Starting phenix.real_space_refine on Wed Mar 20 21:43:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjo_31625/03_2024/7fjo_31625.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjo_31625/03_2024/7fjo_31625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjo_31625/03_2024/7fjo_31625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjo_31625/03_2024/7fjo_31625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjo_31625/03_2024/7fjo_31625.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjo_31625/03_2024/7fjo_31625.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 123 5.16 5 C 18207 2.51 5 N 4694 2.21 5 O 5523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 28": "NH1" <-> "NH2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G ARG 48": "NH1" <-> "NH2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "H ARG 28": "NH1" <-> "NH2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "J ARG 28": "NH1" <-> "NH2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J GLU 101": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K ARG 48": "NH1" <-> "NH2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L ARG 48": "NH1" <-> "NH2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C GLU 1111": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28547 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "G" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 108} Chain: "H" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "J" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "K" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 108} Chain: "L" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 108} Chain: "A" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7696 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 48, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7696 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 48, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 7678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7678 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 7 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 18.08, per 1000 atoms: 0.63 Number of scatterers: 28547 At special positions: 0 Unit cell: (193.23, 163.587, 157, 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 123 16.00 O 5523 8.00 N 4694 7.00 C 18207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 94 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.16 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.09 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 282 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 10.45 Conformation dependent library (CDL) restraints added in 4.9 seconds 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6782 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 63 sheets defined 19.6% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.587A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.512A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.133A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.546A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.656A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.562A 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 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 963 removed outlier: 4.253A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.820A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.482A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.581A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.677A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) 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: 4.056A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.502A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.868A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.580A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.589A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.549A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.869A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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: 3.870A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.615A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.587A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.667A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 removed outlier: 6.946A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE C 759 " --> pdb=" O TYR C 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 755 through 759' Processing helix chain 'C' and resid 760 through 783 removed outlier: 4.341A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.845A 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 866 through 885 removed outlier: 3.616A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.543A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.535A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.581A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (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: 3.758A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1147 Processing sheet with id=AA1, first strand: chain 'F' and resid 18 through 23 removed outlier: 3.589A pdb=" N CYS F 22 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 59 through 60 removed outlier: 3.519A pdb=" N SER F 59 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE F 34 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER G 7 " --> pdb=" O SER G 22 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER G 22 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.265A pdb=" N LEU G 11 " --> pdb=" O GLU G 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 30 through 31 removed outlier: 3.625A pdb=" N LYS G 36 " --> pdb=" O TYR G 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.707A pdb=" N TRP G 41 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N HIS G 55 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU G 39 " --> pdb=" O HIS G 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 18 through 23 removed outlier: 3.589A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 59 through 60 removed outlier: 3.519A pdb=" N SER H 59 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 18 through 23 removed outlier: 3.589A pdb=" N CYS J 22 " --> pdb=" O ALA J 79 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP J 73 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 59 through 60 removed outlier: 3.519A pdb=" N SER J 59 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER K 7 " --> pdb=" O SER K 22 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER K 22 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.265A pdb=" N LEU K 11 " --> pdb=" O GLU K 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 30 through 31 removed outlier: 3.625A pdb=" N LYS K 36 " --> pdb=" O TYR K 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 59 through 60 removed outlier: 6.707A pdb=" N TRP K 41 " --> pdb=" O LEU K 53 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N HIS K 55 " --> pdb=" O LEU K 39 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU K 39 " --> pdb=" O HIS K 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.265A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.625A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.707A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N HIS L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU L 39 " --> pdb=" O HIS L 55 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.794A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.672A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.823A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.646A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.292A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.006A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 355 removed outlier: 4.395A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.864A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.648A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.999A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.866A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.207A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.969A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.673A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.564A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.427A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.616A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 354 through 355 removed outlier: 4.394A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.864A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.650A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.079A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AF1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.860A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 718 through 720 Processing sheet with id=AF3, first strand: chain 'B' and resid 718 through 720 removed outlier: 3.644A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF5, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.919A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.533A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.343A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AF9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.983A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 354 through 355 removed outlier: 4.394A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 394 through 395 removed outlier: 3.864A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.649A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.971A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AG6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.862A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG9, first strand: chain 'C' and resid 1094 through 1097 1063 hydrogen bonds defined for protein. 2868 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: 12.40 Time building geometry restraints manager: 11.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6982 1.33 - 1.47: 8667 1.47 - 1.61: 13383 1.61 - 1.75: 3 1.75 - 1.89: 153 Bond restraints: 29188 Sorted by residual: bond pdb=" CA GLY K 106 " pdb=" C GLY K 106 " ideal model delta sigma weight residual 1.518 1.627 -0.110 1.48e-02 4.57e+03 5.50e+01 bond pdb=" CA GLY L 106 " pdb=" C GLY L 106 " ideal model delta sigma weight residual 1.518 1.627 -0.109 1.48e-02 4.57e+03 5.44e+01 bond pdb=" CA GLY G 106 " pdb=" C GLY G 106 " ideal model delta sigma weight residual 1.518 1.626 -0.109 1.48e-02 4.57e+03 5.42e+01 bond pdb=" N GLY B 648 " pdb=" CA GLY B 648 " ideal model delta sigma weight residual 1.450 1.500 -0.049 1.01e-02 9.80e+03 2.37e+01 bond pdb=" CA CYS B 617 " pdb=" C CYS B 617 " ideal model delta sigma weight residual 1.522 1.589 -0.067 1.39e-02 5.18e+03 2.34e+01 ... (remaining 29183 not shown) Histogram of bond angle deviations from ideal: 96.58 - 104.30: 384 104.30 - 112.02: 12884 112.02 - 119.75: 12386 119.75 - 127.47: 13879 127.47 - 135.19: 189 Bond angle restraints: 39722 Sorted by residual: angle pdb=" C CYS A 525 " pdb=" N GLY A 526 " pdb=" CA GLY A 526 " ideal model delta sigma weight residual 121.87 109.58 12.29 1.57e+00 4.06e-01 6.13e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 118.38 -7.68 1.22e+00 6.72e-01 3.97e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.35 -7.65 1.22e+00 6.72e-01 3.93e+01 angle pdb=" N GLY K 106 " pdb=" CA GLY K 106 " pdb=" C GLY K 106 " ideal model delta sigma weight residual 112.25 104.04 8.21 1.34e+00 5.57e-01 3.76e+01 angle pdb=" N GLY G 106 " pdb=" CA GLY G 106 " pdb=" C GLY G 106 " ideal model delta sigma weight residual 112.25 104.04 8.21 1.34e+00 5.57e-01 3.76e+01 ... (remaining 39717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 16315 17.36 - 34.71: 975 34.71 - 52.07: 167 52.07 - 69.43: 83 69.43 - 86.78: 23 Dihedral angle restraints: 17563 sinusoidal: 6996 harmonic: 10567 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -159.72 73.72 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -14.88 -71.12 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -154.39 68.39 1 1.00e+01 1.00e-02 6.06e+01 ... (remaining 17560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3225 0.091 - 0.183: 1197 0.183 - 0.274: 153 0.274 - 0.366: 27 0.366 - 0.457: 4 Chirality restraints: 4606 Sorted by residual: chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA PRO B 986 " pdb=" N PRO B 986 " pdb=" C PRO B 986 " pdb=" CB PRO B 986 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 4603 not shown) Planarity restraints: 5088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.343 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG A1307 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.515 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1302 " -0.326 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG A1302 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A1302 " -0.070 2.00e-02 2.50e+03 pdb=" N2 NAG A1302 " 0.504 2.00e-02 2.50e+03 pdb=" O7 NAG A1302 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " -0.333 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG C1304 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " 0.497 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " -0.071 2.00e-02 2.50e+03 ... (remaining 5085 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 26 2.00 - 2.73: 1057 2.73 - 3.45: 39331 3.45 - 4.18: 68635 4.18 - 4.90: 118461 Nonbonded interactions: 227510 Sorted by model distance: nonbonded pdb=" CE2 TYR G 100 " pdb=" ND2 ASN C 487 " model vdw 1.277 3.420 nonbonded pdb=" CE2 TYR K 100 " pdb=" ND2 ASN B 487 " model vdw 1.278 3.420 nonbonded pdb=" CE2 TYR L 100 " pdb=" ND2 ASN A 487 " model vdw 1.278 3.420 nonbonded pdb=" CD PRO A 230 " pdb=" CD PRO C 521 " model vdw 1.446 3.840 nonbonded pdb=" CD2 TYR K 100 " pdb=" CD2 PHE B 486 " model vdw 1.536 3.640 ... (remaining 227505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 114 o \ r (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 190 or (resid 191 and (name \ N or name CA or name C or name O or name CB )) or resid 192 through 280 or (resi \ d 281 and (name N or name CA or name C or name O or name CB )) or resid 282 thro \ ugh 676 or resid 690 through 744 or (resid 745 and (name N or name CA or name C \ or name O or name CB )) or resid 746 through 747 or (resid 748 and (name N or na \ me CA or name C or name O or name CB )) or resid 749 through 810 or (resid 811 a \ nd (name N or name CA or name C or name O or name CB )) or resid 813 through 827 \ or resid 855 through 866 or (resid 867 through 868 and (name N or name CA or na \ me C or name O or name CB )) or resid 869 through 1147 or resid 1301 through 130 \ 8)) selection = (chain 'B' and (resid 27 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 114 o \ r (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 190 or (resid 191 and (name \ N or name CA or name C or name O or name CB )) or resid 192 through 280 or (resi \ d 281 and (name N or name CA or name C or name O or name CB )) or resid 282 thro \ ugh 676 or resid 690 through 744 or (resid 745 and (name N or name CA or name C \ or name O or name CB )) or resid 746 through 747 or (resid 748 and (name N or na \ me CA or name C or name O or name CB )) or resid 749 through 810 or (resid 811 a \ nd (name N or name CA or name C or name O or name CB )) or resid 813 through 827 \ or resid 855 through 866 or (resid 867 through 868 and (name N or name CA or na \ me C or name O or name CB )) or resid 869 through 1147 or resid 1301 through 130 \ 8)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 95 or (resid 96 through 97 and (na \ me N or name CA or name C or name O or name CB )) or resid 98 through 143 or (re \ sid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 and (name N or name CA or name C or name \ O or name CB )) or resid 215 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 through 308 or (re \ sid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 th \ rough 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) \ or resid 529 through 811 or resid 813 through 1141 or (resid 1142 and (name N o \ r name CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid \ 1145 through 1146 and (name N or name CA or name C or name O or name CB )) or r \ esid 1147 or resid 1301 through 1308)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } 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: 2.350 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: 10.600 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 77.140 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3580 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 : 0.012 0.110 29188 Z= 0.760 Angle : 1.565 12.288 39722 Z= 1.077 Chirality : 0.089 0.457 4606 Planarity : 0.016 0.292 5063 Dihedral : 12.537 86.785 10709 Min Nonbonded Distance : 1.277 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.16 % Favored : 92.39 % Rotamer: Outliers : 3.26 % Allowed : 4.25 % Favored : 92.48 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 3576 helix: -0.31 (0.18), residues: 608 sheet: 0.43 (0.19), residues: 766 loop : -1.28 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP B 886 HIS 0.016 0.002 HIS C1048 PHE 0.060 0.007 PHE B 927 TYR 0.096 0.009 TYR A 707 ARG 0.018 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 535 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 22 CYS cc_start: 0.1615 (OUTLIER) cc_final: 0.0016 (p) REVERT: F 43 GLN cc_start: 0.1288 (OUTLIER) cc_final: 0.0210 (mt0) REVERT: F 78 THR cc_start: 0.2852 (OUTLIER) cc_final: 0.2645 (t) REVERT: F 86 LEU cc_start: 0.0172 (OUTLIER) cc_final: -0.0172 (mp) REVERT: G 93 TYR cc_start: -0.0724 (OUTLIER) cc_final: -0.1015 (m-80) REVERT: H 22 CYS cc_start: 0.2458 (OUTLIER) cc_final: 0.0380 (p) REVERT: H 43 GLN cc_start: -0.0031 (OUTLIER) cc_final: -0.0945 (mp10) REVERT: J 22 CYS cc_start: 0.1548 (OUTLIER) cc_final: 0.0097 (t) REVERT: J 51 ILE cc_start: -0.3377 (OUTLIER) cc_final: -0.3675 (mt) REVERT: J 109 GLN cc_start: 0.2176 (OUTLIER) cc_final: 0.1895 (mm110) REVERT: K 111 GLU cc_start: -0.2670 (OUTLIER) cc_final: -0.3640 (tp30) REVERT: K 112 ILE cc_start: 0.5508 (OUTLIER) cc_final: 0.5178 (mm) REVERT: L 21 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5635 (tt) REVERT: A 320 VAL cc_start: 0.5664 (t) cc_final: 0.4889 (t) REVERT: A 1041 ASP cc_start: 0.5934 (t0) cc_final: 0.5677 (t0) REVERT: A 1048 HIS cc_start: 0.4012 (t70) cc_final: 0.3041 (t-170) REVERT: B 365 TYR cc_start: 0.8712 (m-80) cc_final: 0.8408 (m-80) REVERT: B 378 LYS cc_start: 0.8799 (pttt) cc_final: 0.8531 (ptpp) REVERT: B 392 PHE cc_start: 0.7530 (m-80) cc_final: 0.5663 (m-10) REVERT: B 519 HIS cc_start: 0.7322 (m90) cc_final: 0.7101 (m90) REVERT: C 389 ASP cc_start: 0.8205 (p0) cc_final: 0.7908 (t0) outliers start: 102 outliers final: 19 residues processed: 625 average time/residue: 0.3518 time to fit residues: 359.3202 Evaluate side-chains 323 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 291 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 93 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 102 ASN Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 109 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 8.9990 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 282 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 326 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 ASN H 109 GLN J 102 ASN L 6 GLN A 409 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 450 ASN A 481 ASN A 493 GLN A 913 GLN A 955 ASN A1135 ASN B 394 ASN B 409 GLN B 448 ASN B 450 ASN B 493 GLN B 804 GLN B 926 GLN B 935 GLN B 978 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 439 ASN C 448 ASN C 450 ASN C 481 ASN C 493 GLN C 519 HIS C 907 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4531 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29188 Z= 0.228 Angle : 0.689 14.726 39722 Z= 0.358 Chirality : 0.048 0.285 4606 Planarity : 0.005 0.065 5063 Dihedral : 6.870 65.168 4478 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 3.29 % Allowed : 10.04 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.35 (0.14), residues: 3576 helix: 1.16 (0.20), residues: 629 sheet: 0.30 (0.17), residues: 953 loop : -0.96 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 64 HIS 0.011 0.002 HIS K 55 PHE 0.020 0.002 PHE C 970 TYR 0.031 0.002 TYR K 100 ARG 0.005 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 357 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 22 CYS cc_start: 0.1190 (OUTLIER) cc_final: 0.0626 (p) REVERT: J 22 CYS cc_start: 0.0369 (OUTLIER) cc_final: -0.1376 (t) REVERT: K 111 GLU cc_start: -0.2817 (OUTLIER) cc_final: -0.3717 (tp30) REVERT: L 21 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5739 (tt) REVERT: L 93 TYR cc_start: 0.0745 (OUTLIER) cc_final: -0.0146 (m-80) REVERT: L 108 THR cc_start: -0.3367 (OUTLIER) cc_final: -0.4184 (p) REVERT: A 656 VAL cc_start: 0.6842 (p) cc_final: 0.6321 (p) REVERT: A 902 MET cc_start: 0.6498 (mmm) cc_final: 0.5989 (mmp) REVERT: A 964 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5795 (tppt) REVERT: A 1041 ASP cc_start: 0.6721 (t0) cc_final: 0.6087 (t0) REVERT: B 274 THR cc_start: 0.5834 (m) cc_final: 0.5618 (t) REVERT: B 392 PHE cc_start: 0.7467 (m-80) cc_final: 0.5683 (m-80) REVERT: C 1064 HIS cc_start: 0.5009 (OUTLIER) cc_final: 0.4733 (m90) outliers start: 103 outliers final: 51 residues processed: 438 average time/residue: 0.3523 time to fit residues: 256.1003 Evaluate side-chains 297 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 238 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1102 TRP Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1064 HIS Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.8980 chunk 101 optimal weight: 0.0970 chunk 272 optimal weight: 0.7980 chunk 222 optimal weight: 0.9980 chunk 90 optimal weight: 0.0980 chunk 327 optimal weight: 1.9990 chunk 353 optimal weight: 0.1980 chunk 291 optimal weight: 20.0000 chunk 324 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 262 optimal weight: 2.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN L 44 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN B 481 ASN B1048 HIS ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 751 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 957 GLN C1054 GLN C1108 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4788 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29188 Z= 0.168 Angle : 0.599 11.641 39722 Z= 0.306 Chirality : 0.045 0.568 4606 Planarity : 0.004 0.077 5063 Dihedral : 6.276 59.698 4446 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 2.53 % Allowed : 13.31 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.06 (0.14), residues: 3576 helix: 1.58 (0.21), residues: 626 sheet: 0.34 (0.17), residues: 998 loop : -0.78 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 56 HIS 0.009 0.001 HIS K 55 PHE 0.024 0.001 PHE C 823 TYR 0.020 0.001 TYR C1067 ARG 0.017 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 271 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 22 CYS cc_start: 0.0804 (OUTLIER) cc_final: -0.0160 (p) REVERT: J 22 CYS cc_start: -0.0477 (OUTLIER) cc_final: -0.1591 (t) REVERT: K 93 TYR cc_start: 0.4152 (OUTLIER) cc_final: 0.2169 (t80) REVERT: K 111 GLU cc_start: -0.2997 (OUTLIER) cc_final: -0.3820 (tp30) REVERT: L 21 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5669 (tt) REVERT: L 93 TYR cc_start: 0.1494 (OUTLIER) cc_final: 0.0266 (m-80) REVERT: L 108 THR cc_start: -0.2449 (OUTLIER) cc_final: -0.3361 (p) REVERT: A 697 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7665 (ptm) REVERT: A 964 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5977 (tppt) REVERT: B 392 PHE cc_start: 0.6889 (m-80) cc_final: 0.5761 (m-80) outliers start: 79 outliers final: 40 residues processed: 331 average time/residue: 0.3281 time to fit residues: 187.2078 Evaluate side-chains 277 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 228 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 chunk 169 optimal weight: 9.9990 chunk 36 optimal weight: 30.0000 chunk 156 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 347 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 762 GLN A 784 GLN A 901 GLN A1048 HIS B 655 HIS B 913 GLN B 978 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 388 ASN C 498 GLN C 751 ASN C 804 GLN C 913 GLN C1048 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.7720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 29188 Z= 0.341 Angle : 0.816 25.911 39722 Z= 0.410 Chirality : 0.053 0.976 4606 Planarity : 0.005 0.052 5063 Dihedral : 6.815 76.819 4439 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.19 % Rotamer: Outliers : 3.81 % Allowed : 12.80 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.54 (0.14), residues: 3576 helix: 0.72 (0.20), residues: 632 sheet: 0.12 (0.17), residues: 937 loop : -0.95 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP C1102 HIS 0.010 0.002 HIS C1088 PHE 0.057 0.003 PHE A 559 TYR 0.061 0.002 TYR L 38 ARG 0.006 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 283 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 93 TYR cc_start: 0.4689 (OUTLIER) cc_final: 0.2917 (t80) REVERT: L 21 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5600 (tt) REVERT: L 93 TYR cc_start: 0.1856 (OUTLIER) cc_final: 0.0400 (m-80) REVERT: B 392 PHE cc_start: 0.6959 (m-80) cc_final: 0.5683 (m-80) REVERT: B 563 GLN cc_start: 0.6402 (mt0) cc_final: 0.6076 (mt0) REVERT: B 695 TYR cc_start: 0.6424 (p90) cc_final: 0.6210 (p90) REVERT: B 957 GLN cc_start: 0.7903 (tp40) cc_final: 0.7662 (tp-100) REVERT: C 955 ASN cc_start: 0.7329 (m110) cc_final: 0.7120 (m-40) outliers start: 119 outliers final: 57 residues processed: 381 average time/residue: 0.3533 time to fit residues: 222.4893 Evaluate side-chains 260 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 200 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 0.5980 chunk 197 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 259 optimal weight: 0.1980 chunk 143 optimal weight: 6.9990 chunk 296 optimal weight: 30.0000 chunk 240 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 177 optimal weight: 0.0070 chunk 312 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 450 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 978 ASN C 784 GLN C 926 GLN C1054 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.8750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 29188 Z= 0.243 Angle : 0.614 12.663 39722 Z= 0.316 Chirality : 0.046 0.551 4606 Planarity : 0.004 0.057 5063 Dihedral : 5.869 58.614 4432 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 2.56 % Allowed : 14.78 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.16 (0.14), residues: 3576 helix: 1.45 (0.21), residues: 625 sheet: 0.32 (0.17), residues: 979 loop : -0.85 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C1102 HIS 0.008 0.001 HIS K 55 PHE 0.028 0.002 PHE B1075 TYR 0.045 0.002 TYR B 351 ARG 0.011 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 224 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 MET cc_start: -0.3623 (ttt) cc_final: -0.4264 (mtt) REVERT: K 76 ASP cc_start: 0.6037 (m-30) cc_final: 0.5464 (p0) REVERT: K 93 TYR cc_start: 0.4564 (OUTLIER) cc_final: 0.2715 (t80) REVERT: L 21 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5446 (tt) REVERT: L 93 TYR cc_start: 0.2113 (OUTLIER) cc_final: 0.0792 (m-80) REVERT: A 190 ARG cc_start: 0.3830 (ptt180) cc_final: 0.3580 (ptt-90) REVERT: A 565 PHE cc_start: 0.4165 (m-80) cc_final: 0.3940 (m-80) REVERT: A 740 MET cc_start: 0.7734 (tpp) cc_final: 0.7344 (ttt) REVERT: B 781 VAL cc_start: 0.8959 (t) cc_final: 0.8737 (t) REVERT: B 1108 ASN cc_start: 0.6969 (m-40) cc_final: 0.6758 (m-40) REVERT: C 241 LEU cc_start: 0.3711 (OUTLIER) cc_final: 0.3392 (mp) REVERT: C 900 MET cc_start: 0.6498 (mpp) cc_final: 0.6149 (mtm) outliers start: 80 outliers final: 44 residues processed: 288 average time/residue: 0.3440 time to fit residues: 166.8081 Evaluate side-chains 223 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 175 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1003 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 4.9990 chunk 313 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 204 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 348 optimal weight: 1.9990 chunk 289 optimal weight: 8.9990 chunk 161 optimal weight: 0.2980 chunk 28 optimal weight: 0.0000 chunk 115 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 957 GLN C 751 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.9311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29188 Z= 0.177 Angle : 0.565 11.864 39722 Z= 0.286 Chirality : 0.043 0.254 4606 Planarity : 0.004 0.058 5063 Dihedral : 5.541 59.871 4432 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.45 % Rotamer: Outliers : 2.24 % Allowed : 16.06 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.08 (0.14), residues: 3576 helix: 1.58 (0.21), residues: 635 sheet: 0.37 (0.17), residues: 927 loop : -0.80 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C1102 HIS 0.008 0.001 HIS A1088 PHE 0.031 0.001 PHE C 168 TYR 0.020 0.001 TYR J 32 ARG 0.009 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 198 time to evaluate : 3.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 41 TRP cc_start: 0.1716 (m100) cc_final: 0.1285 (m100) REVERT: K 76 ASP cc_start: 0.6026 (m-30) cc_final: 0.5421 (p0) REVERT: K 93 TYR cc_start: 0.4581 (OUTLIER) cc_final: 0.3030 (t80) REVERT: L 93 TYR cc_start: 0.1853 (OUTLIER) cc_final: 0.0450 (m-80) REVERT: A 740 MET cc_start: 0.7759 (tpp) cc_final: 0.7400 (ttt) REVERT: B 216 LEU cc_start: 0.6745 (mt) cc_final: 0.5759 (tp) REVERT: B 408 ARG cc_start: 0.8731 (mmm160) cc_final: 0.8413 (tpm170) REVERT: B 781 VAL cc_start: 0.8990 (t) cc_final: 0.8783 (t) outliers start: 70 outliers final: 46 residues processed: 252 average time/residue: 0.3453 time to fit residues: 147.5853 Evaluate side-chains 222 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 174 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 4.9990 chunk 39 optimal weight: 40.0000 chunk 198 optimal weight: 5.9990 chunk 254 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 346 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 498 GLN B 926 GLN B 978 ASN C 317 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 1.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 29188 Z= 0.335 Angle : 0.754 20.118 39722 Z= 0.386 Chirality : 0.050 0.393 4606 Planarity : 0.005 0.093 5063 Dihedral : 6.248 59.393 4430 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.26 % Favored : 94.69 % Rotamer: Outliers : 3.26 % Allowed : 15.77 % Favored : 80.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.61 % 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 (0.14), residues: 3576 helix: 1.05 (0.20), residues: 633 sheet: 0.24 (0.17), residues: 906 loop : -1.03 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 102 HIS 0.011 0.002 HIS A1101 PHE 0.030 0.003 PHE B 106 TYR 0.041 0.002 TYR J 106 ARG 0.026 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 185 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 76 ASP cc_start: 0.5815 (m-30) cc_final: 0.5270 (p0) REVERT: K 93 TYR cc_start: 0.4848 (OUTLIER) cc_final: 0.3439 (t80) REVERT: L 93 TYR cc_start: 0.2407 (OUTLIER) cc_final: 0.0891 (m-80) REVERT: A 91 TYR cc_start: 0.4562 (OUTLIER) cc_final: 0.4305 (t80) REVERT: A 796 ASP cc_start: 0.7043 (p0) cc_final: 0.6836 (p0) REVERT: A 878 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9004 (tp) REVERT: A 1049 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8836 (mp) REVERT: B 693 ILE cc_start: 0.8241 (mp) cc_final: 0.7901 (mp) REVERT: C 708 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7666 (m) outliers start: 102 outliers final: 50 residues processed: 267 average time/residue: 0.3607 time to fit residues: 162.2597 Evaluate side-chains 186 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 130 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 chunk 236 optimal weight: 0.6980 chunk 171 optimal weight: 0.0370 chunk 32 optimal weight: 20.0000 chunk 272 optimal weight: 8.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 978 ASN B1002 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 764 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 1.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29188 Z= 0.205 Angle : 0.573 10.872 39722 Z= 0.294 Chirality : 0.044 0.280 4606 Planarity : 0.004 0.062 5063 Dihedral : 5.753 59.778 4430 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 1.82 % Allowed : 17.24 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.24 (0.14), residues: 3576 helix: 1.57 (0.21), residues: 634 sheet: 0.31 (0.17), residues: 929 loop : -0.97 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 64 HIS 0.007 0.001 HIS K 55 PHE 0.026 0.002 PHE B 541 TYR 0.018 0.001 TYR A1138 ARG 0.009 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 132 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 76 ASP cc_start: 0.5674 (m-30) cc_final: 0.5128 (p0) REVERT: K 93 TYR cc_start: 0.4630 (OUTLIER) cc_final: 0.3206 (t80) REVERT: L 93 TYR cc_start: 0.2069 (OUTLIER) cc_final: 0.0633 (m-80) REVERT: A 104 TRP cc_start: 0.3836 (m-90) cc_final: 0.3173 (m-90) REVERT: A 796 ASP cc_start: 0.6749 (p0) cc_final: 0.6447 (p0) outliers start: 57 outliers final: 43 residues processed: 182 average time/residue: 0.3570 time to fit residues: 112.6050 Evaluate side-chains 159 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 114 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 323 optimal weight: 0.5980 chunk 194 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 292 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 322 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A1106 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 1.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29188 Z= 0.226 Angle : 0.579 11.239 39722 Z= 0.295 Chirality : 0.044 0.361 4606 Planarity : 0.004 0.060 5063 Dihedral : 5.672 59.753 4428 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 1.79 % Allowed : 17.47 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.18 (0.14), residues: 3576 helix: 1.75 (0.21), residues: 629 sheet: 0.31 (0.17), residues: 955 loop : -0.97 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 64 HIS 0.006 0.001 HIS J 35 PHE 0.027 0.002 PHE B 194 TYR 0.018 0.001 TYR B1067 ARG 0.006 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 121 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 76 ASP cc_start: 0.5606 (m-30) cc_final: 0.5069 (p0) REVERT: K 92 TYR cc_start: 0.3559 (m-80) cc_final: 0.3157 (m-80) REVERT: K 93 TYR cc_start: 0.4714 (OUTLIER) cc_final: 0.3262 (t80) REVERT: L 93 TYR cc_start: 0.2237 (OUTLIER) cc_final: 0.0820 (m-80) REVERT: A 104 TRP cc_start: 0.3904 (m-90) cc_final: 0.3259 (m-90) REVERT: A 796 ASP cc_start: 0.6778 (p0) cc_final: 0.6508 (p0) REVERT: C 708 SER cc_start: 0.8087 (OUTLIER) cc_final: 0.7882 (p) outliers start: 56 outliers final: 45 residues processed: 170 average time/residue: 0.3674 time to fit residues: 108.2419 Evaluate side-chains 159 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 111 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 2.9990 chunk 341 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 358 optimal weight: 0.8980 chunk 330 optimal weight: 0.7980 chunk 285 optimal weight: 20.0000 chunk 29 optimal weight: 40.0000 chunk 220 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C1083 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 1.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29188 Z= 0.202 Angle : 0.558 10.912 39722 Z= 0.285 Chirality : 0.044 0.269 4606 Planarity : 0.004 0.059 5063 Dihedral : 5.565 59.682 4428 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 1.63 % Allowed : 17.95 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.06 (0.14), residues: 3576 helix: 1.76 (0.21), residues: 638 sheet: 0.48 (0.17), residues: 916 loop : -0.91 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 64 HIS 0.005 0.001 HIS K 55 PHE 0.024 0.001 PHE B 106 TYR 0.025 0.001 TYR A1138 ARG 0.006 0.000 ARG B 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 130 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 MET cc_start: -0.4089 (ttt) cc_final: -0.4598 (mtt) REVERT: K 76 ASP cc_start: 0.5828 (m-30) cc_final: 0.5207 (p0) REVERT: K 92 TYR cc_start: 0.3319 (m-80) cc_final: 0.2965 (m-80) REVERT: K 93 TYR cc_start: 0.4705 (OUTLIER) cc_final: 0.3264 (t80) REVERT: L 93 TYR cc_start: 0.2153 (OUTLIER) cc_final: 0.0737 (m-80) REVERT: A 796 ASP cc_start: 0.6686 (p0) cc_final: 0.6469 (p0) outliers start: 51 outliers final: 42 residues processed: 174 average time/residue: 0.3898 time to fit residues: 112.9978 Evaluate side-chains 156 residues out of total 3181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 112 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 TYR Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 1.9990 chunk 304 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 286 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 293 optimal weight: 9.9990 chunk 36 optimal weight: 30.0000 chunk 52 optimal weight: 40.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 498 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 901 GLN C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.156880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.102927 restraints weight = 77192.781| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 4.48 r_work: 0.3130 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 1.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 29188 Z= 0.486 Angle : 0.794 12.509 39722 Z= 0.410 Chirality : 0.051 0.309 4606 Planarity : 0.005 0.060 5063 Dihedral : 6.673 58.975 4428 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 1.98 % Allowed : 17.79 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.68 (0.14), residues: 3576 helix: 1.11 (0.20), residues: 624 sheet: 0.13 (0.17), residues: 907 loop : -1.26 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 64 HIS 0.009 0.002 HIS A1064 PHE 0.029 0.003 PHE B1075 TYR 0.046 0.002 TYR B 495 ARG 0.018 0.001 ARG C 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6092.42 seconds wall clock time: 111 minutes 13.58 seconds (6673.58 seconds total)