 0.6728 (tp30) cc_final: 0.6462 (mp0) REVERT: C 955 ASP cc_start: 0.7042 (t0) cc_final: 0.6759 (t70) REVERT: C 966 GLN cc_start: 0.7645 (tt0) cc_final: 0.7383 (tt0) REVERT: C 970 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6681 (mp0) REVERT: C 978 HIS cc_start: 0.5640 (m-70) cc_final: 0.5080 (p90) REVERT: C 997 ASP cc_start: 0.7311 (m-30) cc_final: 0.6947 (m-30) REVERT: C 1005 SER cc_start: 0.7495 (m) cc_final: 0.7174 (p) REVERT: C 1014 ARG cc_start: 0.7675 (mtp85) cc_final: 0.7106 (mtm-85) REVERT: D 1 MET cc_start: -0.0693 (tpt) cc_final: -0.1082 (ttm) REVERT: D 3 MET cc_start: 0.2100 (mmm) cc_final: 0.1636 (tpt) REVERT: D 41 GLU cc_start: 0.6891 (tp30) cc_final: 0.5977 (tm-30) REVERT: D 42 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6413 (mm-30) REVERT: D 50 GLN cc_start: 0.7439 (mm-40) cc_final: 0.7191 (mm110) REVERT: D 72 GLU cc_start: 0.7079 (mp0) cc_final: 0.6855 (mm-30) REVERT: D 86 VAL cc_start: 0.7609 (t) cc_final: 0.7229 (p) REVERT: D 102 THR cc_start: 0.7416 (p) cc_final: 0.7075 (t) REVERT: D 203 MET cc_start: 0.7292 (ptt) cc_final: 0.7084 (ptt) REVERT: D 242 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6782 (tt0) REVERT: D 244 GLU cc_start: 0.7520 (tt0) cc_final: 0.7248 (tt0) REVERT: D 252 ARG cc_start: 0.6414 (mmm-85) cc_final: 0.5878 (mmt180) REVERT: D 253 ASP cc_start: 0.6578 (m-30) cc_final: 0.6137 (p0) REVERT: D 254 TYR cc_start: 0.6741 (p90) cc_final: 0.6339 (p90) REVERT: D 293 ARG cc_start: 0.7615 (mtt90) cc_final: 0.7286 (mpt180) REVERT: D 297 GLU cc_start: 0.6549 (mm-30) cc_final: 0.5527 (mp0) REVERT: D 335 GLU cc_start: 0.8077 (tt0) cc_final: 0.7823 (tt0) REVERT: D 370 GLU cc_start: 0.7225 (tt0) cc_final: 0.7023 (tp30) REVERT: D 371 GLN cc_start: 0.6945 (tp40) cc_final: 0.6497 (mp10) REVERT: D 421 MET cc_start: 0.7602 (mmm) cc_final: 0.7359 (mmm) REVERT: D 432 ARG cc_start: 0.7287 (mtm180) cc_final: 0.6951 (mtp85) REVERT: D 443 ARG cc_start: 0.7153 (mtp85) cc_final: 0.6882 (mtp-110) REVERT: D 488 GLU cc_start: 0.6910 (pm20) cc_final: 0.6597 (tm-30) REVERT: D 503 MET cc_start: 0.7946 (mtm) cc_final: 0.7719 (mtp) REVERT: D 656 MET cc_start: 0.7749 (mtm) cc_final: 0.7498 (mtt) REVERT: D 662 LYS cc_start: 0.7022 (tttt) cc_final: 0.6616 (mtmm) REVERT: D 668 GLU cc_start: 0.7512 (tt0) cc_final: 0.7279 (tt0) REVERT: D 769 MET cc_start: 0.7119 (ttt) cc_final: 0.6634 (tmt) REVERT: D 775 LYS cc_start: 0.7815 (mttt) cc_final: 0.7564 (mttm) REVERT: D 782 ARG cc_start: 0.7422 (mtm180) cc_final: 0.7186 (mtp-110) REVERT: D 868 THR cc_start: 0.8197 (m) cc_final: 0.7955 (m) REVERT: D 894 GLU cc_start: 0.6808 (tp30) cc_final: 0.6572 (mp0) REVERT: D 966 GLN cc_start: 0.7489 (tt0) cc_final: 0.7197 (tt0) REVERT: D 970 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6756 (mp0) REVERT: D 1005 SER cc_start: 0.7535 (m) cc_final: 0.7323 (p) REVERT: D 1014 ARG cc_start: 0.7744 (mtp85) cc_final: 0.7097 (mtm-85) outliers start: 8 outliers final: 8 residues processed: 801 average time/residue: 1.7320 time to fit residues: 1601.4864 Evaluate side-chains 516 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 508 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 PRO Chi-restraints excluded: chain A residue 561 PRO Chi-restraints excluded: chain B residue 435 PRO Chi-restraints excluded: chain B residue 561 PRO Chi-restraints excluded: chain C residue 435 PRO Chi-restraints excluded: chain C residue 561 PRO Chi-restraints excluded: chain D residue 435 PRO Chi-restraints excluded: chain D residue 561 PRO 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: 5.9990 chunk 208 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 319 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 370 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 366 GLN A 396 HIS A 511 GLN A 647 HIS A 654 HIS A 784 GLN A 825 GLN A 950 HIS ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 366 GLN B 396 HIS B 419 HIS B 647 HIS B 654 HIS B 726 ASN B 784 GLN B 825 GLN B 959 ASN B 986 ASN C 94 HIS 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: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33856 Z= 0.337 Angle : 0.702 9.171 46192 Z= 0.386 Chirality : 0.049 0.199 4832 Planarity : 0.009 0.076 6100 Dihedral : 6.067 77.797 4508 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.37 % Allowed : 6.25 % Favored : 92.38 % 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: -0.26 (0.20), residues: 532 sheet: 0.27 (0.14), residues: 1352 loop : -0.84 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 554 HIS 0.009 0.002 HIS D 217 PHE 0.017 0.002 PHE A 932 TYR 0.025 0.003 TYR C 101 ARG 0.007 0.001 ARG B 449 *********************** 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 624 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 576 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: -0.0334 (tpt) cc_final: -0.0740 (ttm) REVERT: A 41 GLU cc_start: 0.7194 (tp30) cc_final: 0.6358 (tm-30) REVERT: A 42 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6559 (tt0) REVERT: A 48 PRO cc_start: 0.7972 (Cg_exo) cc_final: 0.7723 (Cg_endo) REVERT: A 78 ASP cc_start: 0.7275 (m-30) cc_final: 0.6833 (m-30) REVERT: A 118 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7279 (tp30) REVERT: A 129 ASN cc_start: 0.7224 (m-40) cc_final: 0.6893 (t0) REVERT: A 220 THR cc_start: 0.7508 (p) cc_final: 0.7194 (t) REVERT: A 242 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7182 (tt0) REVERT: A 244 GLU cc_start: 0.7727 (tt0) cc_final: 0.7320 (tp30) REVERT: A 246 GLN cc_start: 0.7376 (tt0) cc_final: 0.7074 (mt0) REVERT: A 252 ARG cc_start: 0.6623 (mmm-85) cc_final: 0.6094 (mmt180) REVERT: A 253 ASP cc_start: 0.6958 (m-30) cc_final: 0.6301 (p0) REVERT: A 293 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7443 (mpt180) REVERT: A 297 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6427 (mm-30) REVERT: A 335 GLU cc_start: 0.8343 (tt0) cc_final: 0.7406 (tm-30) REVERT: A 363 LEU cc_start: 0.7568 (mt) cc_final: 0.7246 (mm) REVERT: A 370 GLU cc_start: 0.7394 (tt0) cc_final: 0.7035 (tm-30) REVERT: A 405 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7600 (ttp-110) REVERT: A 432 ARG cc_start: 0.7338 (mtm180) cc_final: 0.7011 (mtp85) REVERT: A 443 ARG cc_start: 0.7588 (mtp85) cc_final: 0.7213 (mtp-110) REVERT: A 488 GLU cc_start: 0.7140 (pm20) cc_final: 0.6547 (tm-30) REVERT: A 508 ASP cc_start: 0.7544 (m-30) cc_final: 0.7205 (m-30) REVERT: A 662 LYS cc_start: 0.6994 (tttt) cc_final: 0.6700 (mtmm) REVERT: A 746 MET cc_start: 0.7097 (mmm) cc_final: 0.6880 (mmp) REVERT: A 747 ASP cc_start: 0.6596 (p0) cc_final: 0.5771 (m-30) REVERT: A 751 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6977 (mp0) REVERT: A 756 ARG cc_start: 0.7277 (ttm110) cc_final: 0.6597 (mtp180) REVERT: A 758 GLN cc_start: 0.7980 (tt0) cc_final: 0.7769 (tt0) REVERT: A 761 ARG cc_start: 0.7631 (ttt180) cc_final: 0.7347 (mtp85) REVERT: A 769 MET cc_start: 0.7328 (ttt) cc_final: 0.6578 (tmt) REVERT: A 774 LYS cc_start: 0.6792 (tttt) cc_final: 0.6255 (tttt) REVERT: A 775 LYS cc_start: 0.7919 (mttt) cc_final: 0.7596 (mttp) REVERT: A 782 ARG cc_start: 0.7899 (mtm180) cc_final: 0.7504 (mtp180) REVERT: A 784 GLN cc_start: 0.7707 (tp-100) cc_final: 0.7428 (tt0) REVERT: A 966 GLN cc_start: 0.7799 (tt0) cc_final: 0.7590 (tt0) REVERT: A 970 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7013 (mp0) REVERT: A 1001 SER cc_start: 0.7616 (t) cc_final: 0.7206 (m) REVERT: A 1005 SER cc_start: 0.7512 (m) cc_final: 0.7044 (p) REVERT: A 1014 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7384 (mtm-85) REVERT: B 39 ASN cc_start: 0.8193 (t0) cc_final: 0.7992 (t0) REVERT: B 41 GLU cc_start: 0.7229 (tp30) cc_final: 0.6363 (tm-30) REVERT: B 42 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6509 (tt0) REVERT: B 48 PRO cc_start: 0.8006 (Cg_exo) cc_final: 0.7796 (Cg_endo) REVERT: B 220 THR cc_start: 0.7540 (p) cc_final: 0.7186 (t) REVERT: B 242 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7172 (tt0) REVERT: B 244 GLU cc_start: 0.7723 (tt0) cc_final: 0.7299 (tp30) REVERT: B 246 GLN cc_start: 0.7350 (tt0) cc_final: 0.7078 (mt0) REVERT: B 252 ARG cc_start: 0.6681 (mmm-85) cc_final: 0.6167 (mmt180) REVERT: B 253 ASP cc_start: 0.6991 (m-30) cc_final: 0.6383 (p0) REVERT: B 293 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7411 (mpt180) REVERT: B 297 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6375 (mm-30) REVERT: B 335 GLU cc_start: 0.8317 (tt0) cc_final: 0.7411 (tm-30) REVERT: B 370 GLU cc_start: 0.7429 (tt0) cc_final: 0.7191 (tp30) REVERT: B 432 ARG cc_start: 0.7328 (mtm180) cc_final: 0.7006 (mtp85) REVERT: B 443 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7216 (mtp-110) REVERT: B 488 GLU cc_start: 0.7159 (pm20) cc_final: 0.6589 (tm-30) REVERT: B 508 ASP cc_start: 0.7517 (m-30) cc_final: 0.7195 (m-30) REVERT: B 662 LYS cc_start: 0.6929 (tttt) cc_final: 0.6658 (mtmm) REVERT: B 682 GLU cc_start: 0.6898 (tt0) cc_final: 0.6570 (tp30) REVERT: B 746 MET cc_start: 0.7025 (mmm) cc_final: 0.6720 (mmm) REVERT: B 751 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6806 (mp0) REVERT: B 756 ARG cc_start: 0.7285 (ttm110) cc_final: 0.6640 (mtp180) REVERT: B 761 ARG cc_start: 0.7520 (ttt180) cc_final: 0.7312 (mtp85) REVERT: B 769 MET cc_start: 0.7320 (ttt) cc_final: 0.6682 (tmt) REVERT: B 782 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7516 (mtp180) REVERT: B 783 ASP cc_start: 0.8320 (m-30) cc_final: 0.8073 (m-30) REVERT: B 784 GLN cc_start: 0.7691 (tp-100) cc_final: 0.7437 (tt0) REVERT: B 966 GLN cc_start: 0.7777 (tt0) cc_final: 0.7561 (tt0) REVERT: B 970 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6982 (mp0) REVERT: B 1001 SER cc_start: 0.7611 (t) cc_final: 0.7210 (m) REVERT: B 1005 SER cc_start: 0.7577 (m) cc_final: 0.7151 (p) REVERT: B 1014 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7398 (mtm-85) REVERT: B 1022 CYS cc_start: 0.7476 (p) cc_final: 0.7155 (p) REVERT: C 1 MET cc_start: -0.0208 (tpt) cc_final: -0.0920 (ttm) REVERT: C 41 GLU cc_start: 0.7123 (tp30) cc_final: 0.6275 (tm-30) REVERT: C 42 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6534 (tt0) REVERT: C 50 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7152 (mm110) REVERT: C 86 VAL cc_start: 0.7902 (t) cc_final: 0.7460 (p) REVERT: C 129 ASN cc_start: 0.7739 (t0) cc_final: 0.7151 (t0) REVERT: C 242 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7122 (tt0) REVERT: C 244 GLU cc_start: 0.7689 (tt0) cc_final: 0.7310 (tp30) REVERT: C 246 GLN cc_start: 0.7429 (tt0) cc_final: 0.7107 (mt0) REVERT: C 252 ARG cc_start: 0.6576 (mmm-85) cc_final: 0.6047 (mmt180) REVERT: C 253 ASP cc_start: 0.6816 (m-30) cc_final: 0.6298 (p0) REVERT: C 254 TYR cc_start: 0.7023 (p90) cc_final: 0.6630 (p90) REVERT: C 297 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6380 (mm-30) REVERT: C 335 GLU cc_start: 0.8316 (tt0) cc_final: 0.7385 (tm-30) REVERT: C 359 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: C 370 GLU cc_start: 0.7381 (tt0) cc_final: 0.7090 (tp30) REVERT: C 432 ARG cc_start: 0.7341 (mtm180) cc_final: 0.7008 (mtp85) REVERT: C 439 GLU cc_start: 0.7624 (tt0) cc_final: 0.6957 (tm-30) REVERT: C 449 ARG cc_start: 0.7766 (ttt-90) cc_final: 0.7556 (mtp85) REVERT: C 488 GLU cc_start: 0.7158 (pm20) cc_final: 0.6606 (tm-30) REVERT: C 660 ASP cc_start: 0.7020 (m-30) cc_final: 0.6491 (p0) REVERT: C 682 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: C 747 ASP cc_start: 0.6875 (p0) cc_final: 0.6625 (p0) REVERT: C 751 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6541 (mp0) REVERT: C 769 MET cc_start: 0.7416 (ttt) cc_final: 0.6697 (tmt) REVERT: C 774 LYS cc_start: 0.7342 (mtmt) cc_final: 0.6751 (ttmt) REVERT: C 775 LYS cc_start: 0.8060 (mttt) cc_final: 0.7734 (mttm) REVERT: C 782 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7593 (mtp-110) REVERT: C 783 ASP cc_start: 0.8239 (m-30) cc_final: 0.7980 (m-30) REVERT: C 812 LYS cc_start: 0.7924 (mttt) cc_final: 0.7710 (mttm) REVERT: C 826 CYS cc_start: 0.6920 (t) cc_final: 0.6461 (p) REVERT: C 955 ASP cc_start: 0.7434 (t0) cc_final: 0.6973 (t70) REVERT: C 966 GLN cc_start: 0.7758 (tt0) cc_final: 0.7528 (tt0) REVERT: C 970 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6981 (mp0) REVERT: C 978 HIS cc_start: 0.5964 (m-70) cc_final: 0.5685 (p-80) REVERT: C 1001 SER cc_start: 0.7696 (t) cc_final: 0.7313 (m) REVERT: C 1005 SER cc_start: 0.7436 (m) cc_final: 0.7091 (p) REVERT: C 1014 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7308 (mtm-85) REVERT: D 1 MET cc_start: -0.0497 (tpt) cc_final: -0.0937 (ttm) REVERT: D 14 ARG cc_start: 0.6397 (tpp80) cc_final: 0.6171 (mmt180) REVERT: D 41 GLU cc_start: 0.7177 (tp30) cc_final: 0.6217 (tm-30) REVERT: D 42 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6429 (tt0) REVERT: D 50 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7275 (mm110) REVERT: D 86 VAL cc_start: 0.7954 (t) cc_final: 0.7510 (p) REVERT: D 220 THR cc_start: 0.7536 (p) cc_final: 0.7244 (t) REVERT: D 238 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7475 (mtm110) REVERT: D 242 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7173 (tt0) REVERT: D 244 GLU cc_start: 0.7768 (tt0) cc_final: 0.7330 (tp30) REVERT: D 252 ARG cc_start: 0.6756 (mmm-85) cc_final: 0.6280 (mmt180) REVERT: D 253 ASP cc_start: 0.6843 (m-30) cc_final: 0.6302 (p0) REVERT: D 254 TYR cc_start: 0.7176 (p90) cc_final: 0.6682 (p90) REVERT: D 293 ARG cc_start: 0.7797 (mtt90) cc_final: 0.7365 (mpt180) REVERT: D 297 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6477 (mm-30) REVERT: D 335 GLU cc_start: 0.8345 (tt0) cc_final: 0.7412 (tm-30) REVERT: D 432 ARG cc_start: 0.7395 (mtm180) cc_final: 0.6990 (mtp85) REVERT: D 439 GLU cc_start: 0.7715 (tt0) cc_final: 0.7079 (tm-30) REVERT: D 443 ARG cc_start: 0.7621 (mtp85) cc_final: 0.7211 (mtp-110) REVERT: D 488 GLU cc_start: 0.7163 (pm20) cc_final: 0.6615 (tm-30) REVERT: D 660 ASP cc_start: 0.6812 (m-30) cc_final: 0.6438 (p0) REVERT: D 662 LYS cc_start: 0.7198 (tttt) cc_final: 0.6825 (mtmt) REVERT: D 682 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6887 (pm20) REVERT: D 747 ASP cc_start: 0.7304 (p0) cc_final: 0.7049 (p0) REVERT: D 751 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6575 (mp0) REVERT: D 756 ARG cc_start: 0.7099 (ttm110) cc_final: 0.6761 (mtp180) REVERT: D 769 MET cc_start: 0.7360 (ttt) cc_final: 0.6561 (tmt) REVERT: D 774 LYS cc_start: 0.7440 (mtmm) cc_final: 0.7139 (mtpp) REVERT: D 775 LYS cc_start: 0.8031 (mttt) cc_final: 0.7719 (mttm) REVERT: D 782 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7537 (mtp-110) REVERT: D 925 ASP cc_start: 0.7390 (m-30) cc_final: 0.7003 (t70) REVERT: D 966 GLN cc_start: 0.7706 (tt0) cc_final: 0.7428 (tt0) REVERT: D 970 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7040 (mp0) REVERT: D 1001 SER cc_start: 0.7735 (t) cc_final: 0.7280 (m) REVERT: D 1005 SER cc_start: 0.7424 (m) cc_final: 0.7157 (p) REVERT: D 1014 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7269 (mtm-85) outliers start: 48 outliers final: 16 residues processed: 597 average time/residue: 1.6893 time to fit residues: 1170.4589 Evaluate side-chains 507 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 488 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 959 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 886 ASN Chi-restraints excluded: chain C residue 1018 GLN Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 1018 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 308 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 20.0000 chunk 400 optimal weight: 0.1980 chunk 330 optimal weight: 10.0000 chunk 368 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 297 optimal weight: 9.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- 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 419 HIS A 605 ASN A 864 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 267 GLN B 605 ASN B 726 ASN B 762 GLN B 950 HIS B 986 ASN C 647 HIS C 762 GLN C 886 ASN C 950 HIS C 959 ASN D 647 HIS D 762 GLN D 950 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 33856 Z= 0.340 Angle : 0.686 9.338 46192 Z= 0.369 Chirality : 0.048 0.189 4832 Planarity : 0.006 0.053 6100 Dihedral : 6.030 74.366 4484 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.24 % Rotamer: Outliers : 1.57 % Allowed : 7.82 % Favored : 90.61 % 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: 544 sheet: 0.57 (0.14), residues: 1332 loop : -0.34 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 554 HIS 0.011 0.002 HIS A 978 PHE 0.011 0.002 PHE B1008 TYR 0.021 0.003 TYR D 101 ARG 0.007 0.001 ARG B 449 *********************** 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 544 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 489 time to evaluate : 4.051 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: -0.0129 (tpt) cc_final: -0.0677 (ttm) REVERT: A 3 MET cc_start: 0.1212 (mmp) cc_final: 0.0771 (mmt) REVERT: A 41 GLU cc_start: 0.7158 (tp30) cc_final: 0.6358 (tm-30) REVERT: A 42 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6637 (tt0) REVERT: A 48 PRO cc_start: 0.8050 (Cg_exo) cc_final: 0.7788 (Cg_endo) REVERT: A 76 GLU cc_start: 0.7628 (mt-10) cc_final: 0.6775 (pp20) REVERT: A 78 ASP cc_start: 0.7260 (m-30) cc_final: 0.6848 (m-30) REVERT: A 118 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7357 (tp30) REVERT: A 129 ASN cc_start: 0.7262 (m-40) cc_final: 0.6924 (t0) REVERT: A 206 MET cc_start: 0.8467 (mtm) cc_final: 0.8002 (mtt) REVERT: A 220 THR cc_start: 0.7597 (p) cc_final: 0.7248 (t) REVERT: A 242 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7192 (tt0) REVERT: A 244 GLU cc_start: 0.7714 (tt0) cc_final: 0.7282 (tp30) REVERT: A 246 GLN cc_start: 0.7489 (tt0) cc_final: 0.7146 (mt0) REVERT: A 252 ARG cc_start: 0.6718 (mmm-85) cc_final: 0.6209 (mmt180) REVERT: A 253 ASP cc_start: 0.7022 (m-30) cc_final: 0.6307 (p0) REVERT: A 293 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7403 (mpt180) REVERT: A 297 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6358 (mm-30) REVERT: A 335 GLU cc_start: 0.8333 (tt0) cc_final: 0.7461 (tm-30) REVERT: A 359 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: A 363 LEU cc_start: 0.7637 (mt) cc_final: 0.7280 (mm) REVERT: A 405 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7619 (ttp-110) REVERT: A 432 ARG cc_start: 0.7350 (mtm180) cc_final: 0.7019 (mtp85) REVERT: A 439 GLU cc_start: 0.7726 (tt0) cc_final: 0.7136 (tm-30) REVERT: A 443 ARG cc_start: 0.7631 (mtp85) cc_final: 0.7198 (mtp-110) REVERT: A 488 GLU cc_start: 0.7107 (pm20) cc_final: 0.6498 (tm-30) REVERT: A 662 LYS cc_start: 0.7148 (tttt) cc_final: 0.6793 (mtmm) REVERT: A 751 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7010 (mp0) REVERT: A 756 ARG cc_start: 0.7325 (ttm110) cc_final: 0.6636 (mtp180) REVERT: A 758 GLN cc_start: 0.8054 (tt0) cc_final: 0.7767 (tt0) REVERT: A 761 ARG cc_start: 0.7591 (ttt180) cc_final: 0.7340 (mtp85) REVERT: A 762 GLN cc_start: 0.7358 (mm-40) cc_final: 0.7120 (mp-120) REVERT: A 769 MET cc_start: 0.7297 (ttt) cc_final: 0.6506 (tmt) REVERT: A 774 LYS cc_start: 0.6787 (tttt) cc_final: 0.6278 (tttt) REVERT: A 775 LYS cc_start: 0.7931 (mttt) cc_final: 0.7607 (mttp) REVERT: A 782 ARG cc_start: 0.7880 (mtm180) cc_final: 0.7470 (mtp180) REVERT: A 784 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7399 (tt0) REVERT: A 966 GLN cc_start: 0.7802 (tt0) cc_final: 0.7591 (tt0) REVERT: A 970 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7041 (mp0) REVERT: A 1001 SER cc_start: 0.7662 (t) cc_final: 0.7201 (m) REVERT: A 1005 SER cc_start: 0.7502 (m) cc_final: 0.7081 (p) REVERT: A 1014 ARG cc_start: 0.8129 (mtp85) cc_final: 0.7440 (mtm-85) REVERT: B 41 GLU cc_start: 0.7182 (tp30) cc_final: 0.6373 (tm-30) REVERT: B 42 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6568 (tt0) REVERT: B 48 PRO cc_start: 0.8049 (Cg_exo) cc_final: 0.7809 (Cg_endo) REVERT: B 78 ASP cc_start: 0.7212 (m-30) cc_final: 0.7004 (m-30) REVERT: B 129 ASN cc_start: 0.7766 (t0) cc_final: 0.7283 (t0) REVERT: B 158 ARG cc_start: 0.7881 (mtp180) cc_final: 0.7576 (mtm110) REVERT: B 206 MET cc_start: 0.8494 (mtm) cc_final: 0.8084 (mtt) REVERT: B 220 THR cc_start: 0.7589 (p) cc_final: 0.7215 (t) REVERT: B 242 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7155 (tt0) REVERT: B 244 GLU cc_start: 0.7697 (tt0) cc_final: 0.7263 (tp30) REVERT: B 246 GLN cc_start: 0.7468 (tt0) cc_final: 0.7140 (mt0) REVERT: B 252 ARG cc_start: 0.6756 (mmm-85) cc_final: 0.6261 (mmt180) REVERT: B 253 ASP cc_start: 0.7013 (m-30) cc_final: 0.6326 (p0) REVERT: B 293 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7598 (mtt180) REVERT: B 297 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6400 (mm-30) REVERT: B 335 GLU cc_start: 0.8340 (tt0) cc_final: 0.7459 (tm-30) REVERT: B 432 ARG cc_start: 0.7349 (mtm180) cc_final: 0.7027 (mtp85) REVERT: B 439 GLU cc_start: 0.7722 (tt0) cc_final: 0.7108 (tm-30) REVERT: B 443 ARG cc_start: 0.7635 (mtp85) cc_final: 0.7217 (mtp-110) REVERT: B 488 GLU cc_start: 0.7105 (pm20) cc_final: 0.6517 (tm-30) REVERT: B 508 ASP cc_start: 0.7568 (m-30) cc_final: 0.7214 (m-30) REVERT: B 662 LYS cc_start: 0.7151 (tttt) cc_final: 0.6773 (mtmm) REVERT: B 751 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6836 (mp0) REVERT: B 756 ARG cc_start: 0.7344 (ttm110) cc_final: 0.6521 (mtp180) REVERT: B 761 ARG cc_start: 0.7582 (ttt180) cc_final: 0.7286 (mtp85) REVERT: B 769 MET cc_start: 0.7334 (ttt) cc_final: 0.6548 (tmt) REVERT: B 774 LYS cc_start: 0.7366 (mtpp) cc_final: 0.6559 (tttt) REVERT: B 782 ARG cc_start: 0.7885 (mtm180) cc_final: 0.7495 (mtp180) REVERT: B 783 ASP cc_start: 0.8348 (m-30) cc_final: 0.8120 (m-30) REVERT: B 784 GLN cc_start: 0.7692 (tp-100) cc_final: 0.7398 (tt0) REVERT: B 966 GLN cc_start: 0.7790 (tt0) cc_final: 0.7586 (tt0) REVERT: B 970 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7079 (mp0) REVERT: B 1001 SER cc_start: 0.7668 (t) cc_final: 0.7219 (m) REVERT: B 1005 SER cc_start: 0.7495 (m) cc_final: 0.7103 (p) REVERT: B 1014 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7405 (mtm-85) REVERT: B 1022 CYS cc_start: 0.7471 (p) cc_final: 0.7249 (p) REVERT: C 1 MET cc_start: -0.0080 (tpt) cc_final: -0.0809 (ttm) REVERT: C 41 GLU cc_start: 0.7133 (tp30) cc_final: 0.6308 (tm-30) REVERT: C 42 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6589 (tt0) REVERT: C 50 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7170 (mm110) REVERT: C 129 ASN cc_start: 0.7757 (t0) cc_final: 0.7260 (t0) REVERT: C 242 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7132 (tt0) REVERT: C 244 GLU cc_start: 0.7809 (tt0) cc_final: 0.7356 (tp30) REVERT: C 246 GLN cc_start: 0.7563 (tt0) cc_final: 0.7216 (mt0) REVERT: C 252 ARG cc_start: 0.6691 (mmm-85) cc_final: 0.6183 (mmt180) REVERT: C 253 ASP cc_start: 0.7022 (m-30) cc_final: 0.6282 (p0) REVERT: C 254 TYR cc_start: 0.7093 (p90) cc_final: 0.6585 (p90) REVERT: C 297 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6385 (mm-30) REVERT: C 335 GLU cc_start: 0.8336 (tt0) cc_final: 0.7456 (tm-30) REVERT: C 359 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: C 370 GLU cc_start: 0.7440 (tt0) cc_final: 0.7025 (tm-30) REVERT: C 432 ARG cc_start: 0.7344 (mtm180) cc_final: 0.7021 (mtp85) REVERT: C 439 GLU cc_start: 0.7705 (tt0) cc_final: 0.7018 (tm-30) REVERT: C 488 GLU cc_start: 0.7081 (pm20) cc_final: 0.6508 (tm-30) REVERT: C 508 ASP cc_start: 0.7580 (m-30) cc_final: 0.7349 (m-30) REVERT: C 662 LYS cc_start: 0.7303 (tttt) cc_final: 0.6798 (mtmm) REVERT: C 682 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: C 751 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6670 (mp0) REVERT: C 758 GLN cc_start: 0.7955 (tt0) cc_final: 0.7743 (tt0) REVERT: C 769 MET cc_start: 0.7336 (ttt) cc_final: 0.6466 (tmt) REVERT: C 774 LYS cc_start: 0.7477 (mtmt) cc_final: 0.6651 (tttt) REVERT: C 775 LYS cc_start: 0.8091 (mttt) cc_final: 0.7753 (mttm) REVERT: C 782 ARG cc_start: 0.7943 (mtm180) cc_final: 0.7604 (mtp180) REVERT: C 783 ASP cc_start: 0.8252 (m-30) cc_final: 0.7956 (m-30) REVERT: C 812 LYS cc_start: 0.7983 (mttt) cc_final: 0.7737 (mttm) REVERT: C 826 CYS cc_start: 0.7493 (t) cc_final: 0.7254 (p) REVERT: C 858 ARG cc_start: 0.8288 (ttt-90) cc_final: 0.7950 (ttt90) REVERT: C 966 GLN cc_start: 0.7828 (tt0) cc_final: 0.7612 (tt0) REVERT: C 970 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7041 (mp0) REVERT: C 1001 SER cc_start: 0.7662 (t) cc_final: 0.7216 (m) REVERT: C 1005 SER cc_start: 0.7435 (m) cc_final: 0.7073 (p) REVERT: C 1014 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7377 (mtm-85) REVERT: C 1022 CYS cc_start: 0.7522 (p) cc_final: 0.7299 (p) REVERT: D 1 MET cc_start: -0.0311 (tpt) cc_final: -0.0750 (ttm) REVERT: D 39 ASN cc_start: 0.8180 (t0) cc_final: 0.7864 (t0) REVERT: D 41 GLU cc_start: 0.7219 (tp30) cc_final: 0.6258 (tm-30) REVERT: D 42 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6551 (tt0) REVERT: D 50 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7235 (mm110) REVERT: D 129 ASN cc_start: 0.7727 (t0) cc_final: 0.7239 (t0) REVERT: D 206 MET cc_start: 0.8560 (mtm) cc_final: 0.8286 (mtt) REVERT: D 220 THR cc_start: 0.7567 (p) cc_final: 0.7223 (t) REVERT: D 242 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7111 (tt0) REVERT: D 244 GLU cc_start: 0.7804 (tt0) cc_final: 0.7357 (tp30) REVERT: D 252 ARG cc_start: 0.6825 (mmm-85) cc_final: 0.6421 (mmt180) REVERT: D 253 ASP cc_start: 0.6997 (m-30) cc_final: 0.6236 (p0) REVERT: D 254 TYR cc_start: 0.7142 (p90) cc_final: 0.6623 (p90) REVERT: D 293 ARG cc_start: 0.7878 (mtt90) cc_final: 0.7593 (mtt180) REVERT: D 297 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6379 (mm-30) REVERT: D 335 GLU cc_start: 0.8315 (tt0) cc_final: 0.7438 (tm-30) REVERT: D 359 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: D 369 ASP cc_start: 0.7487 (p0) cc_final: 0.7034 (p0) REVERT: D 432 ARG cc_start: 0.7373 (mtm180) cc_final: 0.7008 (mtp85) REVERT: D 439 GLU cc_start: 0.7750 (tt0) cc_final: 0.7119 (tm-30) REVERT: D 443 ARG cc_start: 0.7645 (mtp85) cc_final: 0.7215 (mtp-110) REVERT: D 488 GLU cc_start: 0.7129 (pm20) cc_final: 0.6560 (tm-30) REVERT: D 662 LYS cc_start: 0.7273 (tttt) cc_final: 0.6790 (mtmm) REVERT: D 682 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: D 725 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: D 751 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6771 (mp0) REVERT: D 756 ARG cc_start: 0.7264 (ttm110) cc_final: 0.6670 (mtp180) REVERT: D 758 GLN cc_start: 0.7991 (tt0) cc_final: 0.7747 (tt0) REVERT: D 769 MET cc_start: 0.7257 (ttt) cc_final: 0.6334 (tmt) REVERT: D 774 LYS cc_start: 0.7464 (mtmm) cc_final: 0.6690 (tttt) REVERT: D 775 LYS cc_start: 0.8117 (mttt) cc_final: 0.7750 (mttm) REVERT: D 782 ARG cc_start: 0.7931 (mtm180) cc_final: 0.7582 (mtp180) REVERT: D 925 ASP cc_start: 0.7449 (m-30) cc_final: 0.7084 (t0) REVERT: D 966 GLN cc_start: 0.7786 (tt0) cc_final: 0.7557 (tt0) REVERT: D 970 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7071 (mp0) REVERT: D 1001 SER cc_start: 0.7692 (t) cc_final: 0.7220 (m) REVERT: D 1005 SER cc_start: 0.7419 (m) cc_final: 0.7131 (p) REVERT: D 1014 ARG cc_start: 0.7978 (mtp85) cc_final: 0.7344 (mtm-85) REVERT: D 1022 CYS cc_start: 0.7516 (p) cc_final: 0.7301 (p) outliers start: 55 outliers final: 21 residues processed: 527 average time/residue: 1.7502 time to fit residues: 1067.6467 Evaluate side-chains 507 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 480 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 959 ASN Chi-restraints excluded: chain B residue 1018 GLN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 1018 GLN Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 924 SER Chi-restraints excluded: chain D residue 1018 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 9.9990 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 249 optimal weight: 0.6980 chunk 372 optimal weight: 8.9990 chunk 394 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 353 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 864 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 726 ASN B 959 ASN B 986 ASN C 959 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33856 Z= 0.213 Angle : 0.587 9.378 46192 Z= 0.312 Chirality : 0.045 0.176 4832 Planarity : 0.004 0.042 6100 Dihedral : 5.642 70.504 4484 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.86 % Favored : 97.04 % Rotamer: Outliers : 1.17 % Allowed : 8.99 % Favored : 89.84 % 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: 0.11 (0.13), residues: 4088 helix: 0.21 (0.21), residues: 552 sheet: 0.65 (0.14), residues: 1344 loop : -0.26 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 554 HIS 0.013 0.001 HIS C 978 PHE 0.009 0.001 PHE A 226 TYR 0.019 0.002 TYR D 101 ARG 0.004 0.000 ARG A 858 *********************** 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 557 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 516 time to evaluate : 4.187 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: -0.0139 (tpt) cc_final: -0.0706 (ttm) REVERT: A 3 MET cc_start: 0.1470 (mmp) cc_final: 0.1054 (tmm) REVERT: A 41 GLU cc_start: 0.7157 (tp30) cc_final: 0.6396 (tm-30) REVERT: A 42 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6641 (tt0) REVERT: A 48 PRO cc_start: 0.8029 (Cg_exo) cc_final: 0.7794 (Cg_endo) REVERT: A 76 GLU cc_start: 0.7593 (mt-10) cc_final: 0.6834 (pp20) REVERT: A 78 ASP cc_start: 0.7256 (m-30) cc_final: 0.6850 (m-30) REVERT: A 118 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7372 (tp30) REVERT: A 131 ASP cc_start: 0.6427 (t70) cc_final: 0.6109 (p0) REVERT: A 220 THR cc_start: 0.7606 (p) cc_final: 0.7240 (t) REVERT: A 242 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7117 (tt0) REVERT: A 244 GLU cc_start: 0.7726 (tt0) cc_final: 0.7291 (tp30) REVERT: A 246 GLN cc_start: 0.7513 (tt0) cc_final: 0.7169 (mt0) REVERT: A 252 ARG cc_start: 0.6702 (mmm-85) cc_final: 0.6234 (mmt180) REVERT: A 253 ASP cc_start: 0.7072 (m-30) cc_final: 0.6335 (p0) REVERT: A 254 TYR cc_start: 0.7170 (p90) cc_final: 0.6591 (p90) REVERT: A 293 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7420 (mpt180) REVERT: A 297 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6358 (mm-30) REVERT: A 335 GLU cc_start: 0.8328 (tt0) cc_final: 0.7428 (tm-30) REVERT: A 359 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: A 363 LEU cc_start: 0.7655 (mt) cc_final: 0.7293 (mm) REVERT: A 405 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7657 (ttp-110) REVERT: A 432 ARG cc_start: 0.7301 (mtm180) cc_final: 0.6985 (mtp85) REVERT: A 439 GLU cc_start: 0.7700 (tt0) cc_final: 0.7154 (tm-30) REVERT: A 443 ARG cc_start: 0.7620 (mtp85) cc_final: 0.7191 (mtp-110) REVERT: A 488 GLU cc_start: 0.7062 (pm20) cc_final: 0.6393 (tm-30) REVERT: A 662 LYS cc_start: 0.7252 (tttt) cc_final: 0.6880 (mtmm) REVERT: A 751 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7006 (mp0) REVERT: A 756 ARG cc_start: 0.7310 (ttm110) cc_final: 0.6584 (mtp180) REVERT: A 758 GLN cc_start: 0.8038 (tt0) cc_final: 0.7764 (tt0) REVERT: A 761 ARG cc_start: 0.7620 (ttt180) cc_final: 0.7328 (mtp85) REVERT: A 762 GLN cc_start: 0.7380 (mm-40) cc_final: 0.7162 (mp-120) REVERT: A 769 MET cc_start: 0.7261 (ttt) cc_final: 0.6291 (tmt) REVERT: A 774 LYS cc_start: 0.6751 (tttt) cc_final: 0.6208 (tttt) REVERT: A 775 LYS cc_start: 0.7895 (mttt) cc_final: 0.7544 (mttp) REVERT: A 782 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7479 (mtp180) REVERT: A 784 GLN cc_start: 0.7630 (tp-100) cc_final: 0.7393 (tt0) REVERT: A 966 GLN cc_start: 0.7840 (tt0) cc_final: 0.7621 (tt0) REVERT: A 970 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7001 (mp0) REVERT: A 1001 SER cc_start: 0.7665 (t) cc_final: 0.7242 (m) REVERT: A 1005 SER cc_start: 0.7387 (m) cc_final: 0.6979 (p) REVERT: A 1014 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7393 (mtm-85) REVERT: B 41 GLU cc_start: 0.7123 (tp30) cc_final: 0.6386 (tm-30) REVERT: B 42 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6600 (tt0) REVERT: B 48 PRO cc_start: 0.8024 (Cg_exo) cc_final: 0.7796 (Cg_endo) REVERT: B 76 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6797 (pp20) REVERT: B 78 ASP cc_start: 0.7262 (m-30) cc_final: 0.7015 (m-30) REVERT: B 129 ASN cc_start: 0.7701 (t0) cc_final: 0.7261 (t0) REVERT: B 158 ARG cc_start: 0.7885 (mtp180) cc_final: 0.7560 (mtm110) REVERT: B 220 THR cc_start: 0.7575 (p) cc_final: 0.7201 (t) REVERT: B 242 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7104 (tt0) REVERT: B 244 GLU cc_start: 0.7742 (tt0) cc_final: 0.7314 (tp30) REVERT: B 246 GLN cc_start: 0.7501 (tt0) cc_final: 0.7189 (mt0) REVERT: B 253 ASP cc_start: 0.7024 (m-30) cc_final: 0.6320 (p0) REVERT: B 254 TYR cc_start: 0.7148 (p90) cc_final: 0.6612 (p90) REVERT: B 293 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7600 (mtt180) REVERT: B 297 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6333 (mm-30) REVERT: B 335 GLU cc_start: 0.8338 (tt0) cc_final: 0.7458 (tm-30) REVERT: B 337 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7888 (ttp-110) REVERT: B 339 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: B 369 ASP cc_start: 0.7374 (p0) cc_final: 0.7007 (p0) REVERT: B 432 ARG cc_start: 0.7302 (mtm180) cc_final: 0.6991 (mtp85) REVERT: B 439 GLU cc_start: 0.7713 (tt0) cc_final: 0.7162 (tm-30) REVERT: B 443 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7211 (mtp-110) REVERT: B 488 GLU cc_start: 0.7079 (pm20) cc_final: 0.6431 (tm-30) REVERT: B 662 LYS cc_start: 0.7279 (tttt) cc_final: 0.6890 (mtmm) REVERT: B 751 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6818 (mp0) REVERT: B 756 ARG cc_start: 0.7313 (ttm110) cc_final: 0.6517 (mtp180) REVERT: B 761 ARG cc_start: 0.7607 (ttt180) cc_final: 0.7331 (mtp85) REVERT: B 762 GLN cc_start: 0.7378 (mp10) cc_final: 0.6766 (tm-30) REVERT: B 769 MET cc_start: 0.7299 (ttt) cc_final: 0.6399 (tmt) REVERT: B 774 LYS cc_start: 0.7339 (mtpp) cc_final: 0.6528 (tttt) REVERT: B 782 ARG cc_start: 0.7852 (mtm180) cc_final: 0.7485 (mtp180) REVERT: B 783 ASP cc_start: 0.8325 (m-30) cc_final: 0.8084 (m-30) REVERT: B 966 GLN cc_start: 0.7814 (tt0) cc_final: 0.7603 (tt0) REVERT: B 970 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7039 (mp0) REVERT: B 1001 SER cc_start: 0.7656 (t) cc_final: 0.7236 (m) REVERT: B 1005 SER cc_start: 0.7398 (m) cc_final: 0.7003 (p) REVERT: B 1014 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7381 (mtm-85) REVERT: C 1 MET cc_start: -0.0005 (tpt) cc_final: -0.0564 (ttm) REVERT: C 40 SER cc_start: 0.7747 (p) cc_final: 0.7352 (t) REVERT: C 41 GLU cc_start: 0.7117 (tp30) cc_final: 0.6287 (tm-30) REVERT: C 42 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6570 (tt0) REVERT: C 50 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7049 (mm110) REVERT: C 76 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6740 (pp20) REVERT: C 129 ASN cc_start: 0.7714 (t0) cc_final: 0.7288 (t0) REVERT: C 242 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7063 (tt0) REVERT: C 244 GLU cc_start: 0.7790 (tt0) cc_final: 0.7430 (tt0) REVERT: C 246 GLN cc_start: 0.7555 (tt0) cc_final: 0.7219 (mt0) REVERT: C 252 ARG cc_start: 0.6645 (mmm-85) cc_final: 0.6154 (mmt180) REVERT: C 253 ASP cc_start: 0.7009 (m-30) cc_final: 0.6271 (p0) REVERT: C 254 TYR cc_start: 0.7089 (p90) cc_final: 0.6591 (p90) REVERT: C 297 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6346 (mm-30) REVERT: C 335 GLU cc_start: 0.8336 (tt0) cc_final: 0.7430 (tm-30) REVERT: C 359 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: C 432 ARG cc_start: 0.7291 (mtm180) cc_final: 0.6984 (mtp85) REVERT: C 439 GLU cc_start: 0.7675 (tt0) cc_final: 0.7056 (tm-30) REVERT: C 488 GLU cc_start: 0.7100 (pm20) cc_final: 0.6490 (tm-30) REVERT: C 508 ASP cc_start: 0.7581 (m-30) cc_final: 0.7343 (m-30) REVERT: C 584 ASN cc_start: 0.6802 (m110) cc_final: 0.6118 (m-40) REVERT: C 662 LYS cc_start: 0.7382 (tttt) cc_final: 0.6899 (mtmm) REVERT: C 682 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6894 (pm20) REVERT: C 747 ASP cc_start: 0.7157 (p0) cc_final: 0.6110 (m-30) REVERT: C 751 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6789 (mp0) REVERT: C 758 GLN cc_start: 0.7929 (tt0) cc_final: 0.7699 (tt0) REVERT: C 769 MET cc_start: 0.7268 (ttt) cc_final: 0.6342 (tmt) REVERT: C 774 LYS cc_start: 0.7420 (mtmt) cc_final: 0.6576 (tttt) REVERT: C 775 LYS cc_start: 0.8096 (mttt) cc_final: 0.7758 (mttp) REVERT: C 782 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7597 (mtp180) REVERT: C 783 ASP cc_start: 0.8243 (m-30) cc_final: 0.7977 (m-30) REVERT: C 812 LYS cc_start: 0.7951 (mttt) cc_final: 0.7710 (mttm) REVERT: C 966 GLN cc_start: 0.7826 (tt0) cc_final: 0.7607 (tt0) REVERT: C 970 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7018 (mp0) REVERT: C 1001 SER cc_start: 0.7665 (t) cc_final: 0.7247 (m) REVERT: C 1005 SER cc_start: 0.7420 (m) cc_final: 0.7042 (p) REVERT: C 1014 ARG cc_start: 0.8002 (mtp85) cc_final: 0.7372 (mtm-85) REVERT: D 1 MET cc_start: -0.0244 (tpt) cc_final: -0.0644 (ttm) REVERT: D 39 ASN cc_start: 0.8140 (t0) cc_final: 0.7879 (t0) REVERT: D 41 GLU cc_start: 0.7146 (tp30) cc_final: 0.6276 (tm-30) REVERT: D 42 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6592 (tt0) REVERT: D 50 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7251 (mm110) REVERT: D 76 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6790 (pp20) REVERT: D 129 ASN cc_start: 0.7710 (t0) cc_final: 0.7260 (t0) REVERT: D 131 ASP cc_start: 0.6565 (t70) cc_final: 0.6335 (p0) REVERT: D 220 THR cc_start: 0.7572 (p) cc_final: 0.7207 (t) REVERT: D 242 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7073 (tt0) REVERT: D 244 GLU cc_start: 0.7835 (tt0) cc_final: 0.7391 (tp30) REVERT: D 252 ARG cc_start: 0.6763 (mmm-85) cc_final: 0.6344 (mmt180) REVERT: D 253 ASP cc_start: 0.7009 (m-30) cc_final: 0.6239 (p0) REVERT: D 254 TYR cc_start: 0.7136 (p90) cc_final: 0.6640 (p90) REVERT: D 293 ARG cc_start: 0.7860 (mtt90) cc_final: 0.7379 (mpt180) REVERT: D 297 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6319 (mm-30) REVERT: D 335 GLU cc_start: 0.8309 (tt0) cc_final: 0.7411 (tm-30) REVERT: D 369 ASP cc_start: 0.7386 (p0) cc_final: 0.7006 (p0) REVERT: D 432 ARG cc_start: 0.7341 (mtm180) cc_final: 0.6989 (mtp85) REVERT: D 439 GLU cc_start: 0.7743 (tt0) cc_final: 0.7164 (tm-30) REVERT: D 443 ARG cc_start: 0.7616 (mtp85) cc_final: 0.7194 (mtp-110) REVERT: D 488 GLU cc_start: 0.7089 (pm20) cc_final: 0.6468 (tm-30) REVERT: D 662 LYS cc_start: 0.7297 (tttt) cc_final: 0.6794 (mtmm) REVERT: D 725 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: D 751 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6807 (mp0) REVERT: D 756 ARG cc_start: 0.7270 (ttm110) cc_final: 0.6522 (mtp180) REVERT: D 758 GLN cc_start: 0.7940 (tt0) cc_final: 0.7719 (tt0) REVERT: D 769 MET cc_start: 0.7186 (ttt) cc_final: 0.6256 (tmt) REVERT: D 774 LYS cc_start: 0.7385 (mtmm) cc_final: 0.6664 (tttt) REVERT: D 775 LYS cc_start: 0.8083 (mttt) cc_final: 0.7592 (mttm) REVERT: D 782 ARG cc_start: 0.7894 (mtm180) cc_final: 0.7548 (mtp180) REVERT: D 925 ASP cc_start: 0.7521 (m-30) cc_final: 0.7172 (t0) REVERT: D 966 GLN cc_start: 0.7790 (tt0) cc_final: 0.7551 (tt0) REVERT: D 970 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7079 (mp0) REVERT: D 1001 SER cc_start: 0.7662 (t) cc_final: 0.7239 (m) REVERT: D 1005 SER cc_start: 0.7382 (m) cc_final: 0.7065 (p) REVERT: D 1014 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7389 (mtm-85) outliers start: 41 outliers final: 15 residues processed: 537 average time/residue: 1.7319 time to fit residues: 1083.1912 Evaluate side-chains 512 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 491 time to evaluate : 3.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 752 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 336 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 10.0000 chunk 353 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 726 ASN A 959 ASN A 986 ASN B 584 ASN B 726 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 605 ASN C 959 ASN C 978 HIS D 584 ASN D 605 ASN D 740 HIS D 762 GLN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 33856 Z= 0.304 Angle : 0.651 11.172 46192 Z= 0.346 Chirality : 0.047 0.185 4832 Planarity : 0.005 0.039 6100 Dihedral : 5.790 64.443 4484 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.86 % Favored : 97.04 % Rotamer: Outliers : 1.71 % Allowed : 9.42 % Favored : 88.87 % 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: 0.23 (0.21), residues: 544 sheet: 0.72 (0.14), residues: 1336 loop : -0.18 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 554 HIS 0.009 0.001 HIS C 978 PHE 0.012 0.002 PHE C 275 TYR 0.021 0.002 TYR D 101 ARG 0.005 0.001 ARG B 858 *********************** 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 540 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 480 time to evaluate : 3.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.0023 (tpt) cc_final: -0.0764 (ttm) REVERT: A 3 MET cc_start: 0.1475 (mmp) cc_final: 0.1029 (tmm) REVERT: A 41 GLU cc_start: 0.7216 (tp30) cc_final: 0.6443 (tm-30) REVERT: A 42 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6700 (tt0) REVERT: A 48 PRO cc_start: 0.8001 (Cg_exo) cc_final: 0.7770 (Cg_endo) REVERT: A 76 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6751 (pp20) REVERT: A 78 ASP cc_start: 0.7231 (m-30) cc_final: 0.6831 (m-30) REVERT: A 118 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7366 (tp30) REVERT: A 206 MET cc_start: 0.8496 (mtm) cc_final: 0.8100 (mtt) REVERT: A 220 THR cc_start: 0.7629 (p) cc_final: 0.7261 (t) REVERT: A 242 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7058 (tt0) REVERT: A 244 GLU cc_start: 0.7689 (tt0) cc_final: 0.7275 (tp30) REVERT: A 246 GLN cc_start: 0.7563 (tt0) cc_final: 0.7207 (mt0) REVERT: A 252 ARG cc_start: 0.6723 (mmm-85) cc_final: 0.6261 (mmt180) REVERT: A 254 TYR cc_start: 0.7128 (p90) cc_final: 0.6740 (p90) REVERT: A 293 ARG cc_start: 0.7861 (mtt90) cc_final: 0.7584 (mtt180) REVERT: A 297 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6357 (mm-30) REVERT: A 335 GLU cc_start: 0.8339 (tt0) cc_final: 0.7433 (tm-30) REVERT: A 359 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: A 369 ASP cc_start: 0.7438 (p0) cc_final: 0.7136 (p0) REVERT: A 370 GLU cc_start: 0.7593 (tt0) cc_final: 0.7128 (tm-30) REVERT: A 405 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7610 (ttp-110) REVERT: A 432 ARG cc_start: 0.7380 (mtm180) cc_final: 0.7058 (mtp85) REVERT: A 439 GLU cc_start: 0.7718 (tt0) cc_final: 0.7082 (tm-30) REVERT: A 443 ARG cc_start: 0.7683 (mtp85) cc_final: 0.7246 (mtp-110) REVERT: A 488 GLU cc_start: 0.7163 (pm20) cc_final: 0.6388 (tm-30) REVERT: A 547 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8332 (mp) REVERT: A 662 LYS cc_start: 0.7315 (tttt) cc_final: 0.6910 (mtmm) REVERT: A 751 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6994 (mp0) REVERT: A 756 ARG cc_start: 0.7332 (ttm110) cc_final: 0.6530 (mtp180) REVERT: A 758 GLN cc_start: 0.8014 (tt0) cc_final: 0.7800 (tt0) REVERT: A 761 ARG cc_start: 0.7588 (ttt180) cc_final: 0.7291 (mtp85) REVERT: A 762 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7199 (mp-120) REVERT: A 774 LYS cc_start: 0.6780 (tttt) cc_final: 0.6189 (tttt) REVERT: A 775 LYS cc_start: 0.7900 (mttt) cc_final: 0.7542 (mttp) REVERT: A 782 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7463 (mtp180) REVERT: A 784 GLN cc_start: 0.7725 (tp-100) cc_final: 0.7503 (tt0) REVERT: A 966 GLN cc_start: 0.7838 (tt0) cc_final: 0.7621 (tt0) REVERT: A 970 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7019 (mp0) REVERT: A 1001 SER cc_start: 0.7703 (t) cc_final: 0.7259 (m) REVERT: A 1005 SER cc_start: 0.7446 (m) cc_final: 0.7027 (p) REVERT: A 1014 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7470 (mtm-85) REVERT: B 41 GLU cc_start: 0.7182 (tp30) cc_final: 0.6431 (tm-30) REVERT: B 42 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6638 (tt0) REVERT: B 48 PRO cc_start: 0.7998 (Cg_exo) cc_final: 0.7778 (Cg_endo) REVERT: B 76 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6809 (pp20) REVERT: B 78 ASP cc_start: 0.7243 (m-30) cc_final: 0.7022 (m-30) REVERT: B 129 ASN cc_start: 0.7710 (t0) cc_final: 0.7270 (t0) REVERT: B 220 THR cc_start: 0.7588 (OUTLIER) cc_final: 0.7215 (t) REVERT: B 242 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7148 (tt0) REVERT: B 244 GLU cc_start: 0.7771 (tt0) cc_final: 0.7338 (tp30) REVERT: B 246 GLN cc_start: 0.7558 (tt0) cc_final: 0.7201 (mt0) REVERT: B 253 ASP cc_start: 0.7120 (m-30) cc_final: 0.6364 (p0) REVERT: B 254 TYR cc_start: 0.7121 (p90) cc_final: 0.6546 (p90) REVERT: B 293 ARG cc_start: 0.7879 (mtt90) cc_final: 0.7571 (mtt180) REVERT: B 335 GLU cc_start: 0.8355 (tt0) cc_final: 0.7497 (tm-30) REVERT: B 337 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7936 (ttp-110) REVERT: B 339 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: B 369 ASP cc_start: 0.7417 (p0) cc_final: 0.7176 (p0) REVERT: B 370 GLU cc_start: 0.7576 (tt0) cc_final: 0.7116 (tm-30) REVERT: B 432 ARG cc_start: 0.7383 (mtm180) cc_final: 0.7062 (mtp85) REVERT: B 439 GLU cc_start: 0.7710 (tt0) cc_final: 0.7086 (tm-30) REVERT: B 443 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7271 (mtp-110) REVERT: B 488 GLU cc_start: 0.7158 (pm20) cc_final: 0.6396 (tm-30) REVERT: B 547 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8334 (mp) REVERT: B 662 LYS cc_start: 0.7407 (tttt) cc_final: 0.6956 (mtmm) REVERT: B 725 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: B 751 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6871 (mp0) REVERT: B 756 ARG cc_start: 0.7315 (ttm110) cc_final: 0.6611 (mtp180) REVERT: B 761 ARG cc_start: 0.7598 (ttt180) cc_final: 0.7324 (mtp85) REVERT: B 762 GLN cc_start: 0.7433 (mp10) cc_final: 0.6832 (tm-30) REVERT: B 774 LYS cc_start: 0.7388 (mtpp) cc_final: 0.6580 (tttt) REVERT: B 782 ARG cc_start: 0.7902 (mtm180) cc_final: 0.7519 (mtp180) REVERT: B 783 ASP cc_start: 0.8331 (m-30) cc_final: 0.8106 (m-30) REVERT: B 966 GLN cc_start: 0.7788 (tt0) cc_final: 0.7571 (tt0) REVERT: B 970 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7035 (mp0) REVERT: B 1001 SER cc_start: 0.7691 (t) cc_final: 0.7246 (m) REVERT: B 1005 SER cc_start: 0.7443 (m) cc_final: 0.7036 (p) REVERT: B 1014 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7474 (mtm-85) REVERT: C 3 MET cc_start: 0.1425 (mmp) cc_final: 0.1112 (mmt) REVERT: C 41 GLU cc_start: 0.7121 (tp30) cc_final: 0.6358 (tm-30) REVERT: C 42 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6644 (tt0) REVERT: C 50 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7072 (mm110) REVERT: C 76 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6785 (pp20) REVERT: C 129 ASN cc_start: 0.7730 (t0) cc_final: 0.7314 (t0) REVERT: C 242 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7066 (tt0) REVERT: C 244 GLU cc_start: 0.7786 (tt0) cc_final: 0.7429 (tt0) REVERT: C 246 GLN cc_start: 0.7646 (tt0) cc_final: 0.7275 (mt0) REVERT: C 252 ARG cc_start: 0.6727 (mmm-85) cc_final: 0.6246 (mmt180) REVERT: C 253 ASP cc_start: 0.7114 (m-30) cc_final: 0.6353 (p0) REVERT: C 254 TYR cc_start: 0.7076 (p90) cc_final: 0.6548 (p90) REVERT: C 297 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6343 (mm-30) REVERT: C 335 GLU cc_start: 0.8332 (tt0) cc_final: 0.7464 (tm-30) REVERT: C 359 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: C 370 GLU cc_start: 0.7616 (tt0) cc_final: 0.7165 (tm-30) REVERT: C 432 ARG cc_start: 0.7381 (mtm180) cc_final: 0.7042 (mtp85) REVERT: C 439 GLU cc_start: 0.7709 (tt0) cc_final: 0.7007 (tm-30) REVERT: C 488 GLU cc_start: 0.7045 (pm20) cc_final: 0.6271 (tm-30) REVERT: C 508 ASP cc_start: 0.7606 (m-30) cc_final: 0.7356 (m-30) REVERT: C 547 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8296 (mp) REVERT: C 662 LYS cc_start: 0.7445 (tttt) cc_final: 0.6905 (mtmm) REVERT: C 682 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: C 751 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6831 (mp0) REVERT: C 769 MET cc_start: 0.7277 (ttt) cc_final: 0.6447 (tmt) REVERT: C 774 LYS cc_start: 0.7474 (mtmt) cc_final: 0.6628 (tttt) REVERT: C 775 LYS cc_start: 0.8060 (mttt) cc_final: 0.7719 (mttp) REVERT: C 782 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7571 (mtp180) REVERT: C 783 ASP cc_start: 0.8262 (m-30) cc_final: 0.7991 (m-30) REVERT: C 812 LYS cc_start: 0.7982 (mttt) cc_final: 0.7733 (mttm) REVERT: C 966 GLN cc_start: 0.7836 (tt0) cc_final: 0.7625 (tt0) REVERT: C 970 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7047 (mp0) REVERT: C 1001 SER cc_start: 0.7702 (t) cc_final: 0.7254 (m) REVERT: C 1005 SER cc_start: 0.7432 (m) cc_final: 0.7050 (p) REVERT: C 1014 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7477 (mtm-85) REVERT: D 1 MET cc_start: -0.0135 (tpt) cc_final: -0.0910 (tpt) REVERT: D 39 ASN cc_start: 0.8159 (t0) cc_final: 0.7875 (t0) REVERT: D 41 GLU cc_start: 0.7182 (tp30) cc_final: 0.6341 (tm-30) REVERT: D 42 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6588 (tt0) REVERT: D 50 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7154 (mm110) REVERT: D 76 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6749 (pp20) REVERT: D 129 ASN cc_start: 0.7713 (t0) cc_final: 0.7278 (t0) REVERT: D 220 THR cc_start: 0.7611 (p) cc_final: 0.7244 (t) REVERT: D 242 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7121 (tt0) REVERT: D 244 GLU cc_start: 0.7852 (tt0) cc_final: 0.7457 (tt0) REVERT: D 252 ARG cc_start: 0.6766 (mmm-85) cc_final: 0.6344 (mmt180) REVERT: D 254 TYR cc_start: 0.7135 (p90) cc_final: 0.6791 (p90) REVERT: D 293 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7564 (mtt180) REVERT: D 297 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6351 (mm-30) REVERT: D 335 GLU cc_start: 0.8339 (tt0) cc_final: 0.7466 (tm-30) REVERT: D 359 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: D 369 ASP cc_start: 0.7430 (p0) cc_final: 0.7040 (p0) REVERT: D 432 ARG cc_start: 0.7398 (mtm180) cc_final: 0.7053 (mtp85) REVERT: D 439 GLU cc_start: 0.7728 (tt0) cc_final: 0.7046 (tm-30) REVERT: D 443 ARG cc_start: 0.7698 (mtp85) cc_final: 0.7275 (mtp-110) REVERT: D 488 GLU cc_start: 0.7136 (pm20) cc_final: 0.6411 (tm-30) REVERT: D 547 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8270 (mp) REVERT: D 662 LYS cc_start: 0.7373 (tttt) cc_final: 0.6842 (mtmm) REVERT: D 725 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: D 751 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6918 (mp0) REVERT: D 756 ARG cc_start: 0.7354 (ttm110) cc_final: 0.6556 (mtp180) REVERT: D 758 GLN cc_start: 0.7986 (tt0) cc_final: 0.7776 (tt0) REVERT: D 769 MET cc_start: 0.7230 (ttt) cc_final: 0.6345 (tmt) REVERT: D 774 LYS cc_start: 0.7369 (mtmm) cc_final: 0.6670 (tttt) REVERT: D 775 LYS cc_start: 0.8040 (mttt) cc_final: 0.7507 (mmtm) REVERT: D 782 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7543 (mtp180) REVERT: D 925 ASP cc_start: 0.7660 (m-30) cc_final: 0.7310 (t0) REVERT: D 966 GLN cc_start: 0.7777 (tt0) cc_final: 0.7563 (tt0) REVERT: D 970 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7037 (mp0) REVERT: D 1001 SER cc_start: 0.7701 (t) cc_final: 0.7252 (m) REVERT: D 1005 SER cc_start: 0.7453 (m) cc_final: 0.7100 (p) REVERT: D 1014 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7463 (mtm-85) outliers start: 60 outliers final: 25 residues processed: 517 average time/residue: 1.7242 time to fit residues: 1033.4633 Evaluate side-chains 508 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 470 time to evaluate : 3.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 959 ASN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 924 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.8980 chunk 355 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN B 227 HIS B 584 ASN B 726 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 959 ASN D 94 HIS D 584 ASN D 762 GLN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 33856 Z= 0.355 Angle : 0.695 13.914 46192 Z= 0.369 Chirality : 0.048 0.187 4832 Planarity : 0.005 0.040 6100 Dihedral : 5.922 58.952 4484 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % Rotamer: Outliers : 1.88 % Allowed : 9.50 % Favored : 88.61 % 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: 0.18 (0.13), residues: 4088 helix: 0.16 (0.21), residues: 544 sheet: 0.67 (0.14), residues: 1356 loop : -0.17 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 554 HIS 0.008 0.001 HIS A 31 PHE 0.012 0.002 PHE C 275 TYR 0.022 0.002 TYR D 101 ARG 0.005 0.001 ARG B 447 *********************** 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 535 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 469 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 MET cc_start: 0.1456 (mmp) cc_final: 0.1101 (tmm) REVERT: A 41 GLU cc_start: 0.7183 (tp30) cc_final: 0.6415 (tm-30) REVERT: A 42 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6714 (tt0) REVERT: A 48 PRO cc_start: 0.8025 (Cg_exo) cc_final: 0.7780 (Cg_endo) REVERT: A 78 ASP cc_start: 0.7233 (m-30) cc_final: 0.6835 (m-30) REVERT: A 118 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7369 (tp30) REVERT: A 206 MET cc_start: 0.8466 (mtm) cc_final: 0.8255 (mtt) REVERT: A 220 THR cc_start: 0.7628 (OUTLIER) cc_final: 0.7257 (t) REVERT: A 242 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7117 (tt0) REVERT: A 244 GLU cc_start: 0.7732 (tt0) cc_final: 0.7319 (tp30) REVERT: A 246 GLN cc_start: 0.7632 (tt0) cc_final: 0.7243 (mt0) REVERT: A 254 TYR cc_start: 0.7091 (p90) cc_final: 0.6605 (p90) REVERT: A 293 ARG cc_start: 0.7871 (mtt90) cc_final: 0.7582 (mtt180) REVERT: A 297 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6330 (mm-30) REVERT: A 335 GLU cc_start: 0.8377 (tt0) cc_final: 0.7551 (tm-30) REVERT: A 359 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: A 369 ASP cc_start: 0.7439 (p0) cc_final: 0.7166 (p0) REVERT: A 370 GLU cc_start: 0.7597 (tt0) cc_final: 0.7143 (tm-30) REVERT: A 405 ARG cc_start: 0.7864 (mtt180) cc_final: 0.7590 (ttp-110) REVERT: A 432 ARG cc_start: 0.7402 (mtm180) cc_final: 0.7046 (mtp85) REVERT: A 439 GLU cc_start: 0.7748 (tt0) cc_final: 0.7093 (tm-30) REVERT: A 488 GLU cc_start: 0.7134 (pm20) cc_final: 0.6086 (tm-30) REVERT: A 547 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 662 LYS cc_start: 0.7389 (tttt) cc_final: 0.6912 (mtmm) REVERT: A 751 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6753 (pm20) REVERT: A 756 ARG cc_start: 0.7329 (ttm110) cc_final: 0.6464 (mtp180) REVERT: A 761 ARG cc_start: 0.7579 (ttt180) cc_final: 0.7340 (mtp85) REVERT: A 762 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7208 (mp-120) REVERT: A 782 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7450 (mtp180) REVERT: A 966 GLN cc_start: 0.7849 (tt0) cc_final: 0.7637 (tt0) REVERT: A 970 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7056 (mp0) REVERT: A 1001 SER cc_start: 0.7707 (t) cc_final: 0.7245 (m) REVERT: A 1005 SER cc_start: 0.7467 (m) cc_final: 0.7045 (p) REVERT: A 1014 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7531 (mtm-85) REVERT: B 41 GLU cc_start: 0.7211 (tp30) cc_final: 0.6468 (tm-30) REVERT: B 42 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6660 (tt0) REVERT: B 48 PRO cc_start: 0.8047 (Cg_exo) cc_final: 0.7780 (Cg_endo) REVERT: B 129 ASN cc_start: 0.7770 (t0) cc_final: 0.7322 (t0) REVERT: B 220 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7225 (t) REVERT: B 242 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7128 (tt0) REVERT: B 244 GLU cc_start: 0.7774 (tt0) cc_final: 0.7370 (tp30) REVERT: B 246 GLN cc_start: 0.7619 (tt0) cc_final: 0.7238 (mt0) REVERT: B 253 ASP cc_start: 0.7188 (m-30) cc_final: 0.6386 (p0) REVERT: B 254 TYR cc_start: 0.7043 (p90) cc_final: 0.6498 (p90) REVERT: B 293 ARG cc_start: 0.7895 (mtt90) cc_final: 0.7567 (mtt180) REVERT: B 335 GLU cc_start: 0.8342 (tt0) cc_final: 0.7464 (tm-30) REVERT: B 337 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7962 (ttp-110) REVERT: B 339 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: B 369 ASP cc_start: 0.7436 (p0) cc_final: 0.7178 (p0) REVERT: B 370 GLU cc_start: 0.7581 (tt0) cc_final: 0.7137 (tm-30) REVERT: B 432 ARG cc_start: 0.7396 (mtm180) cc_final: 0.7044 (mtp85) REVERT: B 439 GLU cc_start: 0.7754 (tt0) cc_final: 0.7109 (tm-30) REVERT: B 488 GLU cc_start: 0.7140 (pm20) cc_final: 0.6096 (tm-30) REVERT: B 547 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 662 LYS cc_start: 0.7445 (tttt) cc_final: 0.6955 (mtmm) REVERT: B 725 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: B 751 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6856 (mp0) REVERT: B 756 ARG cc_start: 0.7297 (ttm110) cc_final: 0.6893 (ttm170) REVERT: B 761 ARG cc_start: 0.7629 (ttt180) cc_final: 0.7354 (mtp85) REVERT: B 762 GLN cc_start: 0.7417 (mp10) cc_final: 0.7047 (mp10) REVERT: B 774 LYS cc_start: 0.7424 (mtpp) cc_final: 0.6618 (tttt) REVERT: B 782 ARG cc_start: 0.7900 (mtm180) cc_final: 0.7507 (mtp180) REVERT: B 966 GLN cc_start: 0.7809 (tt0) cc_final: 0.7607 (tt0) REVERT: B 970 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7081 (mp0) REVERT: B 1001 SER cc_start: 0.7709 (t) cc_final: 0.7244 (m) REVERT: B 1005 SER cc_start: 0.7441 (m) cc_final: 0.7039 (p) REVERT: B 1014 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7521 (mtm-85) REVERT: C 3 MET cc_start: 0.1517 (mmp) cc_final: 0.1217 (tmm) REVERT: C 41 GLU cc_start: 0.7175 (tp30) cc_final: 0.6384 (tm-30) REVERT: C 42 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6633 (tt0) REVERT: C 50 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7093 (mm110) REVERT: C 129 ASN cc_start: 0.7756 (t0) cc_final: 0.7341 (t0) REVERT: C 206 MET cc_start: 0.8487 (mtm) cc_final: 0.8184 (mtt) REVERT: C 242 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7139 (tt0) REVERT: C 244 GLU cc_start: 0.7797 (tt0) cc_final: 0.7422 (tt0) REVERT: C 246 GLN cc_start: 0.7727 (tt0) cc_final: 0.7336 (mt0) REVERT: C 252 ARG cc_start: 0.6711 (mmm-85) cc_final: 0.6274 (mmt180) REVERT: C 254 TYR cc_start: 0.7019 (p90) cc_final: 0.6634 (p90) REVERT: C 297 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6366 (mm-30) REVERT: C 335 GLU cc_start: 0.8345 (tt0) cc_final: 0.7444 (tm-30) REVERT: C 359 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: C 369 ASP cc_start: 0.7413 (p0) cc_final: 0.7160 (p0) REVERT: C 432 ARG cc_start: 0.7385 (mtm180) cc_final: 0.7034 (mtp85) REVERT: C 439 GLU cc_start: 0.7758 (tt0) cc_final: 0.7053 (tm-30) REVERT: C 488 GLU cc_start: 0.7151 (pm20) cc_final: 0.6360 (tm-30) REVERT: C 508 ASP cc_start: 0.7664 (m-30) cc_final: 0.7406 (m-30) REVERT: C 547 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8268 (mp) REVERT: C 662 LYS cc_start: 0.7452 (tttt) cc_final: 0.6869 (mtmm) REVERT: C 751 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6933 (mp0) REVERT: C 769 MET cc_start: 0.7259 (ttt) cc_final: 0.6350 (tmt) REVERT: C 774 LYS cc_start: 0.7509 (mtmt) cc_final: 0.6640 (tttt) REVERT: C 775 LYS cc_start: 0.8030 (mttt) cc_final: 0.7664 (mttp) REVERT: C 782 ARG cc_start: 0.7968 (mtm180) cc_final: 0.7599 (mtp180) REVERT: C 783 ASP cc_start: 0.8397 (m-30) cc_final: 0.8092 (m-30) REVERT: C 812 LYS cc_start: 0.7981 (mttt) cc_final: 0.7731 (mttm) REVERT: C 966 GLN cc_start: 0.7823 (tt0) cc_final: 0.7609 (tt0) REVERT: C 970 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7055 (mp0) REVERT: C 1001 SER cc_start: 0.7720 (t) cc_final: 0.7254 (m) REVERT: C 1005 SER cc_start: 0.7430 (m) cc_final: 0.7040 (p) REVERT: C 1014 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7527 (mtm-85) REVERT: D 1 MET cc_start: 0.0055 (tpt) cc_final: -0.0264 (ttm) REVERT: D 39 ASN cc_start: 0.8217 (t0) cc_final: 0.7917 (t0) REVERT: D 41 GLU cc_start: 0.7162 (tp30) cc_final: 0.6343 (tm-30) REVERT: D 42 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6633 (tt0) REVERT: D 50 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7100 (mm110) REVERT: D 129 ASN cc_start: 0.7784 (t0) cc_final: 0.7348 (t0) REVERT: D 220 THR cc_start: 0.7608 (p) cc_final: 0.7252 (t) REVERT: D 242 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7071 (tt0) REVERT: D 244 GLU cc_start: 0.7817 (tt0) cc_final: 0.7420 (tt0) REVERT: D 254 TYR cc_start: 0.7133 (p90) cc_final: 0.6711 (p90) REVERT: D 293 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7561 (mtt180) REVERT: D 335 GLU cc_start: 0.8343 (tt0) cc_final: 0.7440 (tm-30) REVERT: D 339 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7294 (tt0) REVERT: D 359 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: D 369 ASP cc_start: 0.7432 (p0) cc_final: 0.7076 (p0) REVERT: D 432 ARG cc_start: 0.7423 (mtm180) cc_final: 0.7042 (mtp85) REVERT: D 439 GLU cc_start: 0.7766 (tt0) cc_final: 0.7086 (tm-30) REVERT: D 488 GLU cc_start: 0.7112 (pm20) cc_final: 0.6869 (pm20) REVERT: D 508 ASP cc_start: 0.7604 (m-30) cc_final: 0.7350 (m-30) REVERT: D 547 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8249 (mp) REVERT: D 662 LYS cc_start: 0.7421 (tttt) cc_final: 0.6805 (mtmm) REVERT: D 725 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: D 751 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6885 (mp0) REVERT: D 756 ARG cc_start: 0.7335 (ttm110) cc_final: 0.6526 (mtp180) REVERT: D 758 GLN cc_start: 0.8017 (tt0) cc_final: 0.7789 (tt0) REVERT: D 769 MET cc_start: 0.7219 (ttt) cc_final: 0.6308 (tmt) REVERT: D 774 LYS cc_start: 0.7338 (mtmm) cc_final: 0.6629 (tttt) REVERT: D 775 LYS cc_start: 0.8025 (mttt) cc_final: 0.7691 (mttp) REVERT: D 782 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7554 (mtp180) REVERT: D 925 ASP cc_start: 0.7755 (m-30) cc_final: 0.7411 (t0) REVERT: D 966 GLN cc_start: 0.7793 (tt0) cc_final: 0.7570 (tt0) REVERT: D 970 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7058 (mp0) REVERT: D 1001 SER cc_start: 0.7713 (t) cc_final: 0.7247 (m) REVERT: D 1005 SER cc_start: 0.7460 (m) cc_final: 0.7091 (p) REVERT: D 1014 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7505 (mtm-85) outliers start: 66 outliers final: 26 residues processed: 510 average time/residue: 1.7390 time to fit residues: 1029.5979 Evaluate side-chains 504 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 464 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 1018 GLN Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 924 SER Chi-restraints excluded: chain D residue 1018 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 224 optimal weight: 20.0000 chunk 288 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 332 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 393 optimal weight: 0.2980 chunk 246 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 784 GLN A 959 ASN A 986 ASN B 584 ASN B 605 ASN B 726 ASN B 784 GLN B 959 ASN B 986 ASN C 647 HIS C 959 ASN D 584 ASN D 647 HIS ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3719 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= 0.194 Angle : 0.574 10.456 46192 Z= 0.301 Chirality : 0.044 0.165 4832 Planarity : 0.004 0.033 6100 Dihedral : 5.438 55.164 4484 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.64 % Favored : 97.26 % Rotamer: Outliers : 1.20 % Allowed : 10.59 % Favored : 88.21 % 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: 0.31 (0.13), residues: 4088 helix: 0.36 (0.21), residues: 560 sheet: 0.76 (0.14), residues: 1336 loop : -0.11 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 554 HIS 0.004 0.001 HIS B 978 PHE 0.010 0.001 PHE B 226 TYR 0.018 0.002 TYR D 101 ARG 0.004 0.000 ARG D 858 *********************** 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 534 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 492 time to evaluate : 4.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 MET cc_start: 0.1457 (mmp) cc_final: 0.1140 (tmm) REVERT: A 41 GLU cc_start: 0.7183 (tp30) cc_final: 0.6404 (tm-30) REVERT: A 42 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6714 (tt0) REVERT: A 48 PRO cc_start: 0.8030 (Cg_exo) cc_final: 0.7782 (Cg_endo) REVERT: A 76 GLU cc_start: 0.7638 (mt-10) cc_final: 0.6797 (pp20) REVERT: A 78 ASP cc_start: 0.7239 (m-30) cc_final: 0.6801 (m-30) REVERT: A 118 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7419 (tp30) REVERT: A 165 ASP cc_start: 0.7434 (t0) cc_final: 0.7151 (t70) REVERT: A 206 MET cc_start: 0.8425 (mtm) cc_final: 0.8090 (mtt) REVERT: A 220 THR cc_start: 0.7591 (p) cc_final: 0.7221 (t) REVERT: A 242 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7102 (tt0) REVERT: A 244 GLU cc_start: 0.7739 (tt0) cc_final: 0.7342 (tp30) REVERT: A 246 GLN cc_start: 0.7624 (tt0) cc_final: 0.7238 (mt0) REVERT: A 254 TYR cc_start: 0.7104 (p90) cc_final: 0.6609 (p90) REVERT: A 293 ARG cc_start: 0.7873 (mtt90) cc_final: 0.7419 (mpt180) REVERT: A 297 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6327 (mm-30) REVERT: A 335 GLU cc_start: 0.8331 (tt0) cc_final: 0.7480 (tm-30) REVERT: A 359 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: A 369 ASP cc_start: 0.7334 (p0) cc_final: 0.6952 (p0) REVERT: A 370 GLU cc_start: 0.7512 (tt0) cc_final: 0.7047 (tm-30) REVERT: A 405 ARG cc_start: 0.7882 (mtt180) cc_final: 0.7656 (ttp-110) REVERT: A 432 ARG cc_start: 0.7259 (mtm180) cc_final: 0.6940 (mtp85) REVERT: A 439 GLU cc_start: 0.7674 (tt0) cc_final: 0.7109 (tm-30) REVERT: A 443 ARG cc_start: 0.7671 (mtp85) cc_final: 0.7254 (mtp-110) REVERT: A 662 LYS cc_start: 0.7365 (tttt) cc_final: 0.6882 (mtmm) REVERT: A 751 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6969 (mp0) REVERT: A 756 ARG cc_start: 0.7281 (ttm110) cc_final: 0.6442 (mtp180) REVERT: A 761 ARG cc_start: 0.7580 (ttt180) cc_final: 0.7306 (mtp85) REVERT: A 762 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7249 (mp-120) REVERT: A 769 MET cc_start: 0.7188 (ttt) cc_final: 0.6296 (tmt) REVERT: A 774 LYS cc_start: 0.7407 (mtpp) cc_final: 0.6610 (tttt) REVERT: A 782 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7465 (mtp180) REVERT: A 966 GLN cc_start: 0.7870 (tt0) cc_final: 0.7647 (tt0) REVERT: A 970 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7036 (mp0) REVERT: A 1001 SER cc_start: 0.7668 (t) cc_final: 0.7292 (m) REVERT: A 1005 SER cc_start: 0.7375 (m) cc_final: 0.6975 (p) REVERT: A 1014 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7475 (mtm-85) REVERT: B 41 GLU cc_start: 0.7178 (tp30) cc_final: 0.6441 (tm-30) REVERT: B 42 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6640 (tt0) REVERT: B 48 PRO cc_start: 0.8031 (Cg_exo) cc_final: 0.7774 (Cg_endo) REVERT: B 129 ASN cc_start: 0.7714 (t0) cc_final: 0.7298 (t0) REVERT: B 165 ASP cc_start: 0.7407 (t0) cc_final: 0.7183 (t70) REVERT: B 220 THR cc_start: 0.7586 (p) cc_final: 0.7196 (t) REVERT: B 242 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7092 (tt0) REVERT: B 244 GLU cc_start: 0.7744 (tt0) cc_final: 0.7450 (tt0) REVERT: B 246 GLN cc_start: 0.7576 (tt0) cc_final: 0.7221 (mt0) REVERT: B 252 ARG cc_start: 0.6662 (mmm-85) cc_final: 0.6048 (mmm160) REVERT: B 254 TYR cc_start: 0.7067 (p90) cc_final: 0.6675 (p90) REVERT: B 293 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7391 (mpt180) REVERT: B 335 GLU cc_start: 0.8336 (tt0) cc_final: 0.7434 (tm-30) REVERT: B 369 ASP cc_start: 0.7352 (p0) cc_final: 0.6989 (p0) REVERT: B 370 GLU cc_start: 0.7485 (tt0) cc_final: 0.7055 (tm-30) REVERT: B 432 ARG cc_start: 0.7253 (mtm180) cc_final: 0.6934 (mtp85) REVERT: B 439 GLU cc_start: 0.7669 (tt0) cc_final: 0.7113 (tm-30) REVERT: B 488 GLU cc_start: 0.7133 (pm20) cc_final: 0.6067 (tm-30) REVERT: B 662 LYS cc_start: 0.7473 (tttt) cc_final: 0.6960 (mtmm) REVERT: B 751 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6857 (mp0) REVERT: B 756 ARG cc_start: 0.7276 (ttm110) cc_final: 0.6846 (ttm170) REVERT: B 761 ARG cc_start: 0.7608 (ttt180) cc_final: 0.7353 (mtp85) REVERT: B 762 GLN cc_start: 0.7376 (mp10) cc_final: 0.7047 (mp10) REVERT: B 769 MET cc_start: 0.7214 (ttt) cc_final: 0.6322 (tmt) REVERT: B 774 LYS cc_start: 0.7370 (mtpp) cc_final: 0.6561 (tttt) REVERT: B 782 ARG cc_start: 0.7849 (mtm180) cc_final: 0.7476 (mtp180) REVERT: B 966 GLN cc_start: 0.7847 (tt0) cc_final: 0.7631 (tt0) REVERT: B 970 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7026 (mp0) REVERT: B 1001 SER cc_start: 0.7672 (t) cc_final: 0.7292 (m) REVERT: B 1005 SER cc_start: 0.7419 (m) cc_final: 0.7026 (p) REVERT: B 1014 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7437 (mtm-85) REVERT: C 3 MET cc_start: 0.1501 (mmp) cc_final: 0.1233 (tmm) REVERT: C 40 SER cc_start: 0.7772 (p) cc_final: 0.7488 (t) REVERT: C 41 GLU cc_start: 0.7104 (tp30) cc_final: 0.6320 (tm-30) REVERT: C 42 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6668 (tt0) REVERT: C 50 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7042 (mm110) REVERT: C 76 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6746 (pp20) REVERT: C 129 ASN cc_start: 0.7695 (t0) cc_final: 0.7297 (t0) REVERT: C 165 ASP cc_start: 0.7432 (t0) cc_final: 0.7215 (t70) REVERT: C 206 MET cc_start: 0.8436 (mtm) cc_final: 0.8154 (mtt) REVERT: C 242 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7100 (tt0) REVERT: C 244 GLU cc_start: 0.7744 (tt0) cc_final: 0.7411 (tt0) REVERT: C 246 GLN cc_start: 0.7669 (tt0) cc_final: 0.7294 (mt0) REVERT: C 252 ARG cc_start: 0.6669 (mmm-85) cc_final: 0.6262 (mmt180) REVERT: C 254 TYR cc_start: 0.7030 (p90) cc_final: 0.6667 (p90) REVERT: C 297 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6276 (mm-30) REVERT: C 335 GLU cc_start: 0.8340 (tt0) cc_final: 0.7436 (tm-30) REVERT: C 369 ASP cc_start: 0.7329 (p0) cc_final: 0.6965 (p0) REVERT: C 432 ARG cc_start: 0.7257 (mtm180) cc_final: 0.6938 (mtp85) REVERT: C 439 GLU cc_start: 0.7679 (tt0) cc_final: 0.7010 (tm-30) REVERT: C 508 ASP cc_start: 0.7682 (m-30) cc_final: 0.7422 (m-30) REVERT: C 584 ASN cc_start: 0.6788 (m110) cc_final: 0.6019 (m-40) REVERT: C 662 LYS cc_start: 0.7447 (tttt) cc_final: 0.6881 (mtmm) REVERT: C 682 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6810 (tp30) REVERT: C 751 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7099 (mp0) REVERT: C 758 GLN cc_start: 0.7948 (tt0) cc_final: 0.7731 (tt0) REVERT: C 769 MET cc_start: 0.7189 (ttt) cc_final: 0.6326 (tmt) REVERT: C 774 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.6600 (tttt) REVERT: C 775 LYS cc_start: 0.8044 (mttt) cc_final: 0.7714 (mttp) REVERT: C 782 ARG cc_start: 0.7904 (mtm180) cc_final: 0.7562 (mtp180) REVERT: C 783 ASP cc_start: 0.8289 (m-30) cc_final: 0.8010 (m-30) REVERT: C 812 LYS cc_start: 0.7939 (mttt) cc_final: 0.7695 (mttm) REVERT: C 966 GLN cc_start: 0.7847 (tt0) cc_final: 0.7624 (tt0) REVERT: C 970 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7015 (mp0) REVERT: C 1001 SER cc_start: 0.7672 (t) cc_final: 0.7292 (m) REVERT: C 1005 SER cc_start: 0.7408 (m) cc_final: 0.7027 (p) REVERT: C 1014 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7503 (mtm-85) REVERT: D 1 MET cc_start: 0.0307 (tpt) cc_final: -0.0074 (ttm) REVERT: D 39 ASN cc_start: 0.8105 (t0) cc_final: 0.7891 (t0) REVERT: D 41 GLU cc_start: 0.7148 (tp30) cc_final: 0.6377 (tm-30) REVERT: D 42 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6689 (tt0) REVERT: D 50 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7011 (mm110) REVERT: D 129 ASN cc_start: 0.7701 (t0) cc_final: 0.7289 (t0) REVERT: D 220 THR cc_start: 0.7606 (p) cc_final: 0.7226 (t) REVERT: D 242 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7059 (tt0) REVERT: D 244 GLU cc_start: 0.7751 (tt0) cc_final: 0.7378 (tt0) REVERT: D 254 TYR cc_start: 0.7168 (p90) cc_final: 0.6751 (p90) REVERT: D 293 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7413 (mpt180) REVERT: D 335 GLU cc_start: 0.8334 (tt0) cc_final: 0.7445 (tm-30) REVERT: D 339 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7225 (tt0) REVERT: D 359 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: D 369 ASP cc_start: 0.7359 (p0) cc_final: 0.6978 (p0) REVERT: D 432 ARG cc_start: 0.7267 (mtm180) cc_final: 0.6936 (mtp85) REVERT: D 439 GLU cc_start: 0.7718 (tt0) cc_final: 0.7097 (tm-30) REVERT: D 508 ASP cc_start: 0.7604 (m-30) cc_final: 0.7348 (m-30) REVERT: D 547 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8321 (mp) REVERT: D 662 LYS cc_start: 0.7414 (tttt) cc_final: 0.6821 (mtmm) REVERT: D 751 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6915 (mp0) REVERT: D 756 ARG cc_start: 0.7319 (ttm110) cc_final: 0.6502 (mtp180) REVERT: D 769 MET cc_start: 0.7127 (ttt) cc_final: 0.6280 (tmt) REVERT: D 774 LYS cc_start: 0.7266 (mtmm) cc_final: 0.6585 (tttt) REVERT: D 775 LYS cc_start: 0.8046 (mttt) cc_final: 0.7721 (mttp) REVERT: D 782 ARG cc_start: 0.7880 (mtm180) cc_final: 0.7526 (mtp180) REVERT: D 925 ASP cc_start: 0.7714 (m-30) cc_final: 0.7375 (t0) REVERT: D 966 GLN cc_start: 0.7848 (tt0) cc_final: 0.7619 (tt0) REVERT: D 970 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7020 (mp0) REVERT: D 1001 SER cc_start: 0.7668 (t) cc_final: 0.7289 (m) REVERT: D 1005 SER cc_start: 0.7415 (m) cc_final: 0.7040 (p) REVERT: D 1014 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7451 (mtm-85) outliers start: 42 outliers final: 18 residues processed: 521 average time/residue: 1.7396 time to fit residues: 1051.2740 Evaluate side-chains 502 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 479 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 774 LYS Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 633 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 234 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 0.0870 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 784 GLN A 959 ASN A 986 ASN B 584 ASN B 726 ASN B 784 GLN B 959 ASN B 986 ASN C 762 GLN C 959 ASN D 584 ASN ** 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: 0.7952 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 33856 Z= 0.193 Angle : 0.572 11.023 46192 Z= 0.299 Chirality : 0.044 0.161 4832 Planarity : 0.004 0.032 6100 Dihedral : 5.329 51.351 4484 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.79 % Favored : 97.11 % Rotamer: Outliers : 1.14 % Allowed : 10.99 % Favored : 87.87 % 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: 0.36 (0.13), residues: 4088 helix: 0.22 (0.21), residues: 584 sheet: 0.82 (0.14), residues: 1336 loop : -0.04 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 554 HIS 0.005 0.001 HIS B 978 PHE 0.009 0.001 PHE B 226 TYR 0.019 0.002 TYR A 101 ARG 0.004 0.000 ARG C 15 *********************** 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 527 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 487 time to evaluate : 3.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 MET cc_start: 0.1431 (mmp) cc_final: 0.1145 (tmm) REVERT: A 41 GLU cc_start: 0.7195 (tp30) cc_final: 0.6425 (tm-30) REVERT: A 42 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6720 (tt0) REVERT: A 48 PRO cc_start: 0.8038 (Cg_exo) cc_final: 0.7790 (Cg_endo) REVERT: A 76 GLU cc_start: 0.7630 (mt-10) cc_final: 0.6815 (pp20) REVERT: A 78 ASP cc_start: 0.7223 (m-30) cc_final: 0.6811 (m-30) REVERT: A 118 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7417 (tp30) REVERT: A 165 ASP cc_start: 0.7405 (t0) cc_final: 0.7166 (t70) REVERT: A 220 THR cc_start: 0.7596 (p) cc_final: 0.7217 (t) REVERT: A 242 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7097 (tt0) REVERT: A 244 GLU cc_start: 0.7747 (tt0) cc_final: 0.7360 (tp30) REVERT: A 246 GLN cc_start: 0.7609 (tt0) cc_final: 0.7195 (mt0) REVERT: A 254 TYR cc_start: 0.7116 (p90) cc_final: 0.6604 (p90) REVERT: A 293 ARG cc_start: 0.7879 (mtt90) cc_final: 0.7426 (mpt180) REVERT: A 297 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6311 (mm-30) REVERT: A 335 GLU cc_start: 0.8332 (tt0) cc_final: 0.7472 (tm-30) REVERT: A 359 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: A 369 ASP cc_start: 0.7312 (p0) cc_final: 0.7009 (p0) REVERT: A 370 GLU cc_start: 0.7505 (tt0) cc_final: 0.7050 (tm-30) REVERT: A 432 ARG cc_start: 0.7254 (mtm180) cc_final: 0.6942 (mtp85) REVERT: A 439 GLU cc_start: 0.7646 (tt0) cc_final: 0.7104 (tm-30) REVERT: A 662 LYS cc_start: 0.7360 (tttt) cc_final: 0.6884 (mtmm) REVERT: A 751 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6967 (mp0) REVERT: A 756 ARG cc_start: 0.7264 (ttm110) cc_final: 0.6414 (mtp180) REVERT: A 761 ARG cc_start: 0.7557 (ttt180) cc_final: 0.7293 (mtp85) REVERT: A 762 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7213 (mp-120) REVERT: A 769 MET cc_start: 0.7188 (ttt) cc_final: 0.6301 (tmt) REVERT: A 774 LYS cc_start: 0.7411 (mtpp) cc_final: 0.6606 (tttt) REVERT: A 782 ARG cc_start: 0.7871 (mtm180) cc_final: 0.7458 (mtp180) REVERT: A 966 GLN cc_start: 0.7863 (tt0) cc_final: 0.7642 (tt0) REVERT: A 970 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7005 (mp0) REVERT: A 1001 SER cc_start: 0.7666 (t) cc_final: 0.7313 (m) REVERT: A 1005 SER cc_start: 0.7407 (m) cc_final: 0.6987 (p) REVERT: A 1014 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7477 (mtm-85) REVERT: B 1 MET cc_start: 0.0845 (ttp) cc_final: 0.0634 (ttp) REVERT: B 41 GLU cc_start: 0.7174 (tp30) cc_final: 0.6430 (tm-30) REVERT: B 42 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6696 (tt0) REVERT: B 48 PRO cc_start: 0.8040 (Cg_exo) cc_final: 0.7795 (Cg_endo) REVERT: B 76 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6835 (pp20) REVERT: B 129 ASN cc_start: 0.7731 (t0) cc_final: 0.7322 (t0) REVERT: B 165 ASP cc_start: 0.7394 (t0) cc_final: 0.7091 (t70) REVERT: B 220 THR cc_start: 0.7584 (p) cc_final: 0.7188 (t) REVERT: B 242 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7069 (tt0) REVERT: B 244 GLU cc_start: 0.7750 (tt0) cc_final: 0.7457 (tt0) REVERT: B 246 GLN cc_start: 0.7576 (tt0) cc_final: 0.7224 (mt0) REVERT: B 252 ARG cc_start: 0.6648 (mmm-85) cc_final: 0.6040 (mmm160) REVERT: B 254 TYR cc_start: 0.7051 (p90) cc_final: 0.6713 (p90) REVERT: B 293 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7401 (mpt180) REVERT: B 297 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6295 (mm-30) REVERT: B 335 GLU cc_start: 0.8323 (tt0) cc_final: 0.7436 (tm-30) REVERT: B 339 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: B 369 ASP cc_start: 0.7330 (p0) cc_final: 0.6955 (p0) REVERT: B 370 GLU cc_start: 0.7448 (tt0) cc_final: 0.7025 (tm-30) REVERT: B 432 ARG cc_start: 0.7245 (mtm180) cc_final: 0.6937 (mtp85) REVERT: B 439 GLU cc_start: 0.7621 (tt0) cc_final: 0.7094 (tm-30) REVERT: B 443 ARG cc_start: 0.7672 (mtp85) cc_final: 0.7251 (mtp-110) REVERT: B 488 GLU cc_start: 0.7096 (pm20) cc_final: 0.6069 (tm-30) REVERT: B 662 LYS cc_start: 0.7473 (tttt) cc_final: 0.6929 (mtmm) REVERT: B 751 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6867 (mp0) REVERT: B 756 ARG cc_start: 0.7284 (ttm110) cc_final: 0.6858 (ttm170) REVERT: B 761 ARG cc_start: 0.7596 (ttt180) cc_final: 0.7350 (mtp85) REVERT: B 762 GLN cc_start: 0.7286 (mp10) cc_final: 0.6967 (mp10) REVERT: B 769 MET cc_start: 0.7211 (ttt) cc_final: 0.6319 (tmt) REVERT: B 774 LYS cc_start: 0.7414 (mtpp) cc_final: 0.6613 (tttt) REVERT: B 782 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7458 (mtp180) REVERT: B 966 GLN cc_start: 0.7855 (tt0) cc_final: 0.7637 (tt0) REVERT: B 970 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7029 (mp0) REVERT: B 1001 SER cc_start: 0.7667 (t) cc_final: 0.7313 (m) REVERT: B 1005 SER cc_start: 0.7423 (m) cc_final: 0.7010 (p) REVERT: B 1014 ARG cc_start: 0.8133 (mtp85) cc_final: 0.7447 (mtm-85) REVERT: C 3 MET cc_start: 0.1589 (mmp) cc_final: 0.1343 (tmm) REVERT: C 40 SER cc_start: 0.7754 (p) cc_final: 0.7514 (t) REVERT: C 41 GLU cc_start: 0.7124 (tp30) cc_final: 0.6343 (tm-30) REVERT: C 42 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6723 (tt0) REVERT: C 50 GLN cc_start: 0.7549 (mm-40) cc_final: 0.6986 (mm110) REVERT: C 76 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6757 (pp20) REVERT: C 129 ASN cc_start: 0.7691 (t0) cc_final: 0.7296 (t0) REVERT: C 165 ASP cc_start: 0.7413 (t0) cc_final: 0.7163 (t70) REVERT: C 242 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7038 (tt0) REVERT: C 244 GLU cc_start: 0.7744 (tt0) cc_final: 0.7410 (tt0) REVERT: C 246 GLN cc_start: 0.7662 (tt0) cc_final: 0.7289 (mt0) REVERT: C 252 ARG cc_start: 0.6656 (mmm-85) cc_final: 0.6258 (mmt180) REVERT: C 254 TYR cc_start: 0.7053 (p90) cc_final: 0.6694 (p90) REVERT: C 297 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6282 (mm-30) REVERT: C 335 GLU cc_start: 0.8339 (tt0) cc_final: 0.7438 (tm-30) REVERT: C 369 ASP cc_start: 0.7332 (p0) cc_final: 0.6936 (p0) REVERT: C 432 ARG cc_start: 0.7241 (mtm180) cc_final: 0.6929 (mtp85) REVERT: C 439 GLU cc_start: 0.7683 (tt0) cc_final: 0.7036 (tm-30) REVERT: C 508 ASP cc_start: 0.7695 (m-30) cc_final: 0.7433 (m-30) REVERT: C 547 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8301 (mp) REVERT: C 584 ASN cc_start: 0.6807 (m110) cc_final: 0.6023 (m-40) REVERT: C 662 LYS cc_start: 0.7456 (tttt) cc_final: 0.6899 (mtmm) REVERT: C 682 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6834 (tp30) REVERT: C 747 ASP cc_start: 0.6831 (p0) cc_final: 0.6544 (p0) REVERT: C 751 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7087 (mp0) REVERT: C 758 GLN cc_start: 0.7954 (tt0) cc_final: 0.7653 (tt0) REVERT: C 769 MET cc_start: 0.7189 (ttt) cc_final: 0.6324 (tmt) REVERT: C 774 LYS cc_start: 0.7469 (mtmt) cc_final: 0.6627 (tttt) REVERT: C 775 LYS cc_start: 0.8051 (mttt) cc_final: 0.7722 (mttp) REVERT: C 782 ARG cc_start: 0.7894 (mtm180) cc_final: 0.7548 (mtp180) REVERT: C 783 ASP cc_start: 0.8216 (m-30) cc_final: 0.7967 (m-30) REVERT: C 812 LYS cc_start: 0.7947 (mttt) cc_final: 0.7704 (mttm) REVERT: C 966 GLN cc_start: 0.7842 (tt0) cc_final: 0.7621 (tt0) REVERT: C 970 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7039 (mp0) REVERT: C 1001 SER cc_start: 0.7667 (t) cc_final: 0.7314 (m) REVERT: C 1005 SER cc_start: 0.7402 (m) cc_final: 0.7018 (p) REVERT: C 1014 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7458 (mtm-85) REVERT: D 1 MET cc_start: 0.0404 (tpt) cc_final: 0.0060 (pmm) REVERT: D 39 ASN cc_start: 0.8079 (t0) cc_final: 0.7860 (t0) REVERT: D 41 GLU cc_start: 0.7120 (tp30) cc_final: 0.6350 (tm-30) REVERT: D 42 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6649 (tt0) REVERT: D 50 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7017 (mm110) REVERT: D 76 GLU cc_start: 0.7627 (mt-10) cc_final: 0.6877 (pp20) REVERT: D 129 ASN cc_start: 0.7714 (t0) cc_final: 0.7309 (t0) REVERT: D 220 THR cc_start: 0.7596 (p) cc_final: 0.7204 (t) REVERT: D 242 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7053 (tt0) REVERT: D 244 GLU cc_start: 0.7754 (tt0) cc_final: 0.7376 (tt0) REVERT: D 254 TYR cc_start: 0.7203 (p90) cc_final: 0.6784 (p90) REVERT: D 293 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7416 (mpt180) REVERT: D 335 GLU cc_start: 0.8327 (tt0) cc_final: 0.7428 (tm-30) REVERT: D 339 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: D 359 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7196 (tt0) REVERT: D 369 ASP cc_start: 0.7313 (p0) cc_final: 0.6942 (p0) REVERT: D 432 ARG cc_start: 0.7265 (mtm180) cc_final: 0.6931 (mtp85) REVERT: D 439 GLU cc_start: 0.7690 (tt0) cc_final: 0.7086 (tm-30) REVERT: D 508 ASP cc_start: 0.7629 (m-30) cc_final: 0.7126 (m-30) REVERT: D 547 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8281 (mp) REVERT: D 662 LYS cc_start: 0.7424 (tttt) cc_final: 0.6830 (mtmm) REVERT: D 751 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6840 (mp0) REVERT: D 756 ARG cc_start: 0.7316 (ttm110) cc_final: 0.6464 (mtp180) REVERT: D 769 MET cc_start: 0.7133 (ttt) cc_final: 0.6345 (tmt) REVERT: D 774 LYS cc_start: 0.7271 (mtmm) cc_final: 0.6612 (tttt) REVERT: D 775 LYS cc_start: 0.8012 (mttt) cc_final: 0.7690 (mttp) REVERT: D 782 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7535 (mtp180) REVERT: D 925 ASP cc_start: 0.7728 (m-30) cc_final: 0.7389 (t0) REVERT: D 966 GLN cc_start: 0.7848 (tt0) cc_final: 0.7620 (tt0) REVERT: D 970 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7008 (mp0) REVERT: D 1001 SER cc_start: 0.7664 (t) cc_final: 0.7312 (m) REVERT: D 1005 SER cc_start: 0.7405 (m) cc_final: 0.7030 (p) REVERT: D 1014 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7428 (mtm-85) outliers start: 40 outliers final: 27 residues processed: 517 average time/residue: 1.7577 time to fit residues: 1058.2200 Evaluate side-chains 516 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 483 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 605 ASN Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 924 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.0470 chunk 376 optimal weight: 9.9990 chunk 343 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 287 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 331 optimal weight: 7.9990 chunk 346 optimal weight: 4.9990 chunk 365 optimal weight: 1.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 784 GLN A 959 ASN A 986 ASN B 584 ASN B 726 ASN B 784 GLN B 959 ASN B 986 ASN C 762 GLN C 959 ASN D 584 ASN ** 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: 0.7963 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 33856 Z= 0.230 Angle : 0.597 11.972 46192 Z= 0.314 Chirality : 0.045 0.165 4832 Planarity : 0.004 0.032 6100 Dihedral : 5.412 46.418 4484 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.79 % Favored : 97.19 % Rotamer: Outliers : 1.34 % Allowed : 11.10 % Favored : 87.56 % 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: 0.38 (0.13), residues: 4088 helix: 0.43 (0.21), residues: 560 sheet: 0.82 (0.14), residues: 1336 loop : -0.07 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 554 HIS 0.005 0.001 HIS B 978 PHE 0.009 0.001 PHE C 275 TYR 0.019 0.002 TYR A 101 ARG 0.005 0.000 ARG C 858 *********************** 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 525 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 478 time to evaluate : 4.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 MET cc_start: 0.1389 (mmp) cc_final: 0.1121 (tmm) REVERT: A 41 GLU cc_start: 0.7167 (tp30) cc_final: 0.6399 (tm-30) REVERT: A 42 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6725 (tt0) REVERT: A 48 PRO cc_start: 0.8051 (Cg_exo) cc_final: 0.7802 (Cg_endo) REVERT: A 78 ASP cc_start: 0.7223 (m-30) cc_final: 0.6819 (m-30) REVERT: A 118 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7329 (tp30) REVERT: A 220 THR cc_start: 0.7611 (p) cc_final: 0.7231 (t) REVERT: A 242 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7110 (tt0) REVERT: A 244 GLU cc_start: 0.7761 (tt0) cc_final: 0.7375 (tp30) REVERT: A 246 GLN cc_start: 0.7623 (tt0) cc_final: 0.7196 (mt0) REVERT: A 254 TYR cc_start: 0.7179 (p90) cc_final: 0.6665 (p90) REVERT: A 293 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7414 (mpt180) REVERT: A 297 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6339 (mm-30) REVERT: A 335 GLU cc_start: 0.8362 (tt0) cc_final: 0.7547 (tm-30) REVERT: A 359 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: A 369 ASP cc_start: 0.7363 (p0) cc_final: 0.7064 (p0) REVERT: A 370 GLU cc_start: 0.7512 (tt0) cc_final: 0.7065 (tm-30) REVERT: A 432 ARG cc_start: 0.7266 (mtm180) cc_final: 0.6943 (mtp85) REVERT: A 439 GLU cc_start: 0.7676 (tt0) cc_final: 0.7088 (tm-30) REVERT: A 547 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8330 (mp) REVERT: A 662 LYS cc_start: 0.7362 (tttt) cc_final: 0.6880 (mtmm) REVERT: A 751 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6942 (mp0) REVERT: A 756 ARG cc_start: 0.7280 (ttm110) cc_final: 0.6765 (ttm170) REVERT: A 761 ARG cc_start: 0.7568 (ttt180) cc_final: 0.7284 (mtp85) REVERT: A 762 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7139 (mp-120) REVERT: A 774 LYS cc_start: 0.7440 (mtpp) cc_final: 0.6634 (tttt) REVERT: A 782 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7450 (mtp180) REVERT: A 966 GLN cc_start: 0.7836 (tt0) cc_final: 0.7616 (tt0) REVERT: A 970 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7008 (mp0) REVERT: A 1001 SER cc_start: 0.7673 (t) cc_final: 0.7325 (m) REVERT: A 1005 SER cc_start: 0.7404 (m) cc_final: 0.6966 (p) REVERT: A 1014 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7513 (mtm-85) REVERT: B 41 GLU cc_start: 0.7183 (tp30) cc_final: 0.6431 (tm-30) REVERT: B 42 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6708 (tt0) REVERT: B 48 PRO cc_start: 0.8056 (Cg_exo) cc_final: 0.7807 (Cg_endo) REVERT: B 129 ASN cc_start: 0.7711 (t0) cc_final: 0.7300 (t0) REVERT: B 165 ASP cc_start: 0.7482 (t0) cc_final: 0.7239 (t70) REVERT: B 220 THR cc_start: 0.7599 (OUTLIER) cc_final: 0.7205 (t) REVERT: B 242 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7087 (tt0) REVERT: B 244 GLU cc_start: 0.7751 (tt0) cc_final: 0.7448 (tt0) REVERT: B 246 GLN cc_start: 0.7621 (tt0) cc_final: 0.7221 (mt0) REVERT: B 252 ARG cc_start: 0.6670 (mmm-85) cc_final: 0.6034 (mmm160) REVERT: B 254 TYR cc_start: 0.7114 (p90) cc_final: 0.6762 (p90) REVERT: B 293 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7404 (mpt180) REVERT: B 297 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6326 (mm-30) REVERT: B 335 GLU cc_start: 0.8329 (tt0) cc_final: 0.8088 (tt0) REVERT: B 339 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: B 370 GLU cc_start: 0.7455 (tt0) cc_final: 0.7043 (tm-30) REVERT: B 432 ARG cc_start: 0.7265 (mtm180) cc_final: 0.6942 (mtp85) REVERT: B 439 GLU cc_start: 0.7694 (tt0) cc_final: 0.7093 (tm-30) REVERT: B 488 GLU cc_start: 0.7135 (pm20) cc_final: 0.6218 (tm-30) REVERT: B 547 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 662 LYS cc_start: 0.7468 (tttt) cc_final: 0.6912 (mtmm) REVERT: B 751 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6798 (mp0) REVERT: B 756 ARG cc_start: 0.7298 (ttm110) cc_final: 0.6857 (ttm170) REVERT: B 762 GLN cc_start: 0.7303 (mp10) cc_final: 0.6980 (mp10) REVERT: B 769 MET cc_start: 0.7217 (ttt) cc_final: 0.6324 (tmt) REVERT: B 774 LYS cc_start: 0.7430 (mtpp) cc_final: 0.6627 (tttt) REVERT: B 782 ARG cc_start: 0.7856 (mtm180) cc_final: 0.7470 (mtp180) REVERT: B 966 GLN cc_start: 0.7823 (tt0) cc_final: 0.7612 (tt0) REVERT: B 970 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7041 (mp0) REVERT: B 1001 SER cc_start: 0.7681 (t) cc_final: 0.7327 (m) REVERT: B 1005 SER cc_start: 0.7424 (m) cc_final: 0.6999 (p) REVERT: B 1014 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7471 (mtm-85) REVERT: C 3 MET cc_start: 0.1552 (mmp) cc_final: 0.1298 (tmm) REVERT: C 40 SER cc_start: 0.7737 (p) cc_final: 0.7494 (t) REVERT: C 41 GLU cc_start: 0.7163 (tp30) cc_final: 0.6356 (tm-30) REVERT: C 42 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6684 (tt0) REVERT: C 50 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7089 (mm110) REVERT: C 76 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6759 (pp20) REVERT: C 129 ASN cc_start: 0.7718 (t0) cc_final: 0.7315 (t0) REVERT: C 165 ASP cc_start: 0.7464 (t0) cc_final: 0.7211 (t70) REVERT: C 242 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7083 (tt0) REVERT: C 244 GLU cc_start: 0.7754 (tt0) cc_final: 0.7395 (tt0) REVERT: C 246 GLN cc_start: 0.7702 (tt0) cc_final: 0.7326 (mt0) REVERT: C 252 ARG cc_start: 0.6632 (mmm-85) cc_final: 0.6241 (mmt180) REVERT: C 254 TYR cc_start: 0.7042 (p90) cc_final: 0.6727 (p90) REVERT: C 297 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6285 (mm-30) REVERT: C 335 GLU cc_start: 0.8339 (tt0) cc_final: 0.7438 (tm-30) REVERT: C 359 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7183 (tt0) REVERT: C 369 ASP cc_start: 0.7339 (p0) cc_final: 0.7031 (p0) REVERT: C 370 GLU cc_start: 0.7563 (tt0) cc_final: 0.7120 (tm-30) REVERT: C 432 ARG cc_start: 0.7275 (mtm180) cc_final: 0.6940 (mtp85) REVERT: C 439 GLU cc_start: 0.7703 (tt0) cc_final: 0.7000 (tm-30) REVERT: C 508 ASP cc_start: 0.7687 (m-30) cc_final: 0.7425 (m-30) REVERT: C 547 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8292 (mp) REVERT: C 584 ASN cc_start: 0.6816 (m110) cc_final: 0.6020 (m-40) REVERT: C 662 LYS cc_start: 0.7434 (tttt) cc_final: 0.6869 (mtmm) REVERT: C 682 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6836 (tp30) REVERT: C 747 ASP cc_start: 0.6925 (p0) cc_final: 0.6632 (p0) REVERT: C 751 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6959 (mp0) REVERT: C 769 MET cc_start: 0.7207 (ttt) cc_final: 0.6341 (tmt) REVERT: C 774 LYS cc_start: 0.7507 (mtmt) cc_final: 0.6649 (tttt) REVERT: C 775 LYS cc_start: 0.8046 (mttt) cc_final: 0.7670 (mttp) REVERT: C 782 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7556 (mtp180) REVERT: C 783 ASP cc_start: 0.8292 (m-30) cc_final: 0.8031 (m-30) REVERT: C 812 LYS cc_start: 0.7953 (mttt) cc_final: 0.7706 (mttm) REVERT: C 966 GLN cc_start: 0.7847 (tt0) cc_final: 0.7629 (tt0) REVERT: C 970 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7032 (mp0) REVERT: C 1001 SER cc_start: 0.7675 (t) cc_final: 0.7326 (m) REVERT: C 1005 SER cc_start: 0.7429 (m) cc_final: 0.7015 (p) REVERT: C 1014 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7518 (mtm-85) REVERT: D 1 MET cc_start: 0.0399 (tpt) cc_final: 0.0035 (ptp) REVERT: D 39 ASN cc_start: 0.8093 (t0) cc_final: 0.7876 (t0) REVERT: D 41 GLU cc_start: 0.7128 (tp30) cc_final: 0.6358 (tm-30) REVERT: D 42 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6721 (tt0) REVERT: D 50 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7013 (mm110) REVERT: D 76 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6837 (pp20) REVERT: D 129 ASN cc_start: 0.7715 (t0) cc_final: 0.7298 (t0) REVERT: D 220 THR cc_start: 0.7615 (p) cc_final: 0.7233 (t) REVERT: D 242 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7067 (tt0) REVERT: D 244 GLU cc_start: 0.7768 (tt0) cc_final: 0.7388 (tt0) REVERT: D 254 TYR cc_start: 0.7144 (p90) cc_final: 0.6715 (p90) REVERT: D 293 ARG cc_start: 0.7916 (mtt90) cc_final: 0.7414 (mpt180) REVERT: D 297 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6305 (mm-30) REVERT: D 335 GLU cc_start: 0.8332 (tt0) cc_final: 0.7432 (tm-30) REVERT: D 359 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: D 369 ASP cc_start: 0.7284 (p0) cc_final: 0.6942 (p0) REVERT: D 432 ARG cc_start: 0.7280 (mtm180) cc_final: 0.6938 (mtp85) REVERT: D 439 GLU cc_start: 0.7722 (tt0) cc_final: 0.7051 (tm-30) REVERT: D 508 ASP cc_start: 0.7626 (m-30) cc_final: 0.7132 (m-30) REVERT: D 547 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8258 (mp) REVERT: D 662 LYS cc_start: 0.7439 (tttt) cc_final: 0.6831 (mtmm) REVERT: D 751 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6960 (mp0) REVERT: D 756 ARG cc_start: 0.7322 (ttm110) cc_final: 0.6629 (mtp180) REVERT: D 769 MET cc_start: 0.7160 (ttt) cc_final: 0.6368 (tmt) REVERT: D 774 LYS cc_start: 0.7262 (mtmm) cc_final: 0.6590 (tttt) REVERT: D 775 LYS cc_start: 0.8007 (mttt) cc_final: 0.7644 (mttp) REVERT: D 782 ARG cc_start: 0.7887 (mtm180) cc_final: 0.7523 (mtp180) REVERT: D 925 ASP cc_start: 0.7736 (m-30) cc_final: 0.7385 (t0) REVERT: D 966 GLN cc_start: 0.7850 (tt0) cc_final: 0.7631 (tt0) REVERT: D 970 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7011 (mp0) REVERT: D 1001 SER cc_start: 0.7671 (t) cc_final: 0.7328 (m) REVERT: D 1005 SER cc_start: 0.7422 (m) cc_final: 0.7025 (p) REVERT: D 1014 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7515 (mtm-85) outliers start: 47 outliers final: 29 residues processed: 514 average time/residue: 1.6991 time to fit residues: 1015.4181 Evaluate side-chains 510 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 472 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 924 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 8.9990 chunk 387 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 269 optimal weight: 8.9990 chunk 406 optimal weight: 10.0000 chunk 374 optimal weight: 9.9990 chunk 323 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 250 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 647 HIS B 584 ASN B 647 HIS B 726 ASN B 978 HIS C 762 GLN 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: 0.7994 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 : 0.007 0.125 33856 Z= 0.443 Angle : 0.745 12.486 46192 Z= 0.396 Chirality : 0.051 0.194 4832 Planarity : 0.006 0.045 6100 Dihedral : 5.917 41.241 4484 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.31 % Allowed : 11.30 % Favored : 87.39 % 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: 0.28 (0.13), residues: 4088 helix: 0.24 (0.22), residues: 540 sheet: 0.79 (0.14), residues: 1352 loop : -0.14 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 554 HIS 0.009 0.002 HIS A 31 PHE 0.016 0.002 PHE C 275 TYR 0.023 0.003 TYR A 101 ARG 0.006 0.001 ARG A 447 ********************** 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 508 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 462 time to evaluate : 3.814 Fit side-chains revert: symmetry clash REVERT: A 3 MET cc_start: 0.1426 (mmp) cc_final: 0.1131 (tmm) REVERT: A 41 GLU cc_start: 0.7143 (tp30) cc_final: 0.6404 (tm-30) REVERT: A 42 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6723 (tt0) REVERT: A 78 ASP cc_start: 0.7244 (m-30) cc_final: 0.6840 (m-30) REVERT: A 118 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7370 (tp30) REVERT: A 220 THR cc_start: 0.7610 (p) cc_final: 0.7252 (t) REVERT: A 242 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7129 (tt0) REVERT: A 244 GLU cc_start: 0.7761 (tt0) cc_final: 0.7396 (tp30) REVERT: A 246 GLN cc_start: 0.7671 (tt0) cc_final: 0.7295 (mt0) REVERT: A 252 ARG cc_start: 0.6652 (mmm-85) cc_final: 0.6057 (mmm160) REVERT: A 254 TYR cc_start: 0.7147 (p90) cc_final: 0.6854 (p90) REVERT: A 293 ARG cc_start: 0.7893 (mtt90) cc_final: 0.7574 (mtt180) REVERT: A 297 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6378 (mm-30) REVERT: A 359 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: A 370 GLU cc_start: 0.7595 (tt0) cc_final: 0.7163 (tm-30) REVERT: A 432 ARG cc_start: 0.7394 (mtm180) cc_final: 0.7017 (mtp85) REVERT: A 439 GLU cc_start: 0.7842 (tt0) cc_final: 0.7190 (tm-30) REVERT: A 508 ASP cc_start: 0.7656 (m-30) cc_final: 0.7124 (m-30) REVERT: A 547 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8288 (mp) REVERT: A 662 LYS cc_start: 0.7411 (tttt) cc_final: 0.6856 (mtmm) REVERT: A 751 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6726 (pm20) REVERT: A 756 ARG cc_start: 0.7285 (ttm110) cc_final: 0.6877 (ttm170) REVERT: A 761 ARG cc_start: 0.7556 (ttt180) cc_final: 0.7280 (mtp85) REVERT: A 762 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7135 (mp-120) REVERT: A 782 ARG cc_start: 0.7900 (mtm180) cc_final: 0.7464 (mtp180) REVERT: A 966 GLN cc_start: 0.7826 (tt0) cc_final: 0.7620 (tt0) REVERT: A 970 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7068 (mp0) REVERT: A 1001 SER cc_start: 0.7700 (t) cc_final: 0.7254 (m) REVERT: A 1005 SER cc_start: 0.7515 (m) cc_final: 0.7071 (p) REVERT: A 1014 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7538 (mtm-85) REVERT: B 41 GLU cc_start: 0.7158 (tp30) cc_final: 0.6434 (tm-30) REVERT: B 42 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6728 (tt0) REVERT: B 129 ASN cc_start: 0.7792 (t0) cc_final: 0.7351 (t0) REVERT: B 220 THR cc_start: 0.7608 (OUTLIER) cc_final: 0.7238 (t) REVERT: B 242 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7119 (tt0) REVERT: B 244 GLU cc_start: 0.7759 (tt0) cc_final: 0.7447 (tt0) REVERT: B 246 GLN cc_start: 0.7655 (tt0) cc_final: 0.7293 (mt0) REVERT: B 252 ARG cc_start: 0.6617 (mmm-85) cc_final: 0.5964 (mmm160) REVERT: B 254 TYR cc_start: 0.7147 (p90) cc_final: 0.6859 (p90) REVERT: B 293 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7578 (mtt180) REVERT: B 335 GLU cc_start: 0.8329 (tt0) cc_final: 0.7541 (tm-30) REVERT: B 339 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: B 369 ASP cc_start: 0.7435 (p0) cc_final: 0.7200 (p0) REVERT: B 370 GLU cc_start: 0.7573 (tt0) cc_final: 0.7232 (tp30) REVERT: B 432 ARG cc_start: 0.7399 (mtm180) cc_final: 0.7016 (mtp85) REVERT: B 439 GLU cc_start: 0.7836 (tt0) cc_final: 0.7182 (tm-30) REVERT: B 488 GLU cc_start: 0.7169 (pm20) cc_final: 0.6223 (tm-30) REVERT: B 547 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8289 (mp) REVERT: B 662 LYS cc_start: 0.7437 (tttt) cc_final: 0.6855 (mtmm) REVERT: B 746 MET cc_start: 0.7409 (mmm) cc_final: 0.7128 (mmp) REVERT: B 751 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6805 (mp0) REVERT: B 756 ARG cc_start: 0.7298 (ttm110) cc_final: 0.6528 (mtp180) REVERT: B 762 GLN cc_start: 0.7403 (mp10) cc_final: 0.7186 (mp10) REVERT: B 774 LYS cc_start: 0.7479 (mtpp) cc_final: 0.6676 (tttt) REVERT: B 782 ARG cc_start: 0.7890 (mtm180) cc_final: 0.7494 (mtp180) REVERT: B 825 GLN cc_start: 0.7540 (tp-100) cc_final: 0.7105 (mt0) REVERT: B 966 GLN cc_start: 0.7818 (tt0) cc_final: 0.7615 (tt0) REVERT: B 970 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7052 (mp0) REVERT: B 1001 SER cc_start: 0.7713 (t) cc_final: 0.7265 (m) REVERT: B 1005 SER cc_start: 0.7519 (m) cc_final: 0.7081 (p) REVERT: B 1014 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7509 (mtm-85) REVERT: C 3 MET cc_start: 0.1538 (mmp) cc_final: 0.1232 (tmm) REVERT: C 41 GLU cc_start: 0.7153 (tp30) cc_final: 0.6382 (tm-30) REVERT: C 42 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6679 (tt0) REVERT: C 50 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7065 (mm110) REVERT: C 129 ASN cc_start: 0.7772 (t0) cc_final: 0.7317 (t0) REVERT: C 242 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7120 (tt0) REVERT: C 244 GLU cc_start: 0.7791 (tt0) cc_final: 0.7403 (tt0) REVERT: C 246 GLN cc_start: 0.7767 (tt0) cc_final: 0.7385 (mt0) REVERT: C 252 ARG cc_start: 0.6668 (mmm-85) cc_final: 0.6297 (mmt180) REVERT: C 254 TYR cc_start: 0.7085 (p90) cc_final: 0.6785 (p90) REVERT: C 297 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6310 (mm-30) REVERT: C 335 GLU cc_start: 0.8356 (tt0) cc_final: 0.7564 (tm-30) REVERT: C 359 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: C 370 GLU cc_start: 0.7598 (tt0) cc_final: 0.7304 (tp30) REVERT: C 432 ARG cc_start: 0.7394 (mtm180) cc_final: 0.7023 (mtp85) REVERT: C 439 GLU cc_start: 0.7784 (tt0) cc_final: 0.7096 (tm-30) REVERT: C 547 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8279 (mp) REVERT: C 662 LYS cc_start: 0.7479 (tttt) cc_final: 0.6869 (mtmm) REVERT: C 682 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6913 (tp30) REVERT: C 747 ASP cc_start: 0.6915 (p0) cc_final: 0.6589 (p0) REVERT: C 751 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6881 (mp0) REVERT: C 774 LYS cc_start: 0.7521 (mtmt) cc_final: 0.6660 (tttt) REVERT: C 775 LYS cc_start: 0.8012 (mttt) cc_final: 0.7636 (mttp) REVERT: C 782 ARG cc_start: 0.7956 (mtm180) cc_final: 0.7589 (mtp180) REVERT: C 783 ASP cc_start: 0.8418 (m-30) cc_final: 0.8156 (m-30) REVERT: C 812 LYS cc_start: 0.8017 (mttt) cc_final: 0.7764 (mttm) REVERT: C 966 GLN cc_start: 0.7835 (tt0) cc_final: 0.7628 (tt0) REVERT: C 970 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7052 (mp0) REVERT: C 1001 SER cc_start: 0.7689 (t) cc_final: 0.7259 (m) REVERT: C 1005 SER cc_start: 0.7529 (m) cc_final: 0.7105 (p) REVERT: C 1014 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7531 (mtm-85) REVERT: D 1 MET cc_start: 0.0649 (tpt) cc_final: 0.0026 (ptp) REVERT: D 39 ASN cc_start: 0.8241 (t0) cc_final: 0.7940 (t0) REVERT: D 41 GLU cc_start: 0.7172 (tp30) cc_final: 0.6383 (tm-30) REVERT: D 42 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6727 (tt0) REVERT: D 50 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7069 (mm110) REVERT: D 129 ASN cc_start: 0.7775 (t0) cc_final: 0.7333 (t0) REVERT: D 220 THR cc_start: 0.7604 (p) cc_final: 0.7241 (t) REVERT: D 242 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7097 (tt0) REVERT: D 244 GLU cc_start: 0.7828 (tt0) cc_final: 0.7412 (tt0) REVERT: D 252 ARG cc_start: 0.6625 (mmm-85) cc_final: 0.6012 (mmp-170) REVERT: D 254 TYR cc_start: 0.7147 (p90) cc_final: 0.6932 (p90) REVERT: D 293 ARG cc_start: 0.7928 (mtt90) cc_final: 0.7587 (mtt180) REVERT: D 335 GLU cc_start: 0.8346 (tt0) cc_final: 0.7521 (tm-30) REVERT: D 359 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: D 369 ASP cc_start: 0.7426 (p0) cc_final: 0.7049 (p0) REVERT: D 432 ARG cc_start: 0.7394 (mtm180) cc_final: 0.7016 (mtp85) REVERT: D 439 GLU cc_start: 0.7839 (tt0) cc_final: 0.7112 (tm-30) REVERT: D 508 ASP cc_start: 0.7644 (m-30) cc_final: 0.7376 (m-30) REVERT: D 547 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8238 (mp) REVERT: D 649 ASP cc_start: 0.7734 (p0) cc_final: 0.7456 (p0) REVERT: D 662 LYS cc_start: 0.7403 (tttt) cc_final: 0.6766 (mtmm) REVERT: D 756 ARG cc_start: 0.7340 (ttm110) cc_final: 0.6671 (mtp180) REVERT: D 774 LYS cc_start: 0.7304 (mtmm) cc_final: 0.6606 (tttt) REVERT: D 775 LYS cc_start: 0.8021 (mttt) cc_final: 0.7642 (mttp) REVERT: D 782 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7527 (mtp180) REVERT: D 891 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7780 (tm-30) REVERT: D 925 ASP cc_start: 0.7799 (m-30) cc_final: 0.7452 (t0) REVERT: D 966 GLN cc_start: 0.7841 (tt0) cc_final: 0.7635 (tt0) REVERT: D 970 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7037 (mp0) REVERT: D 1001 SER cc_start: 0.7685 (t) cc_final: 0.7255 (m) REVERT: D 1005 SER cc_start: 0.7520 (m) cc_final: 0.7109 (p) REVERT: D 1014 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7520 (mtm-85) outliers start: 46 outliers final: 26 residues processed: 499 average time/residue: 1.7283 time to fit residues: 1002.4875 Evaluate side-chains 491 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 456 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 924 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 0.9990 chunk 344 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 332 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 647 HIS A 978 HIS B 584 ASN B 647 HIS B 726 ASN B 784 GLN B 959 ASN B 978 HIS B 986 ASN C 647 HIS C 959 ASN D 584 ASN D 647 HIS D 762 GLN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120679 restraints weight = 29537.905| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.04 r_work: 0.3226 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 33856 Z= 0.265 Angle : 0.629 12.062 46192 Z= 0.333 Chirality : 0.046 0.171 4832 Planarity : 0.004 0.034 6100 Dihedral : 5.608 36.033 4484 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.26 % Allowed : 11.30 % Favored : 87.44 % 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: 0.31 (0.13), residues: 4088 helix: 0.22 (0.21), residues: 552 sheet: 0.82 (0.14), residues: 1348 loop : -0.12 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 554 HIS 0.008 0.001 HIS A 978 PHE 0.010 0.002 PHE C 275 TYR 0.021 0.002 TYR A 101 ARG 0.005 0.001 ARG D 858 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15724.97 seconds wall clock time: 276 minutes 16.86 seconds (16576.86 seconds total)