Starting phenix.real_space_refine on Fri Aug 9 03:18:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0x_42873/08_2024/8v0x_42873.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0x_42873/08_2024/8v0x_42873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0x_42873/08_2024/8v0x_42873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0x_42873/08_2024/8v0x_42873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0x_42873/08_2024/8v0x_42873.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0x_42873/08_2024/8v0x_42873.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 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 15829 2.51 5 N 4091 2.21 5 O 4762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24796 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.03, per 1000 atoms: 0.57 Number of scatterers: 24796 At special positions: 0 Unit cell: (138.24, 132.84, 174.96, 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 4762 8.00 N 4091 7.00 C 15829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 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=2.04 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=2.05 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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=2.05 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.05 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 A 840 " - pdb=" SG CYS A 851 " 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=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 234 " " NAG A1310 " - " ASN A 801 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 801 " Time building additional restraints: 10.11 Conformation dependent library (CDL) restraints added in 5.9 seconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 51 sheets defined 25.1% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.678A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.149A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 4.104A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.621A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.655A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.601A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.605A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.662A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.913A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.586A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.555A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.873A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.824A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.614A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.794A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.613A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.521A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 4.125A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.888A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.522A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.608A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.171A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.102A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.789A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.564A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.509A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.525A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.784A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.586A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.655A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.692A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.539A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.540A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.563A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.558A pdb=" N PHE C 43 " --> pdb=" O PHE B 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.636A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 104 removed outlier: 4.171A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.364A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.007A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.956A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.173A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 704 removed outlier: 6.643A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS A 790 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASN C 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.282A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.610A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 25 through 30 removed outlier: 4.308A pdb=" N THR B 25 " --> pdb=" O HIS B 66 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.912A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.672A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.041A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 118 through 120 removed outlier: 3.536A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.379A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.554A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.506A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.887A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.613A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.196A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.526A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.397A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'A' and resid 25 through 29 removed outlier: 3.600A pdb=" N THR A 25 " --> pdb=" O HIS A 66 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ARG A 34 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N LEU A 223 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.558A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.558A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.577A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.759A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.369A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.628A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.699A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.519A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AF3, first strand: chain 'A' and resid 718 through 722 removed outlier: 7.155A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.374A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.525A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1094 through 1097 887 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.10 Time building geometry restraints manager: 10.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7922 1.35 - 1.47: 6482 1.47 - 1.60: 10809 1.60 - 1.73: 0 1.73 - 1.86: 141 Bond restraints: 25354 Sorted by residual: bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.23e-02 6.61e+03 6.26e+00 bond pdb=" C1 NAG C1309 " pdb=" O5 NAG C1309 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.42e+00 bond pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.13e+00 ... (remaining 25349 not shown) Histogram of bond angle deviations from ideal: 96.37 - 103.89: 343 103.89 - 111.41: 10521 111.41 - 118.93: 9645 118.93 - 126.45: 13688 126.45 - 133.97: 296 Bond angle restraints: 34493 Sorted by residual: angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 111.77 102.62 9.15 1.04e+00 9.25e-01 7.73e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 121.54 131.86 -10.32 1.91e+00 2.74e-01 2.92e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 126.56 -12.16 2.30e+00 1.89e-01 2.79e+01 angle pdb=" CG1 ILE C 105 " pdb=" CB ILE C 105 " pdb=" CG2 ILE C 105 " ideal model delta sigma weight residual 110.70 96.37 14.33 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C VAL C 130 " pdb=" CA VAL C 130 " pdb=" CB VAL C 130 " ideal model delta sigma weight residual 112.46 118.73 -6.27 1.33e+00 5.65e-01 2.22e+01 ... (remaining 34488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.66: 14504 23.66 - 47.33: 889 47.33 - 70.99: 95 70.99 - 94.65: 36 94.65 - 118.32: 1 Dihedral angle restraints: 15525 sinusoidal: 6420 harmonic: 9105 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 9.36 83.64 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -4.19 -81.81 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -15.47 -70.53 1 1.00e+01 1.00e-02 6.40e+01 ... (remaining 15522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3402 0.075 - 0.150: 563 0.150 - 0.225: 40 0.225 - 0.300: 2 0.300 - 0.375: 2 Chirality restraints: 4009 Sorted by residual: chirality pdb=" CB ILE C 105 " pdb=" CA ILE C 105 " pdb=" CG1 ILE C 105 " pdb=" CG2 ILE C 105 " both_signs ideal model delta sigma weight residual False 2.64 3.02 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE A 101 " pdb=" CA ILE A 101 " pdb=" CG1 ILE A 101 " pdb=" CG2 ILE A 101 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE B 101 " pdb=" CA ILE B 101 " pdb=" CG1 ILE B 101 " pdb=" CG2 ILE B 101 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 4006 not shown) Planarity restraints: 4453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 138 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO B 139 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO B 139 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 139 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 105 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C ILE C 105 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE C 105 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE C 106 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 173 " -0.048 5.00e-02 4.00e+02 7.24e-02 8.39e+00 pdb=" N PRO C 174 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 174 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 174 " -0.040 5.00e-02 4.00e+02 ... (remaining 4450 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7248 2.82 - 3.34: 19813 3.34 - 3.86: 39614 3.86 - 4.38: 42960 4.38 - 4.90: 78621 Nonbonded interactions: 188256 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.304 3.040 nonbonded pdb=" OE1 GLU A 819 " pdb=" OG SER A1055 " model vdw 2.316 3.040 nonbonded pdb=" O PHE C 374 " pdb=" ND2 ASN B 405 " model vdw 2.325 3.120 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.330 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.330 3.040 ... (remaining 188251 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 1147 or resid 1301 through 1309)) selection = (chain 'B' and (resid 24 through 1147 or resid 1301 through 1309)) 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=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: 1.760 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: 0.980 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 69.580 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.100 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 0.096 25354 Z= 0.279 Angle : 0.791 14.331 34493 Z= 0.414 Chirality : 0.052 0.375 4009 Planarity : 0.006 0.104 4424 Dihedral : 14.552 118.315 9540 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 3081 helix: -0.60 (0.17), residues: 682 sheet: -0.19 (0.20), residues: 653 loop : -1.85 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.013 0.001 HIS C 519 PHE 0.047 0.002 PHE C 168 TYR 0.028 0.001 TYR B 170 ARG 0.013 0.001 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 537 LYS cc_start: 0.6882 (mtpp) cc_final: 0.6597 (mttt) REVERT: C 544 ASN cc_start: 0.8754 (m-40) cc_final: 0.8518 (m-40) REVERT: B 303 LEU cc_start: 0.8676 (mt) cc_final: 0.8415 (mt) REVERT: A 287 ASP cc_start: 0.6692 (m-30) cc_final: 0.6463 (m-30) REVERT: A 904 TYR cc_start: 0.7220 (m-10) cc_final: 0.6787 (m-10) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3231 time to fit residues: 147.3031 Evaluate side-chains 212 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.0170 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 0.0870 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS B 544 ASN B 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25354 Z= 0.157 Angle : 0.530 7.418 34493 Z= 0.278 Chirality : 0.044 0.223 4009 Planarity : 0.004 0.076 4424 Dihedral : 6.920 106.953 3951 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.74 % Allowed : 5.89 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3081 helix: 1.24 (0.20), residues: 671 sheet: 0.08 (0.20), residues: 657 loop : -1.74 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.007 0.001 HIS C 519 PHE 0.028 0.001 PHE A 392 TYR 0.015 0.001 TYR C 351 ARG 0.005 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 257 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 493 GLN cc_start: 0.7698 (tt0) cc_final: 0.7397 (tt0) REVERT: C 537 LYS cc_start: 0.6797 (mtpp) cc_final: 0.6530 (mttt) REVERT: C 544 ASN cc_start: 0.8744 (m-40) cc_final: 0.8459 (m-40) REVERT: B 303 LEU cc_start: 0.8626 (mt) cc_final: 0.8315 (mt) REVERT: B 420 ASP cc_start: 0.7738 (m-30) cc_final: 0.7500 (m-30) REVERT: B 646 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7365 (ttt90) REVERT: B 1138 TYR cc_start: 0.7104 (t80) cc_final: 0.6788 (t80) REVERT: A 287 ASP cc_start: 0.6706 (m-30) cc_final: 0.6402 (m-30) REVERT: A 811 LYS cc_start: 0.6916 (mmtm) cc_final: 0.6137 (tttp) REVERT: A 904 TYR cc_start: 0.7131 (m-10) cc_final: 0.6797 (m-10) outliers start: 20 outliers final: 15 residues processed: 267 average time/residue: 0.3360 time to fit residues: 146.4580 Evaluate side-chains 232 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 217 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 881 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.6980 chunk 87 optimal weight: 0.4980 chunk 235 optimal weight: 3.9990 chunk 192 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 283 optimal weight: 0.4980 chunk 306 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 chunk 281 optimal weight: 20.0000 chunk 96 optimal weight: 0.0870 chunk 227 optimal weight: 10.0000 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN A 405 ASN A 960 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25354 Z= 0.139 Angle : 0.496 8.575 34493 Z= 0.257 Chirality : 0.043 0.271 4009 Planarity : 0.004 0.056 4424 Dihedral : 6.364 98.847 3951 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.92 % Allowed : 8.40 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 3081 helix: 1.81 (0.20), residues: 676 sheet: 0.07 (0.20), residues: 645 loop : -1.56 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.000 HIS B 339 PHE 0.026 0.001 PHE A 541 TYR 0.012 0.001 TYR A 489 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 230 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.7637 (m-80) cc_final: 0.7388 (m-80) REVERT: C 430 THR cc_start: 0.7689 (p) cc_final: 0.7416 (m) REVERT: C 537 LYS cc_start: 0.6828 (mtpp) cc_final: 0.6525 (mttt) REVERT: C 544 ASN cc_start: 0.8758 (m-40) cc_final: 0.8452 (m-40) REVERT: B 224 GLU cc_start: 0.7859 (mp0) cc_final: 0.7485 (mp0) REVERT: B 303 LEU cc_start: 0.8635 (mt) cc_final: 0.8301 (mt) REVERT: B 420 ASP cc_start: 0.7658 (m-30) cc_final: 0.7308 (m-30) REVERT: B 646 ARG cc_start: 0.7698 (mtp180) cc_final: 0.7238 (ttt90) REVERT: A 287 ASP cc_start: 0.6681 (m-30) cc_final: 0.6383 (m-30) REVERT: A 811 LYS cc_start: 0.6870 (mmtm) cc_final: 0.6122 (tttt) REVERT: A 904 TYR cc_start: 0.7007 (m-10) cc_final: 0.6720 (m-10) outliers start: 25 outliers final: 15 residues processed: 246 average time/residue: 0.3445 time to fit residues: 137.0946 Evaluate side-chains 234 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 219 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.2980 chunk 213 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 135 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 301 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 269 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25354 Z= 0.161 Angle : 0.495 9.463 34493 Z= 0.256 Chirality : 0.043 0.266 4009 Planarity : 0.004 0.054 4424 Dihedral : 5.898 83.816 3951 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.40 % Allowed : 9.36 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3081 helix: 1.90 (0.20), residues: 689 sheet: -0.02 (0.20), residues: 671 loop : -1.47 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.005 0.001 HIS A 339 PHE 0.026 0.001 PHE A 92 TYR 0.014 0.001 TYR A 91 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.7671 (m-80) cc_final: 0.7384 (m-80) REVERT: C 332 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7099 (mm) REVERT: C 396 TYR cc_start: 0.7925 (m-80) cc_final: 0.7501 (m-80) REVERT: C 430 THR cc_start: 0.7737 (p) cc_final: 0.7493 (m) REVERT: C 537 LYS cc_start: 0.6924 (mtpp) cc_final: 0.6603 (mttt) REVERT: C 544 ASN cc_start: 0.8735 (m-40) cc_final: 0.8415 (m-40) REVERT: C 1073 LYS cc_start: 0.7661 (ptmm) cc_final: 0.7155 (mtpt) REVERT: B 224 GLU cc_start: 0.8138 (mp0) cc_final: 0.7758 (mp0) REVERT: B 646 ARG cc_start: 0.7661 (mtp180) cc_final: 0.7188 (ttt90) REVERT: A 287 ASP cc_start: 0.6722 (m-30) cc_final: 0.6410 (m-30) REVERT: A 811 LYS cc_start: 0.6969 (mmtm) cc_final: 0.6198 (tttp) REVERT: A 904 TYR cc_start: 0.7014 (m-10) cc_final: 0.6781 (m-10) outliers start: 38 outliers final: 29 residues processed: 261 average time/residue: 0.3419 time to fit residues: 145.2637 Evaluate side-chains 252 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 270 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1135 ASN B 314 GLN B 506 GLN B 613 GLN A1083 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25354 Z= 0.380 Angle : 0.628 9.583 34493 Z= 0.326 Chirality : 0.048 0.261 4009 Planarity : 0.004 0.049 4424 Dihedral : 6.155 71.746 3951 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.14 % Allowed : 10.06 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3081 helix: 1.46 (0.20), residues: 683 sheet: -0.21 (0.20), residues: 684 loop : -1.55 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 886 HIS 0.007 0.001 HIS B1064 PHE 0.037 0.002 PHE B 906 TYR 0.017 0.002 TYR C 266 ARG 0.008 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 244 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 332 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7114 (mm) REVERT: C 340 GLU cc_start: 0.8050 (mp0) cc_final: 0.7783 (mp0) REVERT: C 396 TYR cc_start: 0.7922 (m-80) cc_final: 0.7558 (m-80) REVERT: C 430 THR cc_start: 0.7779 (p) cc_final: 0.7552 (m) REVERT: C 434 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8760 (mp) REVERT: C 537 LYS cc_start: 0.7513 (mtpp) cc_final: 0.7269 (tppt) REVERT: C 544 ASN cc_start: 0.8886 (m-40) cc_final: 0.8619 (m-40) REVERT: C 675 GLN cc_start: 0.7010 (pp30) cc_final: 0.6477 (pp30) REVERT: B 224 GLU cc_start: 0.8253 (mp0) cc_final: 0.7845 (mp0) REVERT: B 420 ASP cc_start: 0.7727 (m-30) cc_final: 0.7506 (m-30) REVERT: B 646 ARG cc_start: 0.7660 (mtp180) cc_final: 0.7315 (ttp80) REVERT: B 936 ASP cc_start: 0.7613 (t0) cc_final: 0.7285 (t0) REVERT: B 977 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7810 (mp) REVERT: B 1107 ARG cc_start: 0.7528 (mtt180) cc_final: 0.7057 (mmm160) REVERT: A 287 ASP cc_start: 0.6760 (m-30) cc_final: 0.6508 (m-30) REVERT: A 811 LYS cc_start: 0.7397 (mmtm) cc_final: 0.6447 (tttp) REVERT: A 904 TYR cc_start: 0.7090 (m-10) cc_final: 0.6497 (m-10) REVERT: A 1029 MET cc_start: 0.9026 (tpp) cc_final: 0.8648 (ttm) outliers start: 58 outliers final: 43 residues processed: 284 average time/residue: 0.3390 time to fit residues: 155.3002 Evaluate side-chains 263 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 217 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 4.9990 chunk 271 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 177 optimal weight: 0.0060 chunk 74 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 158 optimal weight: 0.0670 overall best weight: 0.4934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A1083 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25354 Z= 0.146 Angle : 0.525 12.486 34493 Z= 0.267 Chirality : 0.044 0.372 4009 Planarity : 0.004 0.051 4424 Dihedral : 6.216 85.231 3951 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.33 % Allowed : 12.19 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 3081 helix: 2.02 (0.20), residues: 676 sheet: -0.13 (0.20), residues: 665 loop : -1.43 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.002 0.000 HIS A1088 PHE 0.017 0.001 PHE A 371 TYR 0.018 0.001 TYR A1138 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 229 time to evaluate : 2.909 Fit side-chains REVERT: C 200 TYR cc_start: 0.7906 (m-80) cc_final: 0.7576 (m-80) REVERT: C 332 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7033 (mm) REVERT: C 340 GLU cc_start: 0.8036 (mp0) cc_final: 0.7766 (mp0) REVERT: C 396 TYR cc_start: 0.7950 (m-80) cc_final: 0.7505 (m-80) REVERT: C 430 THR cc_start: 0.7740 (p) cc_final: 0.7513 (m) REVERT: C 537 LYS cc_start: 0.7339 (mtpp) cc_final: 0.7121 (tppt) REVERT: C 675 GLN cc_start: 0.6999 (pp30) cc_final: 0.6332 (pp30) REVERT: C 1073 LYS cc_start: 0.7593 (ptmm) cc_final: 0.7009 (mtpt) REVERT: B 224 GLU cc_start: 0.8211 (mp0) cc_final: 0.7880 (mp0) REVERT: B 422 ASN cc_start: 0.8084 (m110) cc_final: 0.7737 (m-40) REVERT: B 646 ARG cc_start: 0.7646 (mtp180) cc_final: 0.7107 (ttt90) REVERT: B 936 ASP cc_start: 0.7474 (t0) cc_final: 0.7149 (t0) REVERT: A 224 GLU cc_start: 0.6744 (mp0) cc_final: 0.6470 (mp0) REVERT: A 287 ASP cc_start: 0.6756 (m-30) cc_final: 0.6456 (m-30) REVERT: A 811 LYS cc_start: 0.7312 (mmtm) cc_final: 0.6508 (tttp) REVERT: A 904 TYR cc_start: 0.7173 (m-10) cc_final: 0.6771 (m-10) outliers start: 36 outliers final: 29 residues processed: 254 average time/residue: 0.3366 time to fit residues: 140.4094 Evaluate side-chains 243 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 10.0000 chunk 34 optimal weight: 0.3980 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 20.0000 chunk 170 optimal weight: 0.6980 chunk 254 optimal weight: 0.3980 chunk 168 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25354 Z= 0.229 Angle : 0.540 10.957 34493 Z= 0.276 Chirality : 0.044 0.255 4009 Planarity : 0.004 0.047 4424 Dihedral : 5.754 58.589 3951 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.69 % Allowed : 12.12 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3081 helix: 1.87 (0.20), residues: 691 sheet: -0.11 (0.21), residues: 596 loop : -1.43 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 886 HIS 0.003 0.001 HIS A1058 PHE 0.019 0.001 PHE A 43 TYR 0.014 0.001 TYR B 421 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 214 time to evaluate : 2.735 Fit side-chains revert: symmetry clash REVERT: C 200 TYR cc_start: 0.7900 (m-80) cc_final: 0.7631 (m-80) REVERT: C 340 GLU cc_start: 0.8066 (mp0) cc_final: 0.7759 (mp0) REVERT: C 396 TYR cc_start: 0.7968 (m-80) cc_final: 0.7530 (m-80) REVERT: C 430 THR cc_start: 0.7774 (p) cc_final: 0.7544 (m) REVERT: C 537 LYS cc_start: 0.7432 (mtpp) cc_final: 0.7204 (tppt) REVERT: C 675 GLN cc_start: 0.6996 (pp30) cc_final: 0.6327 (pp30) REVERT: C 1073 LYS cc_start: 0.7588 (ptmm) cc_final: 0.7017 (mtpt) REVERT: B 32 PHE cc_start: 0.8899 (m-80) cc_final: 0.8688 (m-10) REVERT: B 125 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7541 (m110) REVERT: B 224 GLU cc_start: 0.8265 (mp0) cc_final: 0.7931 (mp0) REVERT: B 422 ASN cc_start: 0.8054 (m110) cc_final: 0.7704 (m-40) REVERT: B 646 ARG cc_start: 0.7627 (mtp180) cc_final: 0.7124 (ttt90) REVERT: B 1107 ARG cc_start: 0.7546 (mtt180) cc_final: 0.7045 (mmm160) REVERT: A 224 GLU cc_start: 0.6784 (mp0) cc_final: 0.6481 (mp0) REVERT: A 287 ASP cc_start: 0.6792 (m-30) cc_final: 0.6500 (m-30) REVERT: A 811 LYS cc_start: 0.7335 (mmtm) cc_final: 0.6525 (tttt) REVERT: A 904 TYR cc_start: 0.7219 (m-10) cc_final: 0.6812 (m-10) outliers start: 46 outliers final: 37 residues processed: 245 average time/residue: 0.3350 time to fit residues: 133.2075 Evaluate side-chains 246 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 208 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 0.0060 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 0.0370 chunk 58 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 236 optimal weight: 0.0060 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN B 125 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25354 Z= 0.133 Angle : 0.490 8.249 34493 Z= 0.252 Chirality : 0.043 0.254 4009 Planarity : 0.003 0.046 4424 Dihedral : 5.233 57.260 3951 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.55 % Allowed : 12.38 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3081 helix: 2.22 (0.20), residues: 685 sheet: -0.00 (0.21), residues: 611 loop : -1.35 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.002 0.000 HIS B1083 PHE 0.020 0.001 PHE B 592 TYR 0.017 0.001 TYR A1138 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 230 time to evaluate : 2.734 Fit side-chains revert: symmetry clash REVERT: C 200 TYR cc_start: 0.7722 (m-80) cc_final: 0.7499 (m-80) REVERT: C 340 GLU cc_start: 0.8041 (mp0) cc_final: 0.7734 (mp0) REVERT: C 396 TYR cc_start: 0.7922 (m-80) cc_final: 0.7499 (m-80) REVERT: C 430 THR cc_start: 0.7724 (p) cc_final: 0.7465 (m) REVERT: C 458 LYS cc_start: 0.7180 (tttt) cc_final: 0.6864 (mttp) REVERT: C 537 LYS cc_start: 0.7300 (mtpp) cc_final: 0.7097 (tppt) REVERT: C 675 GLN cc_start: 0.6974 (pp30) cc_final: 0.6348 (pp30) REVERT: C 902 MET cc_start: 0.8797 (tpt) cc_final: 0.8588 (mmm) REVERT: C 955 ASN cc_start: 0.7091 (m-40) cc_final: 0.6774 (m110) REVERT: C 1073 LYS cc_start: 0.7536 (ptmm) cc_final: 0.7050 (mtpt) REVERT: B 32 PHE cc_start: 0.8905 (m-80) cc_final: 0.8668 (m-10) REVERT: B 224 GLU cc_start: 0.8211 (mp0) cc_final: 0.7914 (mp0) REVERT: B 422 ASN cc_start: 0.8065 (m110) cc_final: 0.7737 (m-40) REVERT: B 646 ARG cc_start: 0.7600 (mtp180) cc_final: 0.7013 (ttt90) REVERT: B 834 ILE cc_start: 0.5377 (OUTLIER) cc_final: 0.5107 (tp) REVERT: B 902 MET cc_start: 0.8135 (tpt) cc_final: 0.7689 (mmt) REVERT: A 224 GLU cc_start: 0.6734 (mp0) cc_final: 0.6490 (mp0) REVERT: A 287 ASP cc_start: 0.6767 (m-30) cc_final: 0.6489 (m-30) REVERT: A 811 LYS cc_start: 0.7327 (mmtm) cc_final: 0.6578 (tttm) REVERT: A 904 TYR cc_start: 0.7128 (m-10) cc_final: 0.6736 (m-10) outliers start: 42 outliers final: 35 residues processed: 254 average time/residue: 0.3407 time to fit residues: 141.3571 Evaluate side-chains 252 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 2.9990 chunk 288 optimal weight: 0.6980 chunk 262 optimal weight: 0.0270 chunk 280 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 220 optimal weight: 20.0000 chunk 85 optimal weight: 0.4980 chunk 253 optimal weight: 0.3980 chunk 265 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN B 125 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25354 Z= 0.142 Angle : 0.494 8.378 34493 Z= 0.253 Chirality : 0.043 0.246 4009 Planarity : 0.003 0.045 4424 Dihedral : 5.029 56.638 3951 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.36 % Allowed : 13.15 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3081 helix: 2.29 (0.20), residues: 686 sheet: 0.06 (0.21), residues: 604 loop : -1.33 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.000 HIS B1083 PHE 0.021 0.001 PHE A 392 TYR 0.015 0.001 TYR B 396 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 217 time to evaluate : 2.878 Fit side-chains revert: symmetry clash REVERT: C 200 TYR cc_start: 0.7752 (m-80) cc_final: 0.7548 (m-80) REVERT: C 340 GLU cc_start: 0.8034 (mp0) cc_final: 0.7724 (mp0) REVERT: C 396 TYR cc_start: 0.7913 (m-80) cc_final: 0.7503 (m-80) REVERT: C 430 THR cc_start: 0.7715 (p) cc_final: 0.7460 (m) REVERT: C 458 LYS cc_start: 0.7168 (tttt) cc_final: 0.6858 (mttp) REVERT: C 675 GLN cc_start: 0.6921 (pp30) cc_final: 0.6295 (pp30) REVERT: C 902 MET cc_start: 0.8843 (tpt) cc_final: 0.8603 (mmm) REVERT: C 955 ASN cc_start: 0.7026 (m-40) cc_final: 0.6666 (m110) REVERT: C 1073 LYS cc_start: 0.7477 (ptmm) cc_final: 0.6989 (mtpt) REVERT: B 224 GLU cc_start: 0.8238 (mp0) cc_final: 0.7947 (mp0) REVERT: B 422 ASN cc_start: 0.8071 (m110) cc_final: 0.7745 (m-40) REVERT: B 646 ARG cc_start: 0.7565 (mtp180) cc_final: 0.7046 (ttt90) REVERT: B 834 ILE cc_start: 0.5458 (OUTLIER) cc_final: 0.5185 (tp) REVERT: B 902 MET cc_start: 0.8138 (tpt) cc_final: 0.7673 (mmt) REVERT: A 224 GLU cc_start: 0.6748 (mp0) cc_final: 0.6514 (mp0) REVERT: A 287 ASP cc_start: 0.6781 (m-30) cc_final: 0.6499 (m-30) REVERT: A 811 LYS cc_start: 0.7327 (mmtm) cc_final: 0.6549 (tttp) REVERT: A 904 TYR cc_start: 0.7118 (m-10) cc_final: 0.6735 (m-10) outliers start: 37 outliers final: 35 residues processed: 239 average time/residue: 0.3374 time to fit residues: 131.2212 Evaluate side-chains 251 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 25354 Z= 0.371 Angle : 0.610 8.454 34493 Z= 0.316 Chirality : 0.047 0.232 4009 Planarity : 0.004 0.047 4424 Dihedral : 5.528 58.203 3951 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.73 % Allowed : 13.19 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 3081 helix: 1.76 (0.20), residues: 687 sheet: -0.08 (0.20), residues: 655 loop : -1.44 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.006 0.001 HIS C1058 PHE 0.029 0.002 PHE A 392 TYR 0.021 0.002 TYR A1138 ARG 0.005 0.001 ARG B 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 220 time to evaluate : 2.843 Fit side-chains revert: symmetry clash REVERT: C 396 TYR cc_start: 0.7982 (m-80) cc_final: 0.7543 (m-80) REVERT: C 430 THR cc_start: 0.7844 (p) cc_final: 0.7559 (m) REVERT: C 506 GLN cc_start: 0.8409 (mp10) cc_final: 0.7951 (mp10) REVERT: C 675 GLN cc_start: 0.7032 (pp30) cc_final: 0.6419 (pp30) REVERT: C 1073 LYS cc_start: 0.7564 (ptmm) cc_final: 0.7029 (mtpt) REVERT: B 224 GLU cc_start: 0.8272 (mp0) cc_final: 0.7946 (mp0) REVERT: B 422 ASN cc_start: 0.8169 (m110) cc_final: 0.7898 (m-40) REVERT: B 646 ARG cc_start: 0.7660 (mtp180) cc_final: 0.7086 (ttt90) REVERT: B 834 ILE cc_start: 0.5525 (OUTLIER) cc_final: 0.5170 (tp) REVERT: B 1107 ARG cc_start: 0.7530 (mtt180) cc_final: 0.7051 (mmm160) REVERT: A 53 ASP cc_start: 0.6847 (t0) cc_final: 0.6317 (t0) REVERT: A 191 GLU cc_start: 0.6613 (tp30) cc_final: 0.6391 (tp30) REVERT: A 287 ASP cc_start: 0.6803 (m-30) cc_final: 0.6591 (m-30) REVERT: A 811 LYS cc_start: 0.7431 (mmtm) cc_final: 0.6631 (tttm) REVERT: A 828 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7133 (tt) REVERT: A 904 TYR cc_start: 0.7073 (m-10) cc_final: 0.6627 (m-10) outliers start: 47 outliers final: 38 residues processed: 251 average time/residue: 0.3432 time to fit residues: 139.1865 Evaluate side-chains 251 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 211 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.5980 chunk 263 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 228 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 68 optimal weight: 0.0170 chunk 247 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 254 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 218 GLN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.183636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144582 restraints weight = 28914.763| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.57 r_work: 0.3144 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25354 Z= 0.167 Angle : 0.524 8.440 34493 Z= 0.269 Chirality : 0.043 0.241 4009 Planarity : 0.004 0.041 4424 Dihedral : 5.176 58.328 3951 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.51 % Allowed : 13.55 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3081 helix: 2.09 (0.20), residues: 684 sheet: -0.07 (0.20), residues: 626 loop : -1.40 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.003 0.001 HIS B1083 PHE 0.020 0.001 PHE A 392 TYR 0.018 0.001 TYR A1138 ARG 0.005 0.000 ARG B 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4941.14 seconds wall clock time: 89 minutes 24.36 seconds (5364.36 seconds total)