Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 07:56:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3e_34465/04_2023/8h3e_34465_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3e_34465/04_2023/8h3e_34465.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3e_34465/04_2023/8h3e_34465_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3e_34465/04_2023/8h3e_34465_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3e_34465/04_2023/8h3e_34465_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3e_34465/04_2023/8h3e_34465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3e_34465/04_2023/8h3e_34465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3e_34465/04_2023/8h3e_34465_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3e_34465/04_2023/8h3e_34465_trim_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.122 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 114 5.16 5 C 15933 2.51 5 N 4131 2.21 5 O 4779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1127": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 24957 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8227 Classifications: {'peptide': 1053} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1001} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8227 Classifications: {'peptide': 1053} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1001} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8227 Classifications: {'peptide': 1053} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1001} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {'NAG': 5, 'Q83': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {'NAG': 5, 'Q83': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {'NAG': 5, 'Q83': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N THR A 33 " occ=0.77 ... (5 atoms not shown) pdb=" CG2 THR A 33 " occ=0.46 residue: pdb=" N HIS A 69 " occ=0.34 ... (8 atoms not shown) pdb=" NE2 HIS A 69 " occ=0.55 residue: pdb=" N VAL A 70 " occ=0.38 ... (5 atoms not shown) pdb=" CG2 VAL A 70 " occ=0.64 residue: pdb=" N THR A 76 " occ=0.73 ... (5 atoms not shown) pdb=" CG2 THR A 76 " occ=0.80 residue: pdb=" N LYS A 77 " occ=0.76 ... (7 atoms not shown) pdb=" NZ LYS A 77 " occ=0.97 residue: pdb=" N ASP A 80 " occ=0.59 ... (6 atoms not shown) pdb=" OD2 ASP A 80 " occ=0.57 residue: pdb=" N ASN A 81 " occ=0.73 ... (6 atoms not shown) pdb=" ND2 ASN A 81 " occ=0.77 residue: pdb=" N SER A 98 " occ=0.66 ... (4 atoms not shown) pdb=" OG SER A 98 " occ=0.86 residue: pdb=" N THR A 109 " occ=0.76 ... (5 atoms not shown) pdb=" CG2 THR A 109 " occ=0.53 residue: pdb=" N ASP A 111 " occ=0.62 ... (6 atoms not shown) pdb=" OD2 ASP A 111 " occ=0.61 residue: pdb=" N ASP A 138 " occ=0.60 ... (6 atoms not shown) pdb=" OD2 ASP A 138 " occ=0.53 residue: pdb=" N TYR A 144 " occ=0.58 ... (10 atoms not shown) pdb=" OH TYR A 144 " occ=0.54 ... (remaining 185 not shown) Time building chain proxies: 12.77, per 1000 atoms: 0.51 Number of scatterers: 24957 At special positions: 0 Unit cell: (145.34, 146.2, 180.6, 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 114 16.00 O 4779 8.00 N 4131 7.00 C 15933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 331 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 331 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 331 " Time building additional restraints: 9.74 Conformation dependent library (CDL) restraints added in 3.7 seconds 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 48 sheets defined 17.7% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 296 through 303 removed outlier: 3.915A pdb=" N LYS A 300 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS A 301 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 303 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 342 removed outlier: 3.967A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 342' Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 418 through 421 No H-bonds generated for 'chain 'A' and resid 418 through 421' Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 756 removed outlier: 3.962A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 779 removed outlier: 3.947A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 822 No H-bonds generated for 'chain 'A' and resid 819 through 822' Processing helix chain 'A' and resid 850 through 856 removed outlier: 3.731A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 883 removed outlier: 3.840A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 907 removed outlier: 3.660A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 920 through 931 Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 950 through 953 No H-bonds generated for 'chain 'A' and resid 950 through 953' Processing helix chain 'A' and resid 960 through 966 removed outlier: 3.989A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 980 No H-bonds generated for 'chain 'A' and resid 977 through 980' Processing helix chain 'A' and resid 986 through 1000 removed outlier: 4.164A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1016 removed outlier: 4.094A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1031 removed outlier: 3.628A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 303 removed outlier: 3.917A pdb=" N LYS B 300 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS B 301 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 303 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 342 removed outlier: 3.967A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 342' Processing helix chain 'B' and resid 365 through 368 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 418 through 421 No H-bonds generated for 'chain 'B' and resid 418 through 421' Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 756 removed outlier: 4.081A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 779 removed outlier: 3.889A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 removed outlier: 3.572A pdb=" N LEU B 822 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 856 removed outlier: 3.665A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 883 removed outlier: 4.016A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 907 removed outlier: 3.650A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 920 through 931 Processing helix chain 'B' and resid 933 through 938 Processing helix chain 'B' and resid 947 through 953 removed outlier: 4.318A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 966 removed outlier: 4.074A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 980 No H-bonds generated for 'chain 'B' and resid 977 through 980' Processing helix chain 'B' and resid 986 through 1000 removed outlier: 4.167A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1016 removed outlier: 4.125A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1031 removed outlier: 3.626A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 303 removed outlier: 3.925A pdb=" N LYS C 300 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS C 301 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 303 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 342 removed outlier: 3.952A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 342' Processing helix chain 'C' and resid 365 through 368 Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 418 through 421 No H-bonds generated for 'chain 'C' and resid 418 through 421' Processing helix chain 'C' and resid 617 through 619 No H-bonds generated for 'chain 'C' and resid 617 through 619' Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 756 removed outlier: 4.075A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 779 removed outlier: 3.917A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL C 772 " --> pdb=" O THR C 768 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 822 No H-bonds generated for 'chain 'C' and resid 819 through 822' Processing helix chain 'C' and resid 850 through 856 removed outlier: 3.701A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 883 removed outlier: 3.833A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 877 " --> pdb=" O TYR C 873 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 879 " --> pdb=" O SER C 875 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 907 removed outlier: 3.655A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 917 Processing helix chain 'C' and resid 920 through 931 Processing helix chain 'C' and resid 933 through 938 Processing helix chain 'C' and resid 947 through 953 removed outlier: 4.311A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 966 removed outlier: 3.979A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 980 No H-bonds generated for 'chain 'C' and resid 977 through 980' Processing helix chain 'C' and resid 986 through 1000 removed outlier: 4.375A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1031 removed outlier: 4.139A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE C1018 " --> pdb=" O ARG C1014 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C1031 " --> pdb=" O THR C1027 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 Processing sheet with id= B, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.361A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 63 through 67 removed outlier: 3.709A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 169 through 171 removed outlier: 4.291A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 102 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.561A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.638A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.795A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 361 through 363 removed outlier: 3.629A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= J, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.670A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.401A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A 574 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 671 through 674 Processing sheet with id= M, first strand: chain 'A' and resid 712 through 714 removed outlier: 3.715A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.662A pdb=" N ALA A1070 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.807A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= Q, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.528A pdb=" N VAL A1096 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 29 through 31 Processing sheet with id= S, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.365A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 63 through 67 removed outlier: 3.712A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 169 through 171 removed outlier: 4.256A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 102 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.666A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.787A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 361 through 363 removed outlier: 3.619A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= Z, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.668A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 671 through 674 Processing sheet with id= AB, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.730A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.649A pdb=" N ALA B1070 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 734 through 736 Processing sheet with id= AE, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AF, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.525A pdb=" N VAL B1096 " --> pdb=" O PHE B1103 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.531A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.338A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 63 through 67 removed outlier: 3.669A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 169 through 171 removed outlier: 3.517A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 102 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.673A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.797A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 361 through 363 removed outlier: 3.617A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AO, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.648A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 551 through 554 Processing sheet with id= AQ, first strand: chain 'C' and resid 671 through 674 Processing sheet with id= AR, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.794A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.679A pdb=" N ALA C1070 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'C' and resid 734 through 736 Processing sheet with id= AU, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AV, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.562A pdb=" N VAL C1096 " --> pdb=" O PHE C1103 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1494 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: 10.05 Time building geometry restraints manager: 10.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4092 1.30 - 1.43: 7074 1.43 - 1.56: 14216 1.56 - 1.69: 1 1.69 - 1.82: 144 Bond restraints: 25527 Sorted by residual: bond pdb=" C12 Q83 C1301 " pdb=" C13 Q83 C1301 " ideal model delta sigma weight residual 1.398 1.540 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C12 Q83 B1301 " pdb=" C13 Q83 B1301 " ideal model delta sigma weight residual 1.398 1.540 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C12 Q83 A1301 " pdb=" C13 Q83 A1301 " ideal model delta sigma weight residual 1.398 1.539 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C14 Q83 C1301 " pdb=" C15 Q83 C1301 " ideal model delta sigma weight residual 1.394 1.523 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C14 Q83 A1301 " pdb=" C15 Q83 A1301 " ideal model delta sigma weight residual 1.394 1.523 -0.129 2.00e-02 2.50e+03 4.13e+01 ... (remaining 25522 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.59: 503 105.59 - 112.70: 13286 112.70 - 119.81: 8190 119.81 - 126.92: 12504 126.92 - 134.03: 242 Bond angle restraints: 34725 Sorted by residual: angle pdb=" C THR C 315 " pdb=" CA THR C 315 " pdb=" CB THR C 315 " ideal model delta sigma weight residual 116.54 110.00 6.54 1.15e+00 7.56e-01 3.23e+01 angle pdb=" CA ALA C 706 " pdb=" C ALA C 706 " pdb=" O ALA C 706 " ideal model delta sigma weight residual 122.13 116.75 5.38 1.13e+00 7.83e-01 2.27e+01 angle pdb=" CA ALA B 706 " pdb=" C ALA B 706 " pdb=" O ALA B 706 " ideal model delta sigma weight residual 122.37 117.09 5.28 1.15e+00 7.56e-01 2.11e+01 angle pdb=" CA ALA A 706 " pdb=" C ALA A 706 " pdb=" O ALA A 706 " ideal model delta sigma weight residual 122.37 117.16 5.21 1.15e+00 7.56e-01 2.05e+01 angle pdb=" CA PRO C1140 " pdb=" N PRO C1140 " pdb=" CD PRO C1140 " ideal model delta sigma weight residual 112.00 105.80 6.20 1.40e+00 5.10e-01 1.96e+01 ... (remaining 34720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12958 17.93 - 35.86: 1628 35.86 - 53.79: 382 53.79 - 71.72: 74 71.72 - 89.65: 30 Dihedral angle restraints: 15072 sinusoidal: 5883 harmonic: 9189 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 176.62 -83.62 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 176.56 -83.56 1 1.00e+01 1.00e-02 8.52e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 175.86 -82.86 1 1.00e+01 1.00e-02 8.41e+01 ... (remaining 15069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3605 0.081 - 0.162: 350 0.162 - 0.242: 6 0.242 - 0.323: 4 0.323 - 0.404: 1 Chirality restraints: 3966 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 3963 not shown) Planarity restraints: 4500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 705 " -0.023 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C VAL C 705 " 0.077 2.00e-02 2.50e+03 pdb=" O VAL C 705 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA C 706 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C1139 " -0.073 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO C1140 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO C1140 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C1140 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 894 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C LEU B 894 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU B 894 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN B 895 " 0.014 2.00e-02 2.50e+03 ... (remaining 4497 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 88 2.55 - 3.14: 17760 3.14 - 3.72: 31897 3.72 - 4.31: 44758 4.31 - 4.90: 81589 Nonbonded interactions: 176092 Sorted by model distance: nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 1.960 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 1.960 2.440 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 1.970 2.440 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 1.972 2.440 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.011 2.440 ... (remaining 176087 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' } 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=0.00 max=1.00 mean=0.80 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: 4.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 24.910 Check model and map are aligned: 0.390 Set scattering table: 0.220 Process input model: 62.680 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 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 : 0.004 0.142 25527 Z= 0.275 Angle : 0.506 6.539 34725 Z= 0.287 Chirality : 0.045 0.404 3966 Planarity : 0.004 0.107 4485 Dihedral : 16.693 89.648 9045 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.14), residues: 3117 helix: -1.25 (0.22), residues: 588 sheet: -0.43 (0.20), residues: 708 loop : -2.12 (0.13), residues: 1821 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 3.364 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 96 average time/residue: 0.3819 time to fit residues: 60.9909 Evaluate side-chains 87 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 2.972 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2140 time to fit residues: 4.8966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 6.9990 chunk 238 optimal weight: 0.0770 chunk 132 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 286 optimal weight: 0.0670 overall best weight: 1.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 25527 Z= 0.205 Angle : 0.563 7.272 34725 Z= 0.299 Chirality : 0.049 0.354 3966 Planarity : 0.004 0.046 4485 Dihedral : 4.961 57.564 3414 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.14), residues: 3117 helix: -1.46 (0.21), residues: 603 sheet: -0.03 (0.20), residues: 645 loop : -2.08 (0.13), residues: 1869 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 93 time to evaluate : 2.825 Fit side-chains outliers start: 77 outliers final: 44 residues processed: 164 average time/residue: 0.3753 time to fit residues: 103.0483 Evaluate side-chains 128 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 84 time to evaluate : 2.958 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2269 time to fit residues: 22.8576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 7.9990 chunk 88 optimal weight: 0.0030 chunk 238 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 286 optimal weight: 0.4980 chunk 309 optimal weight: 0.7980 chunk 255 optimal weight: 0.0970 chunk 284 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 25527 Z= 0.162 Angle : 0.521 7.480 34725 Z= 0.275 Chirality : 0.047 0.349 3966 Planarity : 0.004 0.037 4485 Dihedral : 4.434 33.566 3414 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.14), residues: 3117 helix: -1.34 (0.21), residues: 600 sheet: 0.03 (0.19), residues: 711 loop : -2.01 (0.13), residues: 1806 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 93 time to evaluate : 3.115 Fit side-chains outliers start: 52 outliers final: 17 residues processed: 145 average time/residue: 0.3462 time to fit residues: 85.1316 Evaluate side-chains 103 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 2.900 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2132 time to fit residues: 10.6330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 4.9990 chunk 215 optimal weight: 0.3980 chunk 148 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 304 optimal weight: 4.9990 chunk 150 optimal weight: 0.0010 chunk 272 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 25527 Z= 0.255 Angle : 0.595 15.354 34725 Z= 0.313 Chirality : 0.050 0.357 3966 Planarity : 0.004 0.040 4485 Dihedral : 4.726 29.489 3414 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.14), residues: 3117 helix: -1.55 (0.21), residues: 600 sheet: 0.15 (0.20), residues: 696 loop : -2.06 (0.13), residues: 1821 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 91 time to evaluate : 3.132 Fit side-chains outliers start: 54 outliers final: 30 residues processed: 139 average time/residue: 0.3414 time to fit residues: 79.4793 Evaluate side-chains 118 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 2.835 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2132 time to fit residues: 16.3824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 226 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 210 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 273 optimal weight: 0.1980 chunk 76 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 25527 Z= 0.271 Angle : 0.603 11.059 34725 Z= 0.321 Chirality : 0.050 0.360 3966 Planarity : 0.004 0.041 4485 Dihedral : 4.873 25.244 3414 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.14), residues: 3117 helix: -1.70 (0.20), residues: 603 sheet: 0.21 (0.20), residues: 681 loop : -2.12 (0.13), residues: 1833 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 90 time to evaluate : 3.075 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 24 residues processed: 138 average time/residue: 0.3885 time to fit residues: 91.0859 Evaluate side-chains 106 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 3.300 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2552 time to fit residues: 15.7122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 0.8980 chunk 274 optimal weight: 0.9980 chunk 60 optimal weight: 0.0050 chunk 178 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 304 optimal weight: 0.0970 chunk 253 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 160 optimal weight: 7.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.083 25527 Z= 0.147 Angle : 0.503 16.567 34725 Z= 0.261 Chirality : 0.046 0.339 3966 Planarity : 0.004 0.037 4485 Dihedral : 4.149 18.778 3414 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.14), residues: 3117 helix: -1.30 (0.21), residues: 600 sheet: 0.08 (0.20), residues: 666 loop : -1.88 (0.13), residues: 1851 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 3.188 Fit side-chains outliers start: 25 outliers final: 13 residues processed: 117 average time/residue: 0.4065 time to fit residues: 78.4765 Evaluate side-chains 98 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 2.917 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2699 time to fit residues: 10.3707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 173 optimal weight: 0.0270 chunk 222 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 170 optimal weight: 0.3980 chunk 303 optimal weight: 0.5980 chunk 190 optimal weight: 0.0010 chunk 185 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 overall best weight: 0.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 935 GLN A 955 ASN A 992 GLN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.074 25527 Z= 0.136 Angle : 0.477 14.327 34725 Z= 0.247 Chirality : 0.046 0.336 3966 Planarity : 0.004 0.036 4485 Dihedral : 3.790 16.795 3414 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3117 helix: -1.04 (0.22), residues: 603 sheet: 0.24 (0.20), residues: 663 loop : -1.81 (0.13), residues: 1851 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 2.881 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 98 average time/residue: 0.4481 time to fit residues: 70.5479 Evaluate side-chains 85 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 3.183 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3665 time to fit residues: 6.6566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 0.4980 chunk 121 optimal weight: 3.9990 chunk 181 optimal weight: 0.0270 chunk 91 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 193 optimal weight: 0.0060 chunk 206 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 238 optimal weight: 0.8980 overall best weight: 0.4654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.066 25527 Z= 0.135 Angle : 0.474 14.336 34725 Z= 0.246 Chirality : 0.045 0.335 3966 Planarity : 0.004 0.036 4485 Dihedral : 3.718 16.936 3414 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.14), residues: 3117 helix: -0.90 (0.22), residues: 591 sheet: 0.31 (0.19), residues: 711 loop : -1.73 (0.13), residues: 1815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 3.124 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 93 average time/residue: 0.4067 time to fit residues: 63.1861 Evaluate side-chains 86 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 3.208 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2341 time to fit residues: 5.7127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 0.6980 chunk 290 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 267 optimal weight: 0.0980 chunk 281 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 25527 Z= 0.199 Angle : 0.534 14.684 34725 Z= 0.280 Chirality : 0.047 0.349 3966 Planarity : 0.004 0.037 4485 Dihedral : 4.165 18.756 3414 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3117 helix: -1.20 (0.21), residues: 612 sheet: 0.20 (0.20), residues: 675 loop : -1.75 (0.13), residues: 1830 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 3.185 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 0.4006 time to fit residues: 60.2913 Evaluate side-chains 84 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 3.146 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2249 time to fit residues: 7.1588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 0.6980 chunk 299 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 207 optimal weight: 0.0670 chunk 313 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 193 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.068 25527 Z= 0.143 Angle : 0.486 14.525 34725 Z= 0.253 Chirality : 0.046 0.339 3966 Planarity : 0.004 0.036 4485 Dihedral : 3.884 17.637 3414 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3117 helix: -0.96 (0.22), residues: 591 sheet: 0.26 (0.20), residues: 669 loop : -1.72 (0.13), residues: 1857 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 4.075 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 83 average time/residue: 0.5059 time to fit residues: 70.4290 Evaluate side-chains 80 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 3.017 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2217 time to fit residues: 4.4550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.078516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.065587 restraints weight = 62246.041| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.15 r_work: 0.2918 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 633 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 663 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 25527 Z= 0.358 Angle : 0.648 15.365 34725 Z= 0.344 Chirality : 0.051 0.428 3966 Planarity : 0.005 0.043 4485 Dihedral : 4.842 21.818 3414 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.14), residues: 3117 helix: -1.61 (0.20), residues: 612 sheet: 0.21 (0.19), residues: 711 loop : -1.93 (0.13), residues: 1794 =============================================================================== Job complete usr+sys time: 4117.76 seconds wall clock time: 76 minutes 40.65 seconds (4600.65 seconds total)