Starting phenix.real_space_refine on Mon Jul 6 20:57:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hcb_34658/07_2026/8hcb_34658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hcb_34658/07_2026/8hcb_34658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hcb_34658/07_2026/8hcb_34658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hcb_34658/07_2026/8hcb_34658.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hcb_34658/07_2026/8hcb_34658.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hcb_34658/07_2026/8hcb_34658.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hcb_34658/07_2026/8hcb_34658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hcb_34658/07_2026/8hcb_34658.cif" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4818 atoms to isotropic. 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 156 5.16 5 C 22344 2.51 5 N 5802 2.21 5 O 6885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35187 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "B" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "C" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "E" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1727 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "L" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1727 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1727 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.95, per 1000 atoms: 0.20 Number of scatterers: 35187 At special positions: 0 Unit cell: (183.15, 146.85, 244.2, 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 156 16.00 O 6885 8.00 N 5802 7.00 C 22344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.04 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 199 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 100 " distance=2.03 Simple disulfide: pdb=" SG CYS F 111 " - pdb=" SG CYS F 116 " distance=2.03 Simple disulfide: pdb=" SG CYS F 161 " - pdb=" SG CYS F 217 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 111 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 111 " - pdb=" SG CYS D 116 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.4 seconds 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8322 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 73 sheets defined 18.9% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.731A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.003A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.731A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.735A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.916A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.768A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.561A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.015A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 4.109A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.093A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.073A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.514A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.891A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.653A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.669A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 887 through 891 removed outlier: 4.142A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.531A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.645A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.944A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.253A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.707A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.004A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 4.120A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.561A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.715A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 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 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.678A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.115A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.746A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.785A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 131 Processing helix chain 'F' and resid 28 through 32 removed outlier: 4.123A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 71 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.960A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.780A pdb=" N SER L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.603A pdb=" N LYS L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'D' and resid 66 through 71 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.443A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.585A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 52 removed outlier: 4.450A 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: 3.809A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 141 removed outlier: 4.055A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.586A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.393A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.886A 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 541 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.784A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.747A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.715A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.004A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.004A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 3.854A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.994A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.079A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.013A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.061A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 135 through 141 removed outlier: 10.550A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.513A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.368A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.601A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.252A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.326A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.084A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.600A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.890A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.983A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.274A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 133 through 141 removed outlier: 4.916A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.549A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 356 removed outlier: 4.534A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.740A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.747A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.044A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) 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 'E' and resid 22 through 23 Processing sheet with id=AF1, first strand: chain 'E' and resid 49 through 53 removed outlier: 4.837A pdb=" N LEU E 51 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU E 42 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 121 through 123 removed outlier: 3.559A pdb=" N PHE E 123 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 138 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR E 178 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 159 through 160 removed outlier: 4.635A pdb=" N TRP E 153 " --> pdb=" O GLN E 160 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.542A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET F 87 " --> pdb=" O LEU F 18 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.211A pdb=" N GLY F 10 " --> pdb=" O ILE F 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 35 through 38 removed outlier: 3.529A pdb=" N SER F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER F 50 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR F 63 " --> pdb=" O SER F 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 141 through 148 removed outlier: 3.837A pdb=" N GLY F 160 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA F 158 " --> pdb=" O PRO F 147 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER F 201 " --> pdb=" O CYS F 161 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR F 197 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 172 through 175 removed outlier: 4.555A pdb=" N TYR F 215 " --> pdb=" O VAL F 232 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 12 through 13 removed outlier: 3.703A pdb=" N VAL L 13 " --> pdb=" O GLU L 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 48 through 53 removed outlier: 3.989A pdb=" N SER L 48 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS L 44 " --> pdb=" O SER L 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU L 52 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 67 through 70 Processing sheet with id=AG3, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.958A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.720A pdb=" N TRP L 153 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS L 199 " --> pdb=" O LYS L 212 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 48 through 53 removed outlier: 6.839A pdb=" N LYS G 44 " --> pdb=" O PRO G 49 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU G 51 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU G 42 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR G 92 " --> pdb=" O TYR G 41 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 67 through 70 Processing sheet with id=AG7, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.698A pdb=" N VAL G 138 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN G 143 " --> pdb=" O TYR G 178 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR G 178 " --> pdb=" O ASN G 143 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 159 through 160 removed outlier: 4.600A pdb=" N TRP G 153 " --> pdb=" O GLN G 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA G 198 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS G 199 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS G 212 " --> pdb=" O CYS G 199 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.555A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H 83 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 35 through 39 removed outlier: 6.941A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 141 through 148 removed outlier: 3.911A pdb=" N GLY H 160 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA H 158 " --> pdb=" O PRO H 147 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER H 201 " --> pdb=" O CYS H 161 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 141 through 148 removed outlier: 3.911A pdb=" N GLY H 160 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA H 158 " --> pdb=" O PRO H 147 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER H 201 " --> pdb=" O CYS H 161 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER H 198 " --> pdb=" O VAL H 190 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 172 through 175 Processing sheet with id=AH5, first strand: chain 'D' and resid 6 through 7 removed outlier: 4.202A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 10 through 11 removed outlier: 5.897A pdb=" N GLY D 10 " --> pdb=" O ILE D 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'D' and resid 45 through 50 removed outlier: 4.778A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 141 through 148 removed outlier: 3.809A pdb=" N GLY D 160 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA D 158 " --> pdb=" O PRO D 147 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 165 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR D 197 " --> pdb=" O ASP D 165 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 141 through 148 removed outlier: 3.809A pdb=" N GLY D 160 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA D 158 " --> pdb=" O PRO D 147 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 165 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR D 197 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 190 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 174 through 175 removed outlier: 4.882A pdb=" N TYR D 215 " --> pdb=" O VAL D 232 " (cutoff:3.500A) 1166 hydrogen bonds defined for protein. 3186 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: 8.49 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11197 1.34 - 1.47: 8862 1.47 - 1.59: 15731 1.59 - 1.71: 0 1.71 - 1.83: 195 Bond restraints: 35985 Sorted by residual: bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.38e-02 5.25e+03 1.18e+01 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C PHE B 898 " pdb=" N PRO B 899 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.90e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.86e+00 ... (remaining 35980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 48392 2.46 - 4.93: 519 4.93 - 7.39: 63 7.39 - 9.85: 8 9.85 - 12.31: 2 Bond angle restraints: 48984 Sorted by residual: angle pdb=" C SER D 151 " pdb=" CA SER D 151 " pdb=" CB SER D 151 " ideal model delta sigma weight residual 115.89 110.71 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CB PRO G 18 " pdb=" CG PRO G 18 " pdb=" CD PRO G 18 " ideal model delta sigma weight residual 106.10 93.79 12.31 3.20e+00 9.77e-02 1.48e+01 angle pdb=" CA PRO G 18 " pdb=" N PRO G 18 " pdb=" CD PRO G 18 " ideal model delta sigma weight residual 112.00 106.90 5.10 1.40e+00 5.10e-01 1.33e+01 angle pdb=" C ASN A 532 " pdb=" N LEU A 533 " pdb=" CA LEU A 533 " ideal model delta sigma weight residual 121.54 128.37 -6.83 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N PRO G 18 " pdb=" CD PRO G 18 " pdb=" CG PRO G 18 " ideal model delta sigma weight residual 103.20 97.94 5.26 1.50e+00 4.44e-01 1.23e+01 ... (remaining 48979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 19068 18.09 - 36.19: 1631 36.19 - 54.28: 317 54.28 - 72.38: 50 72.38 - 90.47: 30 Dihedral angle restraints: 21096 sinusoidal: 8160 harmonic: 12936 Sorted by residual: 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 93.00 -176.53 -90.47 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 -176.81 -90.19 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 2.52 -88.52 1 1.00e+01 1.00e-02 9.35e+01 ... (remaining 21093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 5261 0.090 - 0.179: 451 0.179 - 0.269: 6 0.269 - 0.358: 2 0.358 - 0.448: 4 Chirality restraints: 5724 Sorted by residual: chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 5721 not shown) Planarity restraints: 6297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " 0.044 2.00e-02 2.50e+03 3.63e-02 1.65e+01 pdb=" C7 NAG C1306 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO B 373 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 205 " -0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO D 206 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 206 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 206 " -0.036 5.00e-02 4.00e+02 ... (remaining 6294 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5138 2.77 - 3.30: 31552 3.30 - 3.83: 58208 3.83 - 4.37: 63810 4.37 - 4.90: 112553 Nonbonded interactions: 271261 Sorted by model distance: nonbonded pdb=" OG SER D 28 " pdb=" OG1 THR D 31 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.255 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.272 3.040 nonbonded pdb=" O CYS B1032 " pdb=" OG SER B1051 " model vdw 2.279 3.040 ... (remaining 271256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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 group one per residue 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 31.730 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.130 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 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 : 0.003 0.047 36096 Z= 0.156 Angle : 0.622 12.313 49260 Z= 0.306 Chirality : 0.047 0.448 5724 Planarity : 0.005 0.068 6255 Dihedral : 13.606 89.064 12603 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.39 % Allowed : 0.62 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.12), residues: 4383 helix: 1.38 (0.20), residues: 648 sheet: 0.70 (0.16), residues: 1032 loop : -1.33 (0.11), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 59 TYR 0.033 0.001 TYR F 166 PHE 0.018 0.001 PHE A 543 TRP 0.010 0.001 TRP F 36 HIS 0.004 0.000 HIS D 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (35985) covalent geometry : angle 0.60415 / 0.30 (48984) SS BOND : bond 0.00216 / 0.14 ( 57) SS BOND : angle 0.91202 / 0.56 ( 114) hydrogen bonds : bond 0.22311 / 14.50 ( 1135) hydrogen bonds : angle 8.57343 / 6.00 ( 3186) link_BETA1-4 : bond 0.00462 / 0.27 ( 12) link_BETA1-4 : angle 0.89845 / 0.65 ( 36) link_NAG-ASN : bond 0.00626 / 0.37 ( 42) link_NAG-ASN : angle 2.93090 / 2.00 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.263 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 997 ILE cc_start: 0.9260 (pt) cc_final: 0.9034 (pt) REVERT: B 340 GLU cc_start: 0.8644 (tm-30) cc_final: 0.7878 (pt0) REVERT: C 900 MET cc_start: 0.8355 (mpp) cc_final: 0.7979 (mpp) REVERT: F 84 PHE cc_start: 0.6808 (m-80) cc_final: 0.6501 (m-80) REVERT: F 94 ASP cc_start: 0.6860 (t0) cc_final: 0.6562 (p0) REVERT: D 34 MET cc_start: 0.7321 (mpp) cc_final: 0.7094 (mpp) REVERT: D 129 MET cc_start: 0.0045 (mmt) cc_final: -0.0191 (mmt) outliers start: 15 outliers final: 5 residues processed: 167 average time/residue: 0.2124 time to fit residues: 58.3664 Evaluate side-chains 113 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.0970 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 10.0000 overall best weight: 3.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 955 ASN C 907 ASN C1005 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 GLN L 129 GLN G 171 GLN G 194 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.096176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.064363 restraints weight = 172599.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.064798 restraints weight = 120163.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.064108 restraints weight = 88412.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.064284 restraints weight = 95373.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.064460 restraints weight = 80722.416| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 36096 Z= 0.238 Angle : 0.651 11.628 49260 Z= 0.330 Chirality : 0.046 0.435 5724 Planarity : 0.005 0.056 6255 Dihedral : 3.982 24.775 4770 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.12), residues: 4383 helix: 1.70 (0.20), residues: 676 sheet: 0.44 (0.16), residues: 1040 loop : -1.25 (0.12), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 328 TYR 0.018 0.002 TYR A 266 PHE 0.039 0.002 PHE B 329 TRP 0.014 0.002 TRP B 436 HIS 0.009 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (35985) covalent geometry : angle 0.63290 / 0.33 (48984) SS BOND : bond 0.00408 / 0.28 ( 57) SS BOND : angle 1.34367 / 0.91 ( 114) hydrogen bonds : bond 0.04049 / 2.64 ( 1135) hydrogen bonds : angle 6.32667 / 4.43 ( 3186) link_BETA1-4 : bond 0.00276 / 0.14 ( 12) link_BETA1-4 : angle 1.49694 / 0.98 ( 36) link_NAG-ASN : bond 0.00540 / 0.32 ( 42) link_NAG-ASN : angle 2.72911 / 1.68 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 458 LYS cc_start: 0.6724 (mptt) cc_final: 0.6521 (mptt) REVERT: C 900 MET cc_start: 0.8688 (mpp) cc_final: 0.7951 (mpp) REVERT: F 64 TYR cc_start: 0.4583 (m-10) cc_final: 0.4036 (m-80) REVERT: G 170 GLU cc_start: 0.0500 (mp0) cc_final: -0.0673 (mm-30) REVERT: D 98 TYR cc_start: 0.6260 (m-10) cc_final: 0.5951 (m-10) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2148 time to fit residues: 46.3680 Evaluate side-chains 99 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 176 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 297 optimal weight: 0.9980 chunk 362 optimal weight: 20.0000 chunk 382 optimal weight: 40.0000 chunk 66 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 196 ASN C 907 ASN ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.096180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.066334 restraints weight = 174397.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.065250 restraints weight = 114915.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.065123 restraints weight = 104304.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.065485 restraints weight = 100168.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.065412 restraints weight = 81811.004| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36096 Z= 0.148 Angle : 0.554 11.317 49260 Z= 0.279 Chirality : 0.044 0.436 5724 Planarity : 0.004 0.055 6255 Dihedral : 3.870 22.405 4770 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.13), residues: 4383 helix: 1.93 (0.21), residues: 663 sheet: 0.44 (0.16), residues: 1049 loop : -1.21 (0.12), residues: 2671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 498 TYR 0.018 0.001 TYR A1138 PHE 0.020 0.001 PHE B 329 TRP 0.024 0.001 TRP A 64 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (35985) covalent geometry : angle 0.53522 / 0.27 (48984) SS BOND : bond 0.00328 / 0.21 ( 57) SS BOND : angle 1.15526 / 0.79 ( 114) hydrogen bonds : bond 0.03905 / 2.54 ( 1135) hydrogen bonds : angle 5.86319 / 4.10 ( 3186) link_BETA1-4 : bond 0.00302 / 0.17 ( 12) link_BETA1-4 : angle 1.09567 / 0.76 ( 36) link_NAG-ASN : bond 0.00433 / 0.26 ( 42) link_NAG-ASN : angle 2.63429 / 1.68 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 455 LEU cc_start: 0.7223 (mm) cc_final: 0.6883 (mm) REVERT: C 900 MET cc_start: 0.8447 (mpp) cc_final: 0.7975 (mpp) REVERT: C 902 MET cc_start: 0.8752 (mmm) cc_final: 0.8250 (mmt) REVERT: E 123 PHE cc_start: 0.3256 (m-80) cc_final: 0.3035 (m-10) REVERT: F 62 ILE cc_start: 0.6059 (mm) cc_final: 0.5792 (mm) REVERT: F 64 TYR cc_start: 0.4816 (m-10) cc_final: 0.3896 (m-80) REVERT: L 59 ARG cc_start: 0.5418 (tpp80) cc_final: 0.4110 (mmm-85) REVERT: L 65 ASP cc_start: 0.5530 (m-30) cc_final: 0.5065 (m-30) REVERT: G 170 GLU cc_start: -0.0123 (mp0) cc_final: -0.0541 (mm-30) REVERT: H 61 TYR cc_start: 0.7972 (m-10) cc_final: 0.7760 (m-80) REVERT: H 69 LYS cc_start: 0.6269 (mtmt) cc_final: 0.6006 (mtmt) REVERT: D 87 MET cc_start: 0.2709 (ppp) cc_final: 0.2373 (ppp) REVERT: D 98 TYR cc_start: 0.6444 (m-10) cc_final: 0.6149 (m-10) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.2224 time to fit residues: 50.4497 Evaluate side-chains 104 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 438 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 388 optimal weight: 9.9990 chunk 391 optimal weight: 0.9990 chunk 367 optimal weight: 30.0000 chunk 340 optimal weight: 30.0000 chunk 379 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 404 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 955 ASN B 185 ASN B 448 ASN B 474 GLN B 955 ASN C 17 ASN C 196 ASN C 907 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.094308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.062566 restraints weight = 172994.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063096 restraints weight = 122339.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062522 restraints weight = 88074.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062743 restraints weight = 91727.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.062884 restraints weight = 79201.095| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36096 Z= 0.244 Angle : 0.662 12.147 49260 Z= 0.333 Chirality : 0.047 0.470 5724 Planarity : 0.005 0.055 6255 Dihedral : 4.335 30.780 4770 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.89 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.12), residues: 4383 helix: 1.56 (0.20), residues: 664 sheet: 0.26 (0.16), residues: 1015 loop : -1.35 (0.11), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 346 TYR 0.028 0.002 TYR A 266 PHE 0.023 0.002 PHE C 906 TRP 0.018 0.002 TRP B1102 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 (35985) covalent geometry : angle 0.64109 / 0.33 (48984) SS BOND : bond 0.00447 / 0.30 ( 57) SS BOND : angle 1.50189 / 1.03 ( 114) hydrogen bonds : bond 0.04115 / 2.69 ( 1135) hydrogen bonds : angle 5.89942 / 4.12 ( 3186) link_BETA1-4 : bond 0.00384 / 0.19 ( 12) link_BETA1-4 : angle 1.61074 / 1.07 ( 36) link_NAG-ASN : bond 0.00543 / 0.32 ( 42) link_NAG-ASN : angle 2.94933 / 1.84 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 458 LYS cc_start: 0.6260 (mptt) cc_final: 0.4960 (ptpt) REVERT: C 486 PHE cc_start: 0.6864 (t80) cc_final: 0.6012 (t80) REVERT: C 900 MET cc_start: 0.8571 (mpp) cc_final: 0.8310 (mpp) REVERT: E 94 MET cc_start: 0.0350 (tpp) cc_final: 0.0093 (tpp) REVERT: F 62 ILE cc_start: 0.6169 (mm) cc_final: 0.5958 (mm) REVERT: F 64 TYR cc_start: 0.5262 (m-10) cc_final: 0.4121 (m-80) REVERT: D 98 TYR cc_start: 0.5991 (m-10) cc_final: 0.5621 (m-80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2183 time to fit residues: 49.5885 Evaluate side-chains 101 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 30 optimal weight: 20.0000 chunk 224 optimal weight: 0.0870 chunk 333 optimal weight: 4.9990 chunk 144 optimal weight: 30.0000 chunk 200 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 277 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 404 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1071 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 196 ASN C 907 ASN ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.095141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.064281 restraints weight = 171280.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.064157 restraints weight = 114351.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.063892 restraints weight = 84894.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.064048 restraints weight = 85061.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.064112 restraints weight = 76986.860| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36096 Z= 0.141 Angle : 0.568 11.866 49260 Z= 0.284 Chirality : 0.045 0.451 5724 Planarity : 0.004 0.055 6255 Dihedral : 4.110 25.647 4770 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.70 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 4383 helix: 1.75 (0.20), residues: 675 sheet: 0.21 (0.16), residues: 1059 loop : -1.32 (0.12), residues: 2649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 113 TYR 0.021 0.001 TYR G 54 PHE 0.024 0.001 PHE C 981 TRP 0.015 0.001 TRP H 124 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (35985) covalent geometry : angle 0.54755 / 0.28 (48984) SS BOND : bond 0.00362 / 0.24 ( 57) SS BOND : angle 1.35580 / 0.91 ( 114) hydrogen bonds : bond 0.03663 / 2.38 ( 1135) hydrogen bonds : angle 5.62151 / 3.93 ( 3186) link_BETA1-4 : bond 0.00328 / 0.18 ( 12) link_BETA1-4 : angle 1.24693 / 0.87 ( 36) link_NAG-ASN : bond 0.00443 / 0.26 ( 42) link_NAG-ASN : angle 2.71471 / 1.73 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7769 (tp) cc_final: 0.7557 (tt) REVERT: B 458 LYS cc_start: 0.6109 (mptt) cc_final: 0.4854 (ptpp) REVERT: C 486 PHE cc_start: 0.6670 (t80) cc_final: 0.5830 (t80) REVERT: C 900 MET cc_start: 0.8364 (mpp) cc_final: 0.7783 (mpp) REVERT: C 902 MET cc_start: 0.8596 (mmm) cc_final: 0.8384 (tpt) REVERT: E 94 MET cc_start: 0.0504 (tpp) cc_final: 0.0199 (tpp) REVERT: F 64 TYR cc_start: 0.5166 (m-10) cc_final: 0.4116 (m-80) REVERT: H 87 MET cc_start: 0.6170 (mpp) cc_final: 0.5920 (mpp) REVERT: D 98 TYR cc_start: 0.5616 (m-10) cc_final: 0.5312 (m-80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2338 time to fit residues: 51.7360 Evaluate side-chains 98 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 150 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 338 optimal weight: 0.5980 chunk 246 optimal weight: 5.9990 chunk 329 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 144 optimal weight: 0.2980 chunk 352 optimal weight: 30.0000 chunk 374 optimal weight: 20.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 196 ASN C 907 ASN F 81 ASN G 204 GLN ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.094478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.062821 restraints weight = 174996.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.062658 restraints weight = 123866.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.062866 restraints weight = 93677.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.062883 restraints weight = 82571.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063020 restraints weight = 75893.404| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36096 Z= 0.187 Angle : 0.606 12.300 49260 Z= 0.304 Chirality : 0.046 0.455 5724 Planarity : 0.004 0.056 6255 Dihedral : 4.253 28.586 4770 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.07 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.12), residues: 4383 helix: 1.56 (0.20), residues: 683 sheet: 0.13 (0.16), residues: 1036 loop : -1.37 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 78 TYR 0.020 0.002 TYR A 266 PHE 0.022 0.002 PHE C 906 TRP 0.024 0.001 TRP H 124 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (35985) covalent geometry : angle 0.58514 / 0.30 (48984) SS BOND : bond 0.00469 / 0.31 ( 57) SS BOND : angle 1.50552 / 1.01 ( 114) hydrogen bonds : bond 0.03813 / 2.50 ( 1135) hydrogen bonds : angle 5.66448 / 3.95 ( 3186) link_BETA1-4 : bond 0.00254 / 0.14 ( 12) link_BETA1-4 : angle 1.44022 / 0.98 ( 36) link_NAG-ASN : bond 0.00461 / 0.28 ( 42) link_NAG-ASN : angle 2.78026 / 1.76 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 458 LYS cc_start: 0.6147 (mptt) cc_final: 0.4946 (ptpp) REVERT: C 486 PHE cc_start: 0.6901 (t80) cc_final: 0.6102 (t80) REVERT: C 900 MET cc_start: 0.8535 (mpp) cc_final: 0.8144 (mpp) REVERT: E 94 MET cc_start: 0.0631 (tpp) cc_final: 0.0240 (tpp) REVERT: F 62 ILE cc_start: 0.6705 (mm) cc_final: 0.6326 (mm) REVERT: F 64 TYR cc_start: 0.5302 (m-10) cc_final: 0.4282 (m-80) REVERT: H 87 MET cc_start: 0.6270 (mpp) cc_final: 0.6022 (mpp) REVERT: D 87 MET cc_start: 0.2516 (ppp) cc_final: 0.2070 (ppp) REVERT: D 98 TYR cc_start: 0.5477 (m-10) cc_final: 0.5070 (m-80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2200 time to fit residues: 47.5591 Evaluate side-chains 95 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 71 optimal weight: 0.9980 chunk 427 optimal weight: 50.0000 chunk 97 optimal weight: 1.9990 chunk 324 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 419 optimal weight: 0.4980 chunk 391 optimal weight: 8.9990 chunk 354 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 363 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 49 HIS C 196 ASN C 907 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 GLN L 203 HIS G 165 GLN ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.095097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.064612 restraints weight = 173018.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.064529 restraints weight = 121944.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.064079 restraints weight = 95591.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.064198 restraints weight = 95087.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064340 restraints weight = 80756.002| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36096 Z= 0.123 Angle : 0.562 11.712 49260 Z= 0.281 Chirality : 0.045 0.446 5724 Planarity : 0.004 0.058 6255 Dihedral : 4.111 24.454 4770 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.91 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4383 helix: 1.76 (0.20), residues: 689 sheet: 0.16 (0.16), residues: 1046 loop : -1.34 (0.12), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 113 TYR 0.015 0.001 TYR A 266 PHE 0.027 0.001 PHE B 329 TRP 0.021 0.001 TRP H 124 HIS 0.005 0.001 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (35985) covalent geometry : angle 0.54108 / 0.28 (48984) SS BOND : bond 0.00338 / 0.22 ( 57) SS BOND : angle 1.31715 / 0.89 ( 114) hydrogen bonds : bond 0.03528 / 2.31 ( 1135) hydrogen bonds : angle 5.48405 / 3.82 ( 3186) link_BETA1-4 : bond 0.00317 / 0.17 ( 12) link_BETA1-4 : angle 1.23047 / 0.86 ( 36) link_NAG-ASN : bond 0.00442 / 0.26 ( 42) link_NAG-ASN : angle 2.77111 / 1.89 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 458 LYS cc_start: 0.6279 (mptt) cc_final: 0.5043 (ptpp) REVERT: C 486 PHE cc_start: 0.6312 (t80) cc_final: 0.5974 (t80) REVERT: C 900 MET cc_start: 0.8433 (mpp) cc_final: 0.8060 (mpp) REVERT: E 94 MET cc_start: 0.0370 (tpp) cc_final: 0.0116 (tpp) REVERT: F 62 ILE cc_start: 0.7581 (mm) cc_final: 0.6774 (tt) REVERT: F 64 TYR cc_start: 0.5418 (m-10) cc_final: 0.4093 (m-80) REVERT: G 110 GLU cc_start: 0.3127 (mp0) cc_final: 0.2887 (mp0) REVERT: H 87 MET cc_start: 0.6231 (mpp) cc_final: 0.5992 (mpp) REVERT: D 87 MET cc_start: 0.2635 (ppp) cc_final: 0.2155 (ppp) REVERT: D 98 TYR cc_start: 0.5654 (m-10) cc_final: 0.5245 (m-80) REVERT: D 119 ASP cc_start: 0.3573 (m-30) cc_final: 0.3292 (m-30) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2132 time to fit residues: 48.6675 Evaluate side-chains 95 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 134 optimal weight: 10.0000 chunk 320 optimal weight: 20.0000 chunk 199 optimal weight: 8.9990 chunk 279 optimal weight: 0.5980 chunk 371 optimal weight: 40.0000 chunk 406 optimal weight: 9.9990 chunk 378 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 955 ASN B 955 ASN C 185 ASN C 196 ASN C 487 ASN C 907 ASN C1036 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.092385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060772 restraints weight = 178476.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061611 restraints weight = 124567.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.061157 restraints weight = 84886.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061249 restraints weight = 83938.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061287 restraints weight = 81226.938| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 36096 Z= 0.344 Angle : 0.791 13.537 49260 Z= 0.398 Chirality : 0.050 0.499 5724 Planarity : 0.005 0.079 6255 Dihedral : 4.935 36.766 4770 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.32 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.12), residues: 4383 helix: 0.90 (0.19), residues: 674 sheet: -0.11 (0.16), residues: 1025 loop : -1.62 (0.11), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 113 TYR 0.034 0.003 TYR H 98 PHE 0.029 0.003 PHE C 906 TRP 0.027 0.002 TRP H 124 HIS 0.008 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.34 (35985) covalent geometry : angle 0.76861 / 0.39 (48984) SS BOND : bond 0.00545 / 0.36 ( 57) SS BOND : angle 1.99756 / 1.34 ( 114) hydrogen bonds : bond 0.04619 / 3.04 ( 1135) hydrogen bonds : angle 6.12257 / 4.25 ( 3186) link_BETA1-4 : bond 0.00454 / 0.23 ( 12) link_BETA1-4 : angle 1.91468 / 1.24 ( 36) link_NAG-ASN : bond 0.00715 / 0.42 ( 42) link_NAG-ASN : angle 3.25339 / 2.09 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 458 LYS cc_start: 0.6245 (mptt) cc_final: 0.5125 (ptpp) REVERT: C 266 TYR cc_start: 0.8056 (m-80) cc_final: 0.7725 (m-80) REVERT: C 486 PHE cc_start: 0.6890 (t80) cc_final: 0.6317 (t80) REVERT: C 900 MET cc_start: 0.8633 (mpp) cc_final: 0.8198 (mpp) REVERT: F 62 ILE cc_start: 0.6862 (mm) cc_final: 0.6259 (mm) REVERT: F 64 TYR cc_start: 0.6283 (m-10) cc_final: 0.4970 (m-80) REVERT: H 87 MET cc_start: 0.6800 (mpp) cc_final: 0.6502 (mpp) REVERT: H 187 PHE cc_start: -0.0608 (m-80) cc_final: -0.0955 (m-80) REVERT: D 98 TYR cc_start: 0.5921 (m-10) cc_final: 0.5516 (m-80) REVERT: D 119 ASP cc_start: 0.3987 (m-30) cc_final: 0.3716 (m-30) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2254 time to fit residues: 48.3845 Evaluate side-chains 95 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 216 optimal weight: 20.0000 chunk 324 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 293 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 427 optimal weight: 3.9990 chunk 295 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 955 ASN A1058 HIS ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 196 ASN C 907 ASN C1036 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.093908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.063309 restraints weight = 177906.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063601 restraints weight = 118682.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.063617 restraints weight = 99059.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063718 restraints weight = 81613.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.063853 restraints weight = 77622.142| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36096 Z= 0.145 Angle : 0.610 12.078 49260 Z= 0.305 Chirality : 0.046 0.462 5724 Planarity : 0.004 0.074 6255 Dihedral : 4.471 26.297 4770 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.12), residues: 4383 helix: 1.40 (0.20), residues: 689 sheet: -0.08 (0.16), residues: 1053 loop : -1.49 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 995 TYR 0.018 0.001 TYR A 266 PHE 0.023 0.001 PHE C 906 TRP 0.021 0.001 TRP H 124 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (35985) covalent geometry : angle 0.58912 / 0.30 (48984) SS BOND : bond 0.00395 / 0.26 ( 57) SS BOND : angle 1.57131 / 1.01 ( 114) hydrogen bonds : bond 0.03762 / 2.48 ( 1135) hydrogen bonds : angle 5.67597 / 3.95 ( 3186) link_BETA1-4 : bond 0.00349 / 0.19 ( 12) link_BETA1-4 : angle 1.36311 / 0.95 ( 36) link_NAG-ASN : bond 0.00451 / 0.28 ( 42) link_NAG-ASN : angle 2.80953 / 1.83 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 374 PHE cc_start: 0.7533 (t80) cc_final: 0.6626 (t80) REVERT: B 458 LYS cc_start: 0.6147 (mptt) cc_final: 0.5044 (ptpt) REVERT: B 900 MET cc_start: 0.8710 (pmm) cc_final: 0.8474 (pmm) REVERT: C 486 PHE cc_start: 0.6750 (t80) cc_final: 0.6159 (t80) REVERT: C 869 MET cc_start: 0.8773 (ptp) cc_final: 0.8545 (ptm) REVERT: C 900 MET cc_start: 0.8388 (mpp) cc_final: 0.7990 (mpp) REVERT: F 62 ILE cc_start: 0.7351 (mm) cc_final: 0.6331 (tt) REVERT: F 64 TYR cc_start: 0.6007 (m-10) cc_final: 0.4545 (m-80) REVERT: L 113 ARG cc_start: 0.5562 (ttp-170) cc_final: 0.5331 (ptt-90) REVERT: H 87 MET cc_start: 0.6782 (mpp) cc_final: 0.6422 (mpp) REVERT: D 87 MET cc_start: 0.2585 (ppp) cc_final: 0.2055 (ppp) REVERT: D 98 TYR cc_start: 0.5584 (m-10) cc_final: 0.5190 (m-80) REVERT: D 119 ASP cc_start: 0.4239 (m-30) cc_final: 0.3896 (m-30) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2025 time to fit residues: 44.0680 Evaluate side-chains 91 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 126 optimal weight: 6.9990 chunk 373 optimal weight: 2.9990 chunk 322 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 334 optimal weight: 20.0000 chunk 163 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 955 ASN B 121 ASN B 955 ASN C 196 ASN C 907 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.093319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.063160 restraints weight = 178687.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063812 restraints weight = 121960.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063563 restraints weight = 81117.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.063646 restraints weight = 82485.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.063696 restraints weight = 78745.021| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36096 Z= 0.196 Angle : 0.641 12.451 49260 Z= 0.320 Chirality : 0.046 0.464 5724 Planarity : 0.004 0.066 6255 Dihedral : 4.562 30.572 4770 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.82 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.12), residues: 4383 helix: 1.32 (0.20), residues: 689 sheet: -0.12 (0.16), residues: 1036 loop : -1.51 (0.12), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 113 TYR 0.021 0.002 TYR A 266 PHE 0.020 0.002 PHE C 906 TRP 0.019 0.002 TRP H 124 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (35985) covalent geometry : angle 0.61901 / 0.31 (48984) SS BOND : bond 0.00430 / 0.29 ( 57) SS BOND : angle 1.59632 / 1.06 ( 114) hydrogen bonds : bond 0.03905 / 2.57 ( 1135) hydrogen bonds : angle 5.71224 / 3.97 ( 3186) link_BETA1-4 : bond 0.00281 / 0.15 ( 12) link_BETA1-4 : angle 1.56632 / 1.07 ( 36) link_NAG-ASN : bond 0.00498 / 0.30 ( 42) link_NAG-ASN : angle 2.91079 / 1.87 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.7831 (t80) cc_final: 0.6991 (t80) REVERT: A 582 LEU cc_start: 0.7714 (tp) cc_final: 0.7506 (tt) REVERT: A 731 MET cc_start: 0.9140 (pmm) cc_final: 0.8888 (pmm) REVERT: B 458 LYS cc_start: 0.6136 (mptt) cc_final: 0.5041 (ptpt) REVERT: C 486 PHE cc_start: 0.6728 (t80) cc_final: 0.6194 (t80) REVERT: C 900 MET cc_start: 0.8447 (mpp) cc_final: 0.8038 (mpp) REVERT: E 79 LYS cc_start: 0.8201 (mptt) cc_final: 0.7942 (mmtp) REVERT: F 62 ILE cc_start: 0.6429 (mm) cc_final: 0.5361 (tt) REVERT: F 64 TYR cc_start: 0.5625 (m-10) cc_final: 0.4315 (m-80) REVERT: L 113 ARG cc_start: 0.5537 (ttp-170) cc_final: 0.5300 (ptt-90) REVERT: H 87 MET cc_start: 0.6757 (mpp) cc_final: 0.6436 (mpp) REVERT: D 87 MET cc_start: 0.2569 (ppp) cc_final: 0.1993 (ppp) REVERT: D 98 TYR cc_start: 0.5576 (m-10) cc_final: 0.5181 (m-80) REVERT: D 119 ASP cc_start: 0.4093 (m-30) cc_final: 0.3821 (m-30) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2103 time to fit residues: 44.1727 Evaluate side-chains 93 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 50 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 333 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 425 optimal weight: 20.0000 chunk 331 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 341 optimal weight: 20.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 196 ASN C 907 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.093771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063826 restraints weight = 177877.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064454 restraints weight = 126847.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064178 restraints weight = 89030.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.064261 restraints weight = 82702.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.064340 restraints weight = 80947.308| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36096 Z= 0.148 Angle : 0.600 11.783 49260 Z= 0.299 Chirality : 0.046 0.443 5724 Planarity : 0.004 0.058 6255 Dihedral : 4.402 25.644 4770 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 4383 helix: 1.50 (0.20), residues: 689 sheet: -0.11 (0.16), residues: 1043 loop : -1.46 (0.12), residues: 2651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 113 TYR 0.018 0.001 TYR A 266 PHE 0.021 0.001 PHE C 906 TRP 0.017 0.001 TRP H 124 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (35985) covalent geometry : angle 0.57981 / 0.29 (48984) SS BOND : bond 0.00388 / 0.26 ( 57) SS BOND : angle 1.40097 / 0.92 ( 114) hydrogen bonds : bond 0.03637 / 2.39 ( 1135) hydrogen bonds : angle 5.56832 / 3.87 ( 3186) link_BETA1-4 : bond 0.00309 / 0.17 ( 12) link_BETA1-4 : angle 1.35451 / 0.95 ( 36) link_NAG-ASN : bond 0.00444 / 0.27 ( 42) link_NAG-ASN : angle 2.77124 / 1.80 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5123.52 seconds wall clock time: 90 minutes 8.89 seconds (5408.89 seconds total)