Starting phenix.real_space_refine on Tue Feb 20 04:39:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjn_31624/02_2024/7fjn_31624.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjn_31624/02_2024/7fjn_31624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjn_31624/02_2024/7fjn_31624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjn_31624/02_2024/7fjn_31624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjn_31624/02_2024/7fjn_31624.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjn_31624/02_2024/7fjn_31624.pdb" } resolution = 3.25 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 117 5.16 5 C 17116 2.51 5 N 4414 2.21 5 O 5177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" 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 TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 985": "OD1" <-> "OD2" Residue "B GLU 988": "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 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" 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 "I ARG 28": "NH1" <-> "NH2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I GLU 101": "OE1" <-> "OE2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J ARG 48": "NH1" <-> "NH2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L ARG 48": "NH1" <-> "NH2" Residue "L GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26824 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7687 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 48, 'TRANS': 944} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 7691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7691 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 48, 'TRANS': 944} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 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: "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: "I" 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: 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: 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: 14.03, per 1000 atoms: 0.52 Number of scatterers: 26824 At special positions: 0 Unit cell: (189.937, 166.881, 155.902, 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 117 16.00 O 5177 8.00 N 4414 7.00 C 17116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.04 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 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 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: 9.69 Conformation dependent library (CDL) restraints added in 5.2 seconds 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6374 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 56 sheets defined 21.1% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 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 342 removed outlier: 4.398A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.592A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (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: 4.015A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (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: 4.148A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' 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: 3.850A 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 383 through 387 removed outlier: 3.923A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' 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: 4.072A 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 '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=AA2, 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=AA3, 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=AA4, 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=AA5, 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=AA6, 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=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 4.048A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.890A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, 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=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, 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=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, 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=AB6 Processing sheet with id=AB7, 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=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, 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=AC1, 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=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, 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=AC4, 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=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.623A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.823A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, 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=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, 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=AD2, first strand: chain 'B' and resid 718 through 720 Processing sheet with id=AD3, 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=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, 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=AD6, 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=AD7, 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=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, 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=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.609A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, 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=AE4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE5, 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=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, 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: 4.061A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AF1, 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=AF2, first strand: chain 'I' and resid 18 through 23 removed outlier: 3.589A pdb=" N CYS I 22 " --> pdb=" O ALA I 79 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP I 73 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 59 through 60 removed outlier: 3.520A pdb=" N SER I 59 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER J 7 " --> pdb=" O SER J 22 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER J 22 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.265A pdb=" N LEU J 11 " --> pdb=" O GLU J 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'J' and resid 30 through 31 removed outlier: 3.626A pdb=" N LYS J 36 " --> pdb=" O TYR J 31 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 59 through 60 removed outlier: 6.707A pdb=" N TRP J 41 " --> pdb=" O LEU J 53 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N HIS J 55 " --> pdb=" O LEU J 39 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU J 39 " --> pdb=" O HIS J 55 " (cutoff:3.500A) Processing sheet with id=AF8, 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=AF9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.264A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.626A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AG2, 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: 4.920A pdb=" N HIS L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU L 39 " --> pdb=" O HIS L 55 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.82 Time building geometry restraints manager: 10.60 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: 6697 1.33 - 1.47: 8125 1.47 - 1.61: 12454 1.61 - 1.75: 2 1.75 - 1.89: 145 Bond restraints: 27423 Sorted by residual: bond pdb=" CA GLY L 106 " pdb=" C GLY L 106 " ideal model delta sigma weight residual 1.518 1.626 -0.108 1.48e-02 4.57e+03 5.34e+01 bond pdb=" CA GLY J 106 " pdb=" C GLY J 106 " ideal model delta sigma weight residual 1.518 1.625 -0.108 1.48e-02 4.57e+03 5.31e+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 bond pdb=" N CYS B 649 " pdb=" CA CYS B 649 " ideal model delta sigma weight residual 1.457 1.517 -0.059 1.29e-02 6.01e+03 2.11e+01 ... (remaining 27418 not shown) Histogram of bond angle deviations from ideal: 96.58 - 104.30: 360 104.30 - 112.02: 12137 112.02 - 119.75: 11428 119.75 - 127.47: 13221 127.47 - 135.19: 177 Bond angle restraints: 37323 Sorted by residual: angle pdb=" N PRO B 527 " pdb=" CA PRO B 527 " pdb=" C PRO B 527 " ideal model delta sigma weight residual 111.13 121.81 -10.68 1.49e+00 4.50e-01 5.13e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 118.66 -7.96 1.22e+00 6.72e-01 4.26e+01 angle pdb=" N GLY L 106 " pdb=" CA GLY L 106 " pdb=" C GLY L 106 " ideal model delta sigma weight residual 112.25 104.09 8.16 1.34e+00 5.57e-01 3.71e+01 angle pdb=" N GLY J 106 " pdb=" CA GLY J 106 " pdb=" C GLY J 106 " ideal model delta sigma weight residual 112.25 104.09 8.16 1.34e+00 5.57e-01 3.71e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 118.08 -7.38 1.22e+00 6.72e-01 3.66e+01 ... (remaining 37318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 15412 17.36 - 34.73: 876 34.73 - 52.09: 140 52.09 - 69.45: 73 69.45 - 86.81: 23 Dihedral angle restraints: 16524 sinusoidal: 6600 harmonic: 9924 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 16521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3071 0.092 - 0.183: 1115 0.183 - 0.274: 130 0.274 - 0.366: 21 0.366 - 0.457: 3 Chirality restraints: 4340 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 3.94e+00 ... (remaining 4337 not shown) Planarity restraints: 4789 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 4786 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 26 2.23 - 2.90: 10164 2.90 - 3.56: 35451 3.56 - 4.23: 62076 4.23 - 4.90: 104703 Nonbonded interactions: 212420 Sorted by model distance: nonbonded pdb=" CD2 PHE B 486 " pdb=" CE2 TYR L 100 " model vdw 1.560 3.640 nonbonded pdb=" OE1 GLN B 498 " pdb=" CE2 TYR B 501 " model vdw 1.579 3.340 nonbonded pdb=" CZ PHE A 456 " pdb=" CG GLU I 54 " model vdw 1.619 3.740 nonbonded pdb=" CD2 PHE B 486 " pdb=" CD2 TYR L 100 " model vdw 1.668 3.640 nonbonded pdb=" CB GLN C 498 " pdb=" CE2 TYR C 501 " model vdw 1.749 3.740 ... (remaining 212415 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 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 (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 676 or resid 690 thro \ ugh 744 or (resid 745 and (name N or name CA or name C or name O or name CB )) o \ r resid 746 through 747 or (resid 748 and (name N or name CA or name C or name O \ or name CB )) or resid 749 through 810 or (resid 811 and (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 name C or name O or name CB \ )) or resid 869 through 1147 or resid 1301 through 1308)) 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 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 (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 676 or resid 690 thro \ ugh 744 or (resid 745 and (name N or name CA or name C or name O or name CB )) o \ r resid 746 through 747 or (resid 748 and (name N or name CA or name C or name O \ or name CB )) or resid 749 through 810 or (resid 811 and (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 name C or name O or name CB \ )) or resid 869 through 985 or (resid 986 through 987 and (name N or name CA or \ name C or name O or name CB )) or resid 988 through 1147 or resid 1301 through \ 1308)) 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 196 or (re \ sid 197 and (name N or name CA or name C or name O or name CB )) or resid 198 th \ rough 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 or name C or name \ O or name CB )) or resid 219 through 238 or (resid 239 and (name N or name CA o \ r name C or name O or name CB )) or resid 240 through 308 or (resid 309 and (nam \ e N or name CA or name C or name O or name CB )) or resid 310 through 527 or (re \ sid 528 and (name N or name CA or name C or name O or name CB )) or resid 529 th \ rough 811 or resid 813 through 985 or (resid 986 through 987 and (name N or name \ CA or name C or name O or name CB )) or resid 988 through 1141 or (resid 1142 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1143 through 11 \ 44 or (resid 1145 through 1146 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1147 or resid 1301 through 1308)) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.290 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 71.750 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.190 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 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 0.108 27423 Z= 0.752 Angle : 1.560 10.872 37323 Z= 1.069 Chirality : 0.087 0.457 4340 Planarity : 0.017 0.292 4764 Dihedral : 12.294 86.813 10084 Min Nonbonded Distance : 1.560 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.50 % Favored : 92.11 % Rotamer: Outliers : 2.63 % Allowed : 3.79 % Favored : 93.59 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3358 helix: -0.24 (0.18), residues: 597 sheet: 0.39 (0.20), residues: 672 loop : -1.44 (0.12), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.006 TRP B 886 HIS 0.016 0.002 HIS C1048 PHE 0.060 0.008 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) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 311 time to evaluate : 3.192 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: A 497 PHE cc_start: 0.0874 (m-10) cc_final: 0.0209 (m-80) REVERT: I 43 GLN cc_start: -0.3820 (OUTLIER) cc_final: -0.4653 (tt0) REVERT: J 15 VAL cc_start: 0.2425 (OUTLIER) cc_final: 0.2166 (m) REVERT: J 64 VAL cc_start: -0.1875 (OUTLIER) cc_final: -0.2343 (m) REVERT: J 93 TYR cc_start: -0.1781 (OUTLIER) cc_final: -0.2942 (m-80) REVERT: J 111 GLU cc_start: 0.0954 (OUTLIER) cc_final: 0.0644 (pm20) REVERT: L 44 GLN cc_start: 0.3105 (mt0) cc_final: 0.2812 (mp10) outliers start: 77 outliers final: 14 residues processed: 379 average time/residue: 0.3787 time to fit residues: 228.4853 Evaluate side-chains 150 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 0.8980 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 307 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 87 ASN A 334 ASN A 409 GLN A 414 GLN A 474 GLN A 487 ASN A 914 ASN A1088 HIS ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 414 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 804 GLN B 914 ASN B 935 GLN B 978 ASN B1088 HIS C 414 GLN C 474 GLN C 540 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27423 Z= 0.193 Angle : 0.633 12.014 37323 Z= 0.330 Chirality : 0.046 0.276 4340 Planarity : 0.004 0.037 4764 Dihedral : 6.456 59.323 4212 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.63 % Favored : 96.25 % Rotamer: Outliers : 2.15 % Allowed : 7.16 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: -0.32 (0.14), residues: 3358 helix: 1.64 (0.21), residues: 593 sheet: 0.46 (0.18), residues: 865 loop : -1.19 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 64 HIS 0.004 0.001 HIS J 55 PHE 0.023 0.001 PHE A 201 TYR 0.037 0.002 TYR L 93 ARG 0.007 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 137 time to evaluate : 2.946 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: A 497 PHE cc_start: 0.1346 (m-10) cc_final: 0.0963 (m-80) REVERT: B 380 TYR cc_start: 0.7340 (t80) cc_final: 0.7018 (t80) REVERT: J 39 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.4830 (tt) REVERT: J 93 TYR cc_start: -0.2079 (OUTLIER) cc_final: -0.2757 (m-80) outliers start: 63 outliers final: 29 residues processed: 193 average time/residue: 0.3360 time to fit residues: 111.9915 Evaluate side-chains 135 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 57 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 256 optimal weight: 2.9990 chunk 209 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 308 optimal weight: 0.0050 chunk 333 optimal weight: 30.0000 chunk 274 optimal weight: 0.9990 chunk 305 optimal weight: 50.0000 chunk 105 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN B 394 ASN B 955 ASN B1002 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C1005 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 HIS ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 27423 Z= 0.184 Angle : 0.547 13.111 37323 Z= 0.286 Chirality : 0.043 0.225 4340 Planarity : 0.004 0.039 4764 Dihedral : 5.704 58.188 4198 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.68 % Rotamer: Outliers : 1.64 % Allowed : 8.02 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3358 helix: 2.07 (0.22), residues: 604 sheet: 0.49 (0.18), residues: 889 loop : -1.00 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 36 HIS 0.004 0.001 HIS J 55 PHE 0.020 0.001 PHE A 201 TYR 0.018 0.001 TYR L 38 ARG 0.004 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 112 time to evaluate : 2.963 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: B 380 TYR cc_start: 0.7451 (t80) cc_final: 0.7098 (t80) REVERT: J 39 LEU cc_start: 0.5264 (OUTLIER) cc_final: 0.4880 (tt) REVERT: J 55 HIS cc_start: 0.0039 (OUTLIER) cc_final: -0.0226 (t70) REVERT: J 93 TYR cc_start: -0.2535 (OUTLIER) cc_final: -0.3032 (m-80) outliers start: 48 outliers final: 28 residues processed: 154 average time/residue: 0.3452 time to fit residues: 91.2189 Evaluate side-chains 120 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 55 HIS Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 96 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 20.0000 chunk 231 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 309 optimal weight: 50.0000 chunk 327 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 293 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 580 GLN A 901 GLN A 913 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 481 ASN B 764 ASN B 901 GLN B 913 GLN B1002 GLN B1048 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 334 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 901 GLN C 914 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 27423 Z= 0.412 Angle : 0.694 12.000 37323 Z= 0.366 Chirality : 0.047 0.250 4340 Planarity : 0.005 0.069 4764 Dihedral : 6.283 59.046 4195 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.47 % Favored : 95.47 % Rotamer: Outliers : 1.94 % Allowed : 8.94 % Favored : 89.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.52 % 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: -0.24 (0.14), residues: 3358 helix: 1.86 (0.21), residues: 603 sheet: 0.28 (0.17), residues: 891 loop : -1.10 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 56 HIS 0.073 0.003 HIS J 55 PHE 0.019 0.002 PHE C 497 TYR 0.047 0.002 TYR B 204 ARG 0.008 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 90 time to evaluate : 3.290 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: A 497 PHE cc_start: 0.4426 (m-10) cc_final: 0.3953 (m-10) REVERT: B 380 TYR cc_start: 0.7467 (t80) cc_final: 0.7161 (t80) REVERT: H 36 TRP cc_start: 0.3243 (m100) cc_final: 0.1811 (m100) REVERT: J 39 LEU cc_start: 0.5057 (OUTLIER) cc_final: 0.4042 (tt) REVERT: J 93 TYR cc_start: -0.1792 (OUTLIER) cc_final: -0.2855 (m-80) outliers start: 57 outliers final: 26 residues processed: 141 average time/residue: 0.3581 time to fit residues: 87.2452 Evaluate side-chains 93 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 65 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B1135 ASN C 448 ASN C 498 GLN C 901 GLN C 914 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 HIS ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 27423 Z= 0.141 Angle : 0.507 13.861 37323 Z= 0.260 Chirality : 0.042 0.223 4340 Planarity : 0.003 0.045 4764 Dihedral : 5.417 59.361 4193 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 1.23 % Allowed : 9.86 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.13 (0.15), residues: 3358 helix: 2.50 (0.22), residues: 600 sheet: 0.44 (0.17), residues: 892 loop : -0.93 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.010 0.001 HIS J 55 PHE 0.016 0.001 PHE C 106 TYR 0.021 0.001 TYR B 351 ARG 0.008 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 77 time to evaluate : 3.290 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: A 1101 HIS cc_start: 0.6326 (OUTLIER) cc_final: 0.5063 (m-70) REVERT: C 241 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6263 (mt) REVERT: C 1101 HIS cc_start: 0.6855 (OUTLIER) cc_final: 0.6584 (m-70) REVERT: J 93 TYR cc_start: -0.2033 (OUTLIER) cc_final: -0.3042 (m-80) outliers start: 36 outliers final: 20 residues processed: 112 average time/residue: 0.3747 time to fit residues: 74.7542 Evaluate side-chains 85 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 96 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 20.0000 chunk 295 optimal weight: 0.0870 chunk 64 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 327 optimal weight: 7.9990 chunk 272 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 172 optimal weight: 4.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN C 901 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.6439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27423 Z= 0.193 Angle : 0.503 11.025 37323 Z= 0.256 Chirality : 0.042 0.212 4340 Planarity : 0.003 0.050 4764 Dihedral : 5.361 59.095 4189 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 1.30 % Allowed : 9.99 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.28 (0.15), residues: 3358 helix: 2.68 (0.22), residues: 600 sheet: 0.44 (0.17), residues: 903 loop : -0.81 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 36 HIS 0.004 0.001 HIS L 55 PHE 0.016 0.001 PHE A 201 TYR 0.026 0.001 TYR A 200 ARG 0.011 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 65 time to evaluate : 3.344 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: A 497 PHE cc_start: 0.4849 (m-10) cc_final: 0.4383 (m-10) REVERT: A 1101 HIS cc_start: 0.6387 (OUTLIER) cc_final: 0.5183 (m-70) REVERT: B 380 TYR cc_start: 0.7166 (t80) cc_final: 0.6916 (t80) REVERT: C 241 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6262 (mt) REVERT: C 495 TYR cc_start: 0.4470 (m-80) cc_final: 0.4185 (m-80) REVERT: C 1101 HIS cc_start: 0.6616 (OUTLIER) cc_final: 0.6405 (m-70) REVERT: H 28 ARG cc_start: 0.7076 (ptp90) cc_final: 0.5813 (mmm160) REVERT: J 39 LEU cc_start: 0.5029 (OUTLIER) cc_final: 0.4664 (tt) REVERT: J 93 TYR cc_start: -0.1713 (OUTLIER) cc_final: -0.3034 (m-80) outliers start: 38 outliers final: 21 residues processed: 100 average time/residue: 0.3503 time to fit residues: 61.6028 Evaluate side-chains 85 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 59 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 96 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 239 optimal weight: 30.0000 chunk 185 optimal weight: 1.9990 chunk 276 optimal weight: 0.0570 chunk 183 optimal weight: 6.9990 chunk 326 optimal weight: 50.0000 chunk 204 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 914 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.6801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27423 Z= 0.223 Angle : 0.504 10.397 37323 Z= 0.258 Chirality : 0.042 0.289 4340 Planarity : 0.003 0.043 4764 Dihedral : 5.299 59.643 4189 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 1.33 % Allowed : 9.89 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.31 (0.15), residues: 3358 helix: 2.67 (0.22), residues: 603 sheet: 0.46 (0.17), residues: 892 loop : -0.78 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 36 HIS 0.006 0.001 HIS C1083 PHE 0.014 0.001 PHE C 106 TYR 0.017 0.001 TYR A 200 ARG 0.006 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 65 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 PHE cc_start: 0.5051 (m-10) cc_final: 0.4516 (m-10) REVERT: A 1101 HIS cc_start: 0.6671 (OUTLIER) cc_final: 0.5773 (m-70) REVERT: B 380 TYR cc_start: 0.7225 (t80) cc_final: 0.6963 (t80) REVERT: B 571 ASP cc_start: 0.6355 (t0) cc_final: 0.5988 (t0) REVERT: C 241 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6356 (mt) REVERT: C 495 TYR cc_start: 0.4227 (m-80) cc_final: 0.3980 (m-80) REVERT: C 858 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8165 (pp) REVERT: H 28 ARG cc_start: 0.7053 (ptp90) cc_final: 0.5757 (mmm160) REVERT: J 39 LEU cc_start: 0.4929 (OUTLIER) cc_final: 0.4531 (tt) REVERT: J 81 ILE cc_start: -0.1331 (OUTLIER) cc_final: -0.1771 (mt) REVERT: J 93 TYR cc_start: -0.1764 (OUTLIER) cc_final: -0.3045 (m-80) outliers start: 39 outliers final: 24 residues processed: 102 average time/residue: 0.3143 time to fit residues: 57.1979 Evaluate side-chains 86 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 56 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 96 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 0.0970 chunk 130 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 222 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.7066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27423 Z= 0.183 Angle : 0.483 11.547 37323 Z= 0.247 Chirality : 0.042 0.215 4340 Planarity : 0.003 0.043 4764 Dihedral : 5.181 59.602 4189 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.31 % Rotamer: Outliers : 1.40 % Allowed : 10.06 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.40 (0.15), residues: 3358 helix: 2.69 (0.22), residues: 609 sheet: 0.47 (0.17), residues: 892 loop : -0.68 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.003 0.001 HIS L 55 PHE 0.022 0.001 PHE C 565 TYR 0.021 0.001 TYR B 904 ARG 0.006 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 56 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 PHE cc_start: 0.5110 (m-10) cc_final: 0.4628 (m-10) REVERT: A 1101 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.5994 (m-70) REVERT: B 380 TYR cc_start: 0.7494 (t80) cc_final: 0.7235 (t80) REVERT: C 241 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6339 (mt) REVERT: C 495 TYR cc_start: 0.4165 (m-80) cc_final: 0.3936 (m-80) REVERT: C 858 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8118 (pp) REVERT: H 28 ARG cc_start: 0.6866 (ptp90) cc_final: 0.5540 (mmm160) REVERT: J 39 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.4517 (tt) REVERT: J 81 ILE cc_start: -0.1342 (OUTLIER) cc_final: -0.1779 (mt) REVERT: J 93 TYR cc_start: -0.1783 (OUTLIER) cc_final: -0.3069 (m-80) outliers start: 41 outliers final: 25 residues processed: 94 average time/residue: 0.3423 time to fit residues: 57.9628 Evaluate side-chains 83 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 52 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 40.0000 chunk 313 optimal weight: 40.0000 chunk 285 optimal weight: 3.9990 chunk 304 optimal weight: 8.9990 chunk 312 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 239 optimal weight: 30.0000 chunk 93 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 907 ASN A1088 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 354 ASN B 474 GLN B 580 GLN B 901 GLN C 764 ASN C 804 GLN C1119 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.8027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.121 27423 Z= 0.572 Angle : 0.726 9.180 37323 Z= 0.374 Chirality : 0.048 0.233 4340 Planarity : 0.004 0.041 4764 Dihedral : 6.461 59.649 4189 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 1.47 % Allowed : 10.20 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3358 helix: 1.80 (0.21), residues: 624 sheet: 0.31 (0.17), residues: 865 loop : -1.03 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 102 HIS 0.009 0.002 HIS H 35 PHE 0.024 0.002 PHE C 32 TYR 0.029 0.002 TYR C1067 ARG 0.008 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 56 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 380 TYR cc_start: 0.7198 (t80) cc_final: 0.6870 (t80) REVERT: C 858 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8319 (pp) REVERT: H 28 ARG cc_start: 0.7072 (ptp90) cc_final: 0.5910 (mmm160) REVERT: J 39 LEU cc_start: 0.4879 (OUTLIER) cc_final: 0.4505 (tt) REVERT: J 93 TYR cc_start: -0.1381 (OUTLIER) cc_final: -0.2676 (m-80) REVERT: L 78 THR cc_start: 0.6781 (m) cc_final: 0.6558 (m) outliers start: 43 outliers final: 30 residues processed: 96 average time/residue: 0.3288 time to fit residues: 55.9826 Evaluate side-chains 84 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 51 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 97 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 0.0870 chunk 199 optimal weight: 1.9990 chunk 321 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 337 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1088 HIS B 474 GLN B 901 GLN C 804 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 GLN J 96 GLN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.8132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27423 Z= 0.262 Angle : 0.542 9.467 37323 Z= 0.279 Chirality : 0.043 0.221 4340 Planarity : 0.003 0.041 4764 Dihedral : 5.676 59.822 4189 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 1.16 % Allowed : 10.74 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.03 (0.15), residues: 3358 helix: 2.28 (0.22), residues: 623 sheet: 0.32 (0.17), residues: 872 loop : -0.94 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 36 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.001 PHE B 168 TYR 0.032 0.001 TYR B 200 ARG 0.005 0.000 ARG C 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 53 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 380 TYR cc_start: 0.7326 (t80) cc_final: 0.7046 (t80) REVERT: C 858 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8176 (pp) REVERT: H 28 ARG cc_start: 0.7036 (ptp90) cc_final: 0.5925 (mmm160) REVERT: J 39 LEU cc_start: 0.4917 (OUTLIER) cc_final: 0.4506 (tt) REVERT: J 93 TYR cc_start: -0.1532 (OUTLIER) cc_final: -0.2792 (m-80) REVERT: L 78 THR cc_start: 0.6636 (m) cc_final: 0.6400 (m) outliers start: 34 outliers final: 24 residues processed: 84 average time/residue: 0.3317 time to fit residues: 50.0969 Evaluate side-chains 78 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 51 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 97 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 0.7980 chunk 213 optimal weight: 0.6980 chunk 286 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 39 optimal weight: 30.0000 chunk 74 optimal weight: 0.9990 chunk 269 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 276 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN C1119 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.107319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.070578 restraints weight = 99204.796| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.40 r_work: 0.2803 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.8184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27423 Z= 0.140 Angle : 0.492 9.059 37323 Z= 0.253 Chirality : 0.042 0.273 4340 Planarity : 0.003 0.043 4764 Dihedral : 5.255 59.819 4187 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 0.99 % Allowed : 10.98 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3358 helix: 2.63 (0.22), residues: 615 sheet: 0.33 (0.17), residues: 904 loop : -0.77 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 36 HIS 0.004 0.001 HIS H 35 PHE 0.019 0.001 PHE B 168 TYR 0.028 0.001 TYR B 200 ARG 0.005 0.000 ARG C 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5109.48 seconds wall clock time: 94 minutes 42.64 seconds (5682.64 seconds total)