Starting phenix.real_space_refine on Fri Aug 9 03:22:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayw_44000/08_2024/9ayw_44000_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayw_44000/08_2024/9ayw_44000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayw_44000/08_2024/9ayw_44000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayw_44000/08_2024/9ayw_44000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayw_44000/08_2024/9ayw_44000_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayw_44000/08_2024/9ayw_44000_neut.cif" } resolution = 3.0 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= -0.001 sd= 0.069 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 15840 2.51 5 N 4095 2.21 5 O 4764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C 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: 24813 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8131 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "B" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8131 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "C" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8131 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 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 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: "C" 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: 14.26, per 1000 atoms: 0.57 Number of scatterers: 24813 At special positions: 0 Unit cell: (137.16, 128.52, 173.88, 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 4764 8.00 N 4095 7.00 C 15840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 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 234 " " NAG C1310 " - " ASN C 801 " Time building additional restraints: 8.76 Conformation dependent library (CDL) restraints added in 4.6 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: 70 helices and 47 sheets defined 25.6% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.508A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 4.177A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.883A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 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 782 removed outlier: 3.600A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.581A 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 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.665A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.785A 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: 3.568A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.545A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.828A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.232A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.904A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 368' Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.025A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.268A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.840A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 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 758 through 783 removed outlier: 3.576A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.516A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.539A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.566A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.546A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (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: 3.504A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.531A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.837A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.658A pdb=" N ASN C 343 " --> pdb=" O HIS C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.842A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.538A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.674A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 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: 3.576A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 842 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.568A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.517A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.513A 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: 3.617A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.635A 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.509A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.984A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.846A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.477A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.986A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.153A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.557A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.402A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.617A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.704A pdb=" N ALA A 435 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.067A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.830A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.700A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.168A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.567A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.989A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.002A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.705A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.585A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 318 removed outlier: 7.044A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.746A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.691A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.955A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.714A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.948A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.559A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.785A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.040A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.533A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.030A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.541A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.568A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.638A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.101A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.808A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.138A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.591A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 1019 hydrogen bonds defined for protein. 2799 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: 11.21 Time building geometry restraints manager: 9.74 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: 7933 1.35 - 1.48: 6653 1.48 - 1.62: 10647 1.62 - 1.75: 0 1.75 - 1.88: 141 Bond restraints: 25374 Sorted by residual: bond pdb=" C ALA C1056 " pdb=" N PRO C1057 " ideal model delta sigma weight residual 1.332 1.359 -0.027 1.12e-02 7.97e+03 5.79e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " ideal model delta sigma weight residual 1.808 1.881 -0.073 3.30e-02 9.18e+02 4.93e+00 bond pdb=" C LEU B 560 " pdb=" N PRO B 561 " ideal model delta sigma weight residual 1.337 1.358 -0.022 9.80e-03 1.04e+04 4.81e+00 bond pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.81e+00 ... (remaining 25369 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.36: 476 105.36 - 112.53: 12909 112.53 - 119.70: 8378 119.70 - 126.86: 12488 126.86 - 134.03: 270 Bond angle restraints: 34521 Sorted by residual: angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 131.80 -17.40 2.30e+00 1.89e-01 5.72e+01 angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 129.85 -15.45 2.30e+00 1.89e-01 4.52e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 128.73 -14.33 2.30e+00 1.89e-01 3.88e+01 angle pdb=" CA CYS C 649 " pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " ideal model delta sigma weight residual 114.40 123.95 -9.55 2.30e+00 1.89e-01 1.72e+01 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 123.89 -9.49 2.30e+00 1.89e-01 1.70e+01 ... (remaining 34516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 14038 18.02 - 36.03: 1229 36.03 - 54.05: 187 54.05 - 72.07: 54 72.07 - 90.09: 35 Dihedral angle restraints: 15543 sinusoidal: 6438 harmonic: 9105 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 -176.91 -90.09 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -167.38 81.38 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 165.31 -72.31 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 15540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 3987 0.177 - 0.355: 26 0.355 - 0.532: 0 0.532 - 0.709: 0 0.709 - 0.887: 1 Chirality restraints: 4014 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CG LEU A 390 " pdb=" CB LEU A 390 " pdb=" CD1 LEU A 390 " pdb=" CD2 LEU A 390 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 4011 not shown) Planarity restraints: 4455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.005 2.00e-02 2.50e+03 3.69e-02 1.70e+01 pdb=" CG ASN A 343 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 138 " -0.058 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO C 139 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 139 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 139 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.020 2.00e-02 2.50e+03 1.87e-02 6.10e+00 pdb=" CG PHE A 906 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.005 2.00e-02 2.50e+03 ... (remaining 4452 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6696 2.81 - 3.33: 19638 3.33 - 3.86: 39869 3.86 - 4.38: 45735 4.38 - 4.90: 82132 Nonbonded interactions: 194070 Sorted by model distance: nonbonded pdb=" OE2 GLU B 298 " pdb=" OG SER B 316 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.313 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.317 3.040 ... (remaining 194065 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' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.410 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: 0.880 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 68.450 Find NCS groups from input model: 0.980 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:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 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 : 0.005 0.073 25374 Z= 0.314 Angle : 0.784 17.401 34521 Z= 0.414 Chirality : 0.057 0.887 4014 Planarity : 0.006 0.089 4425 Dihedral : 14.170 89.980 9558 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.76 (0.14), residues: 3081 helix: 0.13 (0.18), residues: 627 sheet: 0.79 (0.18), residues: 762 loop : -1.43 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 886 HIS 0.008 0.001 HIS A 339 PHE 0.043 0.002 PHE A 906 TYR 0.036 0.002 TYR C 453 ARG 0.016 0.001 ARG C 995 *********************** 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 286 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 SER cc_start: 0.8794 (p) cc_final: 0.8204 (m) REVERT: B 731 MET cc_start: 0.8910 (ptt) cc_final: 0.8491 (ptt) REVERT: B 851 CYS cc_start: 0.7552 (m) cc_final: 0.7148 (m) REVERT: C 220 PHE cc_start: 0.8144 (m-80) cc_final: 0.7886 (m-80) REVERT: C 995 ARG cc_start: 0.7662 (mtt-85) cc_final: 0.7408 (mtm180) outliers start: 0 outliers final: 1 residues processed: 286 average time/residue: 1.1581 time to fit residues: 390.2352 Evaluate side-chains 202 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 564 GLN A 710 ASN A 804 GLN B 321 GLN B 334 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B1010 GLN B1088 HIS C 448 ASN C 493 GLN C 606 ASN C 762 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25374 Z= 0.227 Angle : 0.547 10.343 34521 Z= 0.287 Chirality : 0.045 0.222 4014 Planarity : 0.004 0.062 4425 Dihedral : 6.321 57.032 3974 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.22 % Allowed : 7.92 % Favored : 90.87 % 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: -0.02 (0.15), residues: 3081 helix: 1.62 (0.20), residues: 645 sheet: 0.95 (0.18), residues: 798 loop : -1.25 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS A 207 PHE 0.024 0.002 PHE A 906 TYR 0.017 0.001 TYR C1067 ARG 0.008 0.000 ARG A 567 *********************** 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 261 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 228 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 731 MET cc_start: 0.9023 (ptt) cc_final: 0.8669 (ptt) REVERT: B 851 CYS cc_start: 0.7648 (m) cc_final: 0.7335 (m) REVERT: C 776 LYS cc_start: 0.7934 (tttp) cc_final: 0.7685 (tttt) outliers start: 33 outliers final: 16 residues processed: 241 average time/residue: 1.0590 time to fit residues: 305.7441 Evaluate side-chains 217 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 201 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 723 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 235 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 306 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 281 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 30 ASN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25374 Z= 0.263 Angle : 0.561 11.574 34521 Z= 0.293 Chirality : 0.046 0.202 4014 Planarity : 0.004 0.048 4425 Dihedral : 5.890 53.583 3972 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.88 % Allowed : 10.87 % Favored : 87.26 % 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: 0.09 (0.15), residues: 3081 helix: 2.05 (0.20), residues: 648 sheet: 0.81 (0.18), residues: 756 loop : -1.16 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS C1048 PHE 0.029 0.002 PHE A 906 TYR 0.018 0.001 TYR C1067 ARG 0.008 0.000 ARG A 567 *********************** 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 272 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 221 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 SER cc_start: 0.8347 (m) cc_final: 0.8131 (p) REVERT: A 904 TYR cc_start: 0.7150 (m-10) cc_final: 0.6950 (m-10) REVERT: B 291 CYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6460 (m) REVERT: B 731 MET cc_start: 0.9041 (ptt) cc_final: 0.8666 (ptt) REVERT: C 33 THR cc_start: 0.8473 (t) cc_final: 0.8058 (m) REVERT: C 776 LYS cc_start: 0.7915 (tttp) cc_final: 0.7687 (tttt) outliers start: 51 outliers final: 34 residues processed: 249 average time/residue: 1.0439 time to fit residues: 311.9292 Evaluate side-chains 237 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 190 optimal weight: 4.9990 chunk 284 optimal weight: 0.6980 chunk 301 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 269 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 564 GLN B 321 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 218 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25374 Z= 0.192 Angle : 0.509 10.887 34521 Z= 0.267 Chirality : 0.044 0.205 4014 Planarity : 0.003 0.048 4425 Dihedral : 5.347 54.319 3972 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.32 % Allowed : 12.15 % Favored : 85.52 % 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: 0.19 (0.15), residues: 3081 helix: 2.09 (0.20), residues: 669 sheet: 0.81 (0.18), residues: 807 loop : -1.15 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS A 207 PHE 0.016 0.001 PHE A 318 TYR 0.016 0.001 TYR C1067 ARG 0.008 0.000 ARG A 567 *********************** 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 286 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 223 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.7862 (pm20) cc_final: 0.7535 (pm20) REVERT: A 443 SER cc_start: 0.8396 (m) cc_final: 0.8149 (p) REVERT: B 731 MET cc_start: 0.9074 (ptt) cc_final: 0.8692 (ptt) REVERT: C 33 THR cc_start: 0.8403 (t) cc_final: 0.8004 (m) REVERT: C 531 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7844 (p) REVERT: C 776 LYS cc_start: 0.7882 (tttp) cc_final: 0.7649 (tttt) outliers start: 63 outliers final: 39 residues processed: 259 average time/residue: 0.9997 time to fit residues: 315.0210 Evaluate side-chains 239 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 503 VAL 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 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A1101 HIS B 49 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 25374 Z= 0.438 Angle : 0.659 13.193 34521 Z= 0.343 Chirality : 0.050 0.240 4014 Planarity : 0.004 0.049 4425 Dihedral : 5.958 52.094 3972 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.24 % Allowed : 13.52 % Favored : 83.24 % 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: -0.12 (0.15), residues: 3081 helix: 1.62 (0.20), residues: 687 sheet: 0.61 (0.18), residues: 765 loop : -1.22 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.006 0.001 HIS C1058 PHE 0.029 0.002 PHE A 906 TYR 0.019 0.002 TYR C1067 ARG 0.008 0.001 ARG A 567 *********************** 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 313 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 225 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7414 (t80) REVERT: A 281 GLU cc_start: 0.7822 (pm20) cc_final: 0.7574 (pm20) REVERT: A 346 THR cc_start: 0.8202 (p) cc_final: 0.7895 (t) REVERT: A 443 SER cc_start: 0.8410 (m) cc_final: 0.8177 (p) REVERT: B 319 ARG cc_start: 0.7048 (mmm-85) cc_final: 0.6776 (mmt90) REVERT: B 731 MET cc_start: 0.9047 (ptt) cc_final: 0.8757 (ptt) REVERT: C 33 THR cc_start: 0.8538 (t) cc_final: 0.8218 (m) REVERT: C 776 LYS cc_start: 0.8014 (tttp) cc_final: 0.7809 (tttt) outliers start: 88 outliers final: 57 residues processed: 285 average time/residue: 1.0135 time to fit residues: 347.5919 Evaluate side-chains 263 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 205 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 998 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 2.9990 chunk 271 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1101 HIS B 321 GLN B 644 GLN B1005 GLN C 69 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25374 Z= 0.270 Angle : 0.567 12.047 34521 Z= 0.296 Chirality : 0.046 0.222 4014 Planarity : 0.004 0.047 4425 Dihedral : 5.523 53.977 3972 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.24 % Allowed : 14.66 % Favored : 82.10 % 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: 0.01 (0.15), residues: 3081 helix: 1.86 (0.20), residues: 684 sheet: 0.61 (0.17), residues: 816 loop : -1.21 (0.14), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS C 69 PHE 0.017 0.002 PHE B 377 TYR 0.017 0.001 TYR C1067 ARG 0.009 0.000 ARG A 567 *********************** 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 302 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 214 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7463 (t80) REVERT: A 281 GLU cc_start: 0.7826 (pm20) cc_final: 0.7587 (pm20) REVERT: A 346 THR cc_start: 0.8190 (p) cc_final: 0.7891 (t) REVERT: A 443 SER cc_start: 0.8333 (m) cc_final: 0.8126 (p) REVERT: B 731 MET cc_start: 0.9112 (ptt) cc_final: 0.8841 (ptt) REVERT: C 33 THR cc_start: 0.8509 (t) cc_final: 0.8190 (m) REVERT: C 531 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7870 (p) outliers start: 88 outliers final: 62 residues processed: 274 average time/residue: 0.9907 time to fit residues: 329.5075 Evaluate side-chains 268 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 204 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 998 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1101 HIS B 644 GLN C 69 HIS C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25374 Z= 0.267 Angle : 0.564 11.428 34521 Z= 0.293 Chirality : 0.046 0.225 4014 Planarity : 0.004 0.052 4425 Dihedral : 5.461 53.365 3972 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.39 % Allowed : 15.14 % Favored : 81.47 % 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: 0.04 (0.15), residues: 3081 helix: 1.93 (0.20), residues: 687 sheet: 0.60 (0.17), residues: 816 loop : -1.20 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS C 69 PHE 0.018 0.002 PHE B 377 TYR 0.017 0.001 TYR C1067 ARG 0.009 0.000 ARG A 567 *********************** 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 305 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 213 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8125 (m-80) cc_final: 0.7820 (m-80) REVERT: A 281 GLU cc_start: 0.7840 (pm20) cc_final: 0.7605 (pm20) REVERT: A 346 THR cc_start: 0.8241 (p) cc_final: 0.7923 (t) REVERT: A 443 SER cc_start: 0.8312 (m) cc_final: 0.8100 (p) REVERT: B 731 MET cc_start: 0.9111 (ptt) cc_final: 0.8836 (ptt) REVERT: B 1139 ASP cc_start: 0.7837 (t0) cc_final: 0.7625 (t70) REVERT: C 33 THR cc_start: 0.8515 (t) cc_final: 0.8208 (m) REVERT: C 177 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5562 (tmm) REVERT: C 218 GLN cc_start: 0.8357 (tp40) cc_final: 0.8128 (tp40) REVERT: C 531 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7876 (p) REVERT: C 904 TYR cc_start: 0.7556 (m-10) cc_final: 0.6245 (m-80) outliers start: 92 outliers final: 71 residues processed: 280 average time/residue: 0.9481 time to fit residues: 323.5688 Evaluate side-chains 282 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 209 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 0.0980 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 236 optimal weight: 7.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1101 HIS B 30 ASN B 360 ASN B 644 GLN B 901 GLN B1005 GLN C 207 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25374 Z= 0.146 Angle : 0.500 11.506 34521 Z= 0.259 Chirality : 0.044 0.217 4014 Planarity : 0.003 0.056 4425 Dihedral : 5.338 59.065 3972 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.21 % Allowed : 16.46 % Favored : 81.33 % 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: 0.30 (0.15), residues: 3081 helix: 2.29 (0.20), residues: 684 sheet: 0.75 (0.17), residues: 807 loop : -1.09 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.006 0.001 HIS C 69 PHE 0.013 0.001 PHE C 592 TYR 0.015 0.001 TYR C1067 ARG 0.008 0.000 ARG A 567 *********************** 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 281 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 221 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8010 (m-80) cc_final: 0.7807 (m-80) REVERT: A 281 GLU cc_start: 0.7883 (pm20) cc_final: 0.7647 (pm20) REVERT: A 443 SER cc_start: 0.8311 (m) cc_final: 0.8091 (p) REVERT: A 904 TYR cc_start: 0.7103 (m-10) cc_final: 0.6873 (m-10) REVERT: B 731 MET cc_start: 0.9140 (ptt) cc_final: 0.8727 (ptt) REVERT: B 1139 ASP cc_start: 0.7877 (t0) cc_final: 0.7650 (t70) REVERT: C 33 THR cc_start: 0.8406 (t) cc_final: 0.8032 (m) REVERT: C 177 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.5615 (tmm) REVERT: C 531 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7918 (p) REVERT: C 1113 GLN cc_start: 0.8173 (mt0) cc_final: 0.7969 (mt0) outliers start: 60 outliers final: 33 residues processed: 260 average time/residue: 0.9814 time to fit residues: 311.8408 Evaluate side-chains 241 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 206 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU 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: 2.9990 chunk 262 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 265 optimal weight: 0.6980 chunk 279 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1101 HIS B 26 GLN B 901 GLN C 69 HIS C 121 ASN C 207 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25374 Z= 0.283 Angle : 0.578 12.346 34521 Z= 0.299 Chirality : 0.046 0.244 4014 Planarity : 0.004 0.056 4425 Dihedral : 5.893 73.703 3972 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.10 % Allowed : 16.91 % Favored : 80.99 % 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: 0.20 (0.15), residues: 3081 helix: 2.09 (0.20), residues: 687 sheet: 0.69 (0.17), residues: 813 loop : -1.11 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS C 69 PHE 0.021 0.002 PHE A 318 TYR 0.017 0.001 TYR C1067 ARG 0.009 0.000 ARG A 567 *********************** 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 266 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 209 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8115 (m-80) cc_final: 0.7839 (m-80) REVERT: A 281 GLU cc_start: 0.7846 (pm20) cc_final: 0.7580 (pm20) REVERT: A 346 THR cc_start: 0.8268 (p) cc_final: 0.7986 (t) REVERT: A 443 SER cc_start: 0.8382 (m) cc_final: 0.8135 (p) REVERT: B 731 MET cc_start: 0.9086 (ptt) cc_final: 0.8808 (ptt) REVERT: C 33 THR cc_start: 0.8487 (t) cc_final: 0.8188 (m) REVERT: C 177 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5600 (tmm) REVERT: C 375 PHE cc_start: 0.4032 (OUTLIER) cc_final: 0.3111 (m-80) REVERT: C 574 ASP cc_start: 0.7209 (t0) cc_final: 0.6937 (t0) REVERT: C 904 TYR cc_start: 0.7528 (m-10) cc_final: 0.6154 (m-80) outliers start: 57 outliers final: 44 residues processed: 250 average time/residue: 1.0110 time to fit residues: 306.2081 Evaluate side-chains 246 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 200 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.2980 chunk 296 optimal weight: 0.0170 chunk 180 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 310 optimal weight: 0.6980 chunk 286 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 chunk 191 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 564 GLN A 784 GLN A1101 HIS B 360 ASN B 505 HIS B 613 GLN C 69 HIS C 121 ASN C 207 HIS C 218 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25374 Z= 0.139 Angle : 0.493 10.587 34521 Z= 0.256 Chirality : 0.044 0.197 4014 Planarity : 0.003 0.055 4425 Dihedral : 5.609 86.145 3972 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.69 % Allowed : 17.42 % Favored : 80.88 % 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: 0.45 (0.15), residues: 3081 helix: 2.50 (0.20), residues: 684 sheet: 0.78 (0.18), residues: 804 loop : -0.99 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.007 0.001 HIS C 69 PHE 0.022 0.001 PHE A 318 TYR 0.016 0.001 TYR C1067 ARG 0.009 0.000 ARG A 567 ********************** 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 255 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 209 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7291 (mp0) REVERT: A 281 GLU cc_start: 0.7878 (pm20) cc_final: 0.7530 (pm20) REVERT: A 443 SER cc_start: 0.8275 (m) cc_final: 0.8048 (p) REVERT: A 503 VAL cc_start: 0.8331 (p) cc_final: 0.8042 (t) REVERT: A 904 TYR cc_start: 0.7141 (m-10) cc_final: 0.6922 (m-10) REVERT: B 50 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8736 (m) REVERT: B 326 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7440 (mp) REVERT: B 574 ASP cc_start: 0.6990 (t0) cc_final: 0.6675 (t0) REVERT: B 731 MET cc_start: 0.9154 (ptt) cc_final: 0.8763 (ptt) REVERT: B 1139 ASP cc_start: 0.7821 (t0) cc_final: 0.7587 (t70) REVERT: C 33 THR cc_start: 0.8388 (t) cc_final: 0.8019 (m) REVERT: C 177 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5623 (tmm) REVERT: C 375 PHE cc_start: 0.3813 (OUTLIER) cc_final: 0.2859 (m-80) REVERT: C 574 ASP cc_start: 0.7233 (t0) cc_final: 0.6944 (t0) REVERT: C 904 TYR cc_start: 0.7466 (m-10) cc_final: 0.6080 (m-80) outliers start: 46 outliers final: 35 residues processed: 240 average time/residue: 0.9622 time to fit residues: 281.8754 Evaluate side-chains 235 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 247 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 254 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1101 HIS B 26 GLN C 69 HIS C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.171299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130147 restraints weight = 26685.089| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.44 r_work: 0.3173 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25374 Z= 0.161 Angle : 0.506 10.686 34521 Z= 0.262 Chirality : 0.044 0.187 4014 Planarity : 0.003 0.053 4425 Dihedral : 5.613 85.702 3972 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.73 % Allowed : 17.68 % Favored : 80.59 % 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: 0.47 (0.15), residues: 3081 helix: 2.44 (0.20), residues: 687 sheet: 0.81 (0.18), residues: 804 loop : -0.95 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS C 69 PHE 0.025 0.001 PHE A 318 TYR 0.016 0.001 TYR C1067 ARG 0.009 0.000 ARG A 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6563.88 seconds wall clock time: 116 minutes 58.58 seconds (7018.58 seconds total)