Starting phenix.real_space_refine on Mon Jul 6 14:33:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cws_30486/07_2026/7cws_30486.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cws_30486/07_2026/7cws_30486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cws_30486/07_2026/7cws_30486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cws_30486/07_2026/7cws_30486.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cws_30486/07_2026/7cws_30486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cws_30486/07_2026/7cws_30486.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cws_30486/07_2026/7cws_30486.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cws_30486/07_2026/7cws_30486.cif" } resolution = 3.4 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 162 5.16 5 C 23111 2.51 5 N 5965 2.21 5 O 7151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.04s 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: 36389 Number of models: 1 Model: "" Number of chains: 33 Chain: "L" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "C" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 789 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "D" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 844 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 844 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 844 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "K" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 789 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "P" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "M" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 789 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 8414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8414 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1024} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8411 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 51, 'TRANS': 1023} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8411 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1024} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" 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: "B" 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: "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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: "b" 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: "c" 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: "d" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 8.21, per 1000 atoms: 0.23 Number of scatterers: 36389 At special positions: 0 Unit cell: (209.04, 216.32, 192.4, 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 162 16.00 O 7151 8.00 N 5965 7.00 C 23111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 87 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 97 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS O 15 " - pdb=" SG CYS O 136 " distance=2.03 Simple disulfide: pdb=" SG CYS O 131 " - pdb=" SG CYS O 166 " distance=2.02 Simple disulfide: pdb=" SG CYS O 291 " - pdb=" SG CYS O 301 " distance=2.03 Simple disulfide: pdb=" SG CYS O 336 " - pdb=" SG CYS O 361 " distance=2.06 Simple disulfide: pdb=" SG CYS O 379 " - pdb=" SG CYS O 432 " distance=2.03 Simple disulfide: pdb=" SG CYS O 480 " - pdb=" SG CYS O 488 " distance=2.03 Simple disulfide: pdb=" SG CYS O 617 " - pdb=" SG CYS O 649 " distance=2.02 Simple disulfide: pdb=" SG CYS O 662 " - pdb=" SG CYS O 671 " distance=2.03 Simple disulfide: pdb=" SG CYS O 738 " - pdb=" SG CYS O 760 " distance=2.03 Simple disulfide: pdb=" SG CYS O 743 " - pdb=" SG CYS O 749 " distance=2.03 Simple disulfide: pdb=" SG CYS O1032 " - pdb=" SG CYS O1043 " distance=2.00 Simple disulfide: pdb=" SG CYS O1082 " - pdb=" SG CYS O1126 " distance=2.00 Simple disulfide: pdb=" SG CYS Q 15 " - pdb=" SG CYS Q 136 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 131 " - pdb=" SG CYS Q 166 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 291 " - pdb=" SG CYS Q 301 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 336 " - pdb=" SG CYS Q 361 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 379 " - pdb=" SG CYS Q 432 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 480 " - pdb=" SG CYS Q 488 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 617 " - pdb=" SG CYS Q 649 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 662 " - pdb=" SG CYS Q 671 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 738 " - pdb=" SG CYS Q 760 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 743 " - pdb=" SG CYS Q 749 " distance=2.02 Simple disulfide: pdb=" SG CYS Q1032 " - pdb=" SG CYS Q1043 " distance=2.04 Simple disulfide: pdb=" SG CYS Q1082 " - pdb=" SG CYS Q1126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 15 " - pdb=" SG CYS R 136 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 166 " distance=2.02 Simple disulfide: pdb=" SG CYS R 291 " - pdb=" SG CYS R 301 " distance=2.09 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.04 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS R 617 " - pdb=" SG CYS R 649 " distance=2.03 Simple disulfide: pdb=" SG CYS R 662 " - pdb=" SG CYS R 671 " distance=2.03 Simple disulfide: pdb=" SG CYS R 738 " - pdb=" SG CYS R 760 " distance=2.02 Simple disulfide: pdb=" SG CYS R 743 " - pdb=" SG CYS R 749 " distance=2.02 Simple disulfide: pdb=" SG CYS R1032 " - pdb=" SG CYS R1043 " distance=2.04 Simple disulfide: pdb=" SG CYS R1082 " - pdb=" SG CYS R1126 " 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 A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG J 1 " - " NAG J 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 1 " - " ASN O 234 " " NAG B 1 " - " ASN O 717 " " NAG J 1 " - " ASN O 801 " " NAG O1201 " - " ASN O 603 " " NAG O1202 " - " ASN O 616 " " NAG O1203 " - " ASN O 657 " " NAG O1204 " - " ASN O 709 " " NAG O1205 " - " ASN O1074 " " NAG Q1301 " - " ASN Q 61 " " NAG Q1302 " - " ASN Q 603 " " NAG Q1303 " - " ASN Q 616 " " NAG Q1304 " - " ASN Q 657 " " NAG Q1305 " - " ASN Q 709 " " NAG Q1306 " - " ASN Q1074 " " NAG R1201 " - " ASN R 603 " " NAG R1202 " - " ASN R 616 " " NAG R1203 " - " ASN R 657 " " NAG R1204 " - " ASN R 709 " " NAG R1205 " - " ASN R1074 " " NAG S 1 " - " ASN O1098 " " NAG T 1 " - " ASN O1134 " " NAG U 1 " - " ASN Q 234 " " NAG V 1 " - " ASN Q 717 " " NAG W 1 " - " ASN Q 801 " " NAG X 1 " - " ASN Q1098 " " NAG Y 1 " - " ASN Q1134 " " NAG a 1 " - " ASN R 717 " " NAG b 1 " - " ASN R 801 " " NAG c 1 " - " ASN R1134 " " NAG d 1 " - " ASN R1098 " Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8544 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 89 sheets defined 16.4% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'L' and resid 29 through 33 Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'N' and resid 29 through 33 Processing helix chain 'K' and resid 80 through 84 removed outlier: 4.334A pdb=" N GLU K 84 " --> pdb=" O THR K 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 33 Processing helix chain 'O' and resid 296 through 304 removed outlier: 3.725A pdb=" N LYS O 300 " --> pdb=" O LEU O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 343 Processing helix chain 'O' and resid 405 through 408 removed outlier: 3.556A pdb=" N ARG O 408 " --> pdb=" O ASP O 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 405 through 408' Processing helix chain 'O' and resid 416 through 421 Processing helix chain 'O' and resid 737 through 743 Processing helix chain 'O' and resid 746 through 754 removed outlier: 3.981A pdb=" N LEU O 752 " --> pdb=" O GLU O 748 " (cutoff:3.500A) Processing helix chain 'O' and resid 755 through 757 No H-bonds generated for 'chain 'O' and resid 755 through 757' Processing helix chain 'O' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU O 763 " --> pdb=" O PHE O 759 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN O 764 " --> pdb=" O CYS O 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU O 773 " --> pdb=" O GLY O 769 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP O 775 " --> pdb=" O ALA O 771 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS O 776 " --> pdb=" O VAL O 772 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR O 778 " --> pdb=" O GLN O 774 " (cutoff:3.500A) Processing helix chain 'O' and resid 816 through 826 removed outlier: 3.635A pdb=" N LEU O 821 " --> pdb=" O PHE O 817 " (cutoff:3.500A) Processing helix chain 'O' and resid 849 through 856 Processing helix chain 'O' and resid 866 through 885 removed outlier: 3.705A pdb=" N LEU O 878 " --> pdb=" O THR O 874 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR O 883 " --> pdb=" O ALA O 879 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY O 885 " --> pdb=" O THR O 881 " (cutoff:3.500A) Processing helix chain 'O' and resid 897 through 909 removed outlier: 3.882A pdb=" N ALA O 903 " --> pdb=" O ALA O 899 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN O 907 " --> pdb=" O ALA O 903 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE O 909 " --> pdb=" O ARG O 905 " (cutoff:3.500A) Processing helix chain 'O' and resid 913 through 941 removed outlier: 3.518A pdb=" N TYR O 917 " --> pdb=" O GLN O 913 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU O 918 " --> pdb=" O ASN O 914 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS O 921 " --> pdb=" O TYR O 917 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU O 922 " --> pdb=" O GLU O 918 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE O 934 " --> pdb=" O ALA O 930 " (cutoff:3.500A) Processing helix chain 'O' and resid 945 through 965 Processing helix chain 'O' and resid 966 through 968 No H-bonds generated for 'chain 'O' and resid 966 through 968' Processing helix chain 'O' and resid 976 through 982 removed outlier: 3.540A pdb=" N ILE O 980 " --> pdb=" O VAL O 976 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU O 981 " --> pdb=" O LEU O 977 " (cutoff:3.500A) Processing helix chain 'O' and resid 985 through 1032 removed outlier: 3.618A pdb=" N ALA O 989 " --> pdb=" O ASP O 985 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL O 991 " --> pdb=" O VAL O 987 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP O 994 " --> pdb=" O GLU O 990 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG O 995 " --> pdb=" O VAL O 991 " (cutoff:3.500A) Processing helix chain 'O' and resid 1140 through 1146 removed outlier: 3.920A pdb=" N GLU O1144 " --> pdb=" O PRO O1140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP O1146 " --> pdb=" O GLN O1142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 343 Processing helix chain 'Q' and resid 364 through 369 removed outlier: 3.681A pdb=" N VAL Q 367 " --> pdb=" O ASP Q 364 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR Q 369 " --> pdb=" O SER Q 366 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 408 removed outlier: 3.555A pdb=" N ARG Q 408 " --> pdb=" O ASP Q 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 405 through 408' Processing helix chain 'Q' and resid 416 through 421 Processing helix chain 'Q' and resid 737 through 743 Processing helix chain 'Q' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU Q 752 " --> pdb=" O GLU Q 748 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU Q 754 " --> pdb=" O SER Q 750 " (cutoff:3.500A) Processing helix chain 'Q' and resid 755 through 757 No H-bonds generated for 'chain 'Q' and resid 755 through 757' Processing helix chain 'Q' and resid 758 through 783 removed outlier: 3.642A pdb=" N ASN Q 764 " --> pdb=" O CYS Q 760 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP Q 775 " --> pdb=" O ALA Q 771 " (cutoff:3.500A) Processing helix chain 'Q' and resid 816 through 826 removed outlier: 3.501A pdb=" N ASP Q 820 " --> pdb=" O SER Q 816 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU Q 821 " --> pdb=" O PHE Q 817 " (cutoff:3.500A) Processing helix chain 'Q' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN Q 856 " --> pdb=" O ALA Q 852 " (cutoff:3.500A) Processing helix chain 'Q' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU Q 878 " --> pdb=" O THR Q 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY Q 885 " --> pdb=" O THR Q 881 " (cutoff:3.500A) Processing helix chain 'Q' and resid 886 through 890 Processing helix chain 'Q' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA Q 903 " --> pdb=" O ALA Q 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR Q 904 " --> pdb=" O MET Q 900 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE Q 909 " --> pdb=" O ARG Q 905 " (cutoff:3.500A) Processing helix chain 'Q' and resid 913 through 940 removed outlier: 3.518A pdb=" N GLU Q 918 " --> pdb=" O ASN Q 914 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS Q 921 " --> pdb=" O TYR Q 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU Q 922 " --> pdb=" O GLU Q 918 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS Q 933 " --> pdb=" O SER Q 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN Q 935 " --> pdb=" O ILE Q 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP Q 936 " --> pdb=" O GLY Q 932 " (cutoff:3.500A) Processing helix chain 'Q' and resid 945 through 965 Processing helix chain 'Q' and resid 966 through 968 No H-bonds generated for 'chain 'Q' and resid 966 through 968' Processing helix chain 'Q' and resid 976 through 984 removed outlier: 3.612A pdb=" N ILE Q 980 " --> pdb=" O VAL Q 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU Q 981 " --> pdb=" O LEU Q 977 " (cutoff:3.500A) Processing helix chain 'Q' and resid 985 through 1032 removed outlier: 4.542A pdb=" N VAL Q 991 " --> pdb=" O VAL Q 987 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG Q 995 " --> pdb=" O VAL Q 991 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1116 through 1118 No H-bonds generated for 'chain 'Q' and resid 1116 through 1118' Processing helix chain 'Q' and resid 1140 through 1146 removed outlier: 4.039A pdb=" N GLU Q1144 " --> pdb=" O PRO Q1140 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP Q1146 " --> pdb=" O GLN Q1142 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 304 removed outlier: 3.749A pdb=" N THR R 299 " --> pdb=" O PRO R 295 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 364 through 368 Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.240A pdb=" N GLN R 409 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 421 Processing helix chain 'R' and resid 737 through 743 Processing helix chain 'R' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU R 752 " --> pdb=" O GLU R 748 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU R 754 " --> pdb=" O SER R 750 " (cutoff:3.500A) Processing helix chain 'R' and resid 755 through 757 No H-bonds generated for 'chain 'R' and resid 755 through 757' Processing helix chain 'R' and resid 758 through 783 removed outlier: 3.643A pdb=" N ASN R 764 " --> pdb=" O CYS R 760 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP R 775 " --> pdb=" O ALA R 771 " (cutoff:3.500A) Processing helix chain 'R' and resid 816 through 826 removed outlier: 3.500A pdb=" N ASP R 820 " --> pdb=" O SER R 816 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU R 821 " --> pdb=" O PHE R 817 " (cutoff:3.500A) Processing helix chain 'R' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN R 856 " --> pdb=" O ALA R 852 " (cutoff:3.500A) Processing helix chain 'R' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU R 878 " --> pdb=" O THR R 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY R 885 " --> pdb=" O THR R 881 " (cutoff:3.500A) Processing helix chain 'R' and resid 886 through 890 Processing helix chain 'R' and resid 897 through 910 removed outlier: 3.544A pdb=" N ALA R 903 " --> pdb=" O ALA R 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR R 904 " --> pdb=" O MET R 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE R 909 " --> pdb=" O ARG R 905 " (cutoff:3.500A) Processing helix chain 'R' and resid 913 through 940 removed outlier: 3.519A pdb=" N GLU R 918 " --> pdb=" O ASN R 914 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS R 921 " --> pdb=" O TYR R 917 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU R 922 " --> pdb=" O GLU R 918 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS R 933 " --> pdb=" O SER R 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN R 935 " --> pdb=" O ILE R 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP R 936 " --> pdb=" O GLY R 932 " (cutoff:3.500A) Processing helix chain 'R' and resid 945 through 965 Processing helix chain 'R' and resid 966 through 968 No H-bonds generated for 'chain 'R' and resid 966 through 968' Processing helix chain 'R' and resid 976 through 984 removed outlier: 3.613A pdb=" N ILE R 980 " --> pdb=" O VAL R 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU R 981 " --> pdb=" O LEU R 977 " (cutoff:3.500A) Processing helix chain 'R' and resid 985 through 1032 removed outlier: 4.598A pdb=" N VAL R 991 " --> pdb=" O VAL R 987 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG R 995 " --> pdb=" O VAL R 991 " (cutoff:3.500A) Processing helix chain 'R' and resid 1116 through 1118 No H-bonds generated for 'chain 'R' and resid 1116 through 1118' Processing helix chain 'R' and resid 1140 through 1146 removed outlier: 4.038A pdb=" N GLU R1144 " --> pdb=" O PRO R1140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP R1146 " --> pdb=" O GLN R1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN L 3 " --> pdb=" O SER L 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 22 through 23 removed outlier: 3.600A pdb=" N ALA L 80 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 46 through 49 Processing sheet with id=AA4, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP C 86 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.734A pdb=" N THR C 91 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL C 100 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 20 through 23 Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.512A pdb=" N GLN D 10 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.553A pdb=" N THR E 69 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.587A pdb=" N ILE E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.338A pdb=" N GLN F 10 " --> pdb=" O GLU F 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 52 through 53 removed outlier: 6.085A pdb=" N TRP F 34 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.524A pdb=" N ILE G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.511A pdb=" N GLN H 10 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TRP H 34 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.553A pdb=" N THR I 69 " --> pdb=" O GLU I 82 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.588A pdb=" N ILE I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN N 3 " --> pdb=" O SER N 26 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA N 80 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 46 through 49 Processing sheet with id=AC5, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP K 86 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR K 50 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.733A pdb=" N THR K 91 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL K 100 " --> pdb=" O THR K 91 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 20 through 23 Processing sheet with id=AC8, first strand: chain 'P' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN P 3 " --> pdb=" O SER P 26 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA P 80 " --> pdb=" O CYS P 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 46 through 49 Processing sheet with id=AD2, first strand: chain 'M' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 9 through 12 removed outlier: 3.733A pdb=" N THR M 91 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL M 100 " --> pdb=" O THR M 91 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 20 through 23 Processing sheet with id=AD5, first strand: chain 'O' and resid 28 through 31 removed outlier: 3.510A pdb=" N SER O 31 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER O 60 " --> pdb=" O SER O 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 36 through 37 removed outlier: 7.274A pdb=" N VAL O 36 " --> pdb=" O LEU O 223 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA O 222 " --> pdb=" O HIS O 207 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS O 207 " --> pdb=" O ALA O 222 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU O 224 " --> pdb=" O SER O 205 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER O 205 " --> pdb=" O GLU O 224 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE O 203 " --> pdb=" O LEU O 226 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP O 228 " --> pdb=" O PHE O 201 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE O 201 " --> pdb=" O ASP O 228 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS O 195 " --> pdb=" O LYS O 202 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU O 191 " --> pdb=" O LYS O 206 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA O 263 " --> pdb=" O ALA O 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 48 through 55 removed outlier: 3.585A pdb=" N THR O 51 " --> pdb=" O PHE O 275 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP O 287 " --> pdb=" O LYS O 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'O' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE O 101 " --> pdb=" O ALA O 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA O 243 " --> pdb=" O ILE O 101 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY O 103 " --> pdb=" O LEU O 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 116 through 120 removed outlier: 6.402A pdb=" N GLU O 132 " --> pdb=" O CYS O 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS O 166 " --> pdb=" O GLU O 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN O 134 " --> pdb=" O ASN O 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN O 164 " --> pdb=" O GLN O 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 311 through 317 removed outlier: 3.933A pdb=" N THR O 599 " --> pdb=" O GLY O 311 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL O 595 " --> pdb=" O THR O 315 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY O 594 " --> pdb=" O GLN O 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 325 through 328 removed outlier: 5.804A pdb=" N ILE O 326 " --> pdb=" O ASN O 542 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 357 through 358 removed outlier: 4.021A pdb=" N VAL O 395 " --> pdb=" O ILE O 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 361 through 362 removed outlier: 6.367A pdb=" N CYS O 361 " --> pdb=" O CYS O 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'O' and resid 378 through 379 Processing sheet with id=AE7, first strand: chain 'O' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'O' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'O' and resid 553 through 554 removed outlier: 3.840A pdb=" N THR O 553 " --> pdb=" O ASP O 586 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 654 through 655 removed outlier: 6.349A pdb=" N GLU O 654 " --> pdb=" O ALA O 694 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR O 696 " --> pdb=" O GLU O 654 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER O 673 " --> pdb=" O ILE O 693 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA O 672 " --> pdb=" O PRO O 665 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 701 through 702 removed outlier: 6.502A pdb=" N ALA O 701 " --> pdb=" O ILE R 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'O' and resid 711 through 715 removed outlier: 3.870A pdb=" N ILE O 714 " --> pdb=" O LYS O1073 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS O1073 " --> pdb=" O ILE O 714 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE O1095 " --> pdb=" O ALA O1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 718 through 728 removed outlier: 7.235A pdb=" N GLY O1059 " --> pdb=" O SER O1055 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N SER O1055 " --> pdb=" O GLY O1059 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL O1061 " --> pdb=" O PRO O1053 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU O1063 " --> pdb=" O SER O1051 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER O1051 " --> pdb=" O LEU O1063 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL O1065 " --> pdb=" O LEU O1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 735 through 736 Processing sheet with id=AF6, first strand: chain 'O' and resid 787 through 788 Processing sheet with id=AF7, first strand: chain 'O' and resid 1120 through 1122 Processing sheet with id=AF8, first strand: chain 'Q' and resid 28 through 31 removed outlier: 7.848A pdb=" N ASN Q 61 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TYR Q 269 " --> pdb=" O ASN Q 61 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA Q 263 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU Q 191 " --> pdb=" O LYS Q 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS Q 195 " --> pdb=" O LYS Q 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE Q 201 " --> pdb=" O ASP Q 228 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP Q 228 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE Q 203 " --> pdb=" O LEU Q 226 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER Q 205 " --> pdb=" O GLU Q 224 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU Q 224 " --> pdb=" O SER Q 205 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS Q 207 " --> pdb=" O ALA Q 222 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA Q 222 " --> pdb=" O HIS Q 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL Q 36 " --> pdb=" O LEU Q 223 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 28 through 31 Processing sheet with id=AG1, first strand: chain 'Q' and resid 48 through 55 Processing sheet with id=AG2, first strand: chain 'Q' and resid 84 through 85 Processing sheet with id=AG3, first strand: chain 'Q' and resid 101 through 104 removed outlier: 6.016A pdb=" N ILE Q 101 " --> pdb=" O ALA Q 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA Q 243 " --> pdb=" O ILE Q 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY Q 103 " --> pdb=" O LEU Q 241 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Q' and resid 116 through 118 removed outlier: 6.403A pdb=" N GLU Q 132 " --> pdb=" O CYS Q 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS Q 166 " --> pdb=" O GLU Q 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN Q 134 " --> pdb=" O ASN Q 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN Q 164 " --> pdb=" O GLN Q 134 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 311 through 319 removed outlier: 3.843A pdb=" N VAL Q 595 " --> pdb=" O THR Q 315 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN Q 317 " --> pdb=" O GLY Q 593 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY Q 593 " --> pdb=" O ASN Q 317 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY Q 594 " --> pdb=" O GLN Q 613 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 325 through 328 removed outlier: 5.847A pdb=" N ILE Q 326 " --> pdb=" O ASN Q 542 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR Q 553 " --> pdb=" O ASP Q 586 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 357 through 358 removed outlier: 4.178A pdb=" N VAL Q 395 " --> pdb=" O ILE Q 358 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS Q 361 " --> pdb=" O CYS Q 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'Q' and resid 378 through 379 Processing sheet with id=AH1, first strand: chain 'Q' and resid 452 through 454 Processing sheet with id=AH2, first strand: chain 'Q' and resid 473 through 474 Processing sheet with id=AH3, first strand: chain 'Q' and resid 654 through 655 removed outlier: 6.388A pdb=" N GLU Q 654 " --> pdb=" O ALA Q 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR Q 696 " --> pdb=" O GLU Q 654 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE Q 670 " --> pdb=" O ILE Q 666 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 711 through 715 removed outlier: 3.844A pdb=" N ILE Q 714 " --> pdb=" O LYS Q1073 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA Q1078 " --> pdb=" O PHE Q1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE Q1095 " --> pdb=" O ALA Q1078 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Q' and resid 718 through 728 removed outlier: 7.166A pdb=" N GLY Q1059 " --> pdb=" O SER Q1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER Q1055 " --> pdb=" O GLY Q1059 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL Q1061 " --> pdb=" O PRO Q1053 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU Q1063 " --> pdb=" O SER Q1051 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER Q1051 " --> pdb=" O LEU Q1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL Q1065 " --> pdb=" O LEU Q1049 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Q' and resid 734 through 736 Processing sheet with id=AH7, first strand: chain 'Q' and resid 787 through 789 removed outlier: 5.660A pdb=" N ILE Q 788 " --> pdb=" O ASN R 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'Q' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA Q1087 " --> pdb=" O SER Q1123 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 27 through 31 removed outlier: 4.095A pdb=" N ALA R 27 " --> pdb=" O TRP R 64 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER R 60 " --> pdb=" O SER R 31 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASN R 61 " --> pdb=" O TYR R 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR R 269 " --> pdb=" O ASN R 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR R 265 " --> pdb=" O PHE R 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU R 191 " --> pdb=" O LYS R 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS R 195 " --> pdb=" O LYS R 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE R 201 " --> pdb=" O ASP R 228 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP R 228 " --> pdb=" O PHE R 201 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE R 203 " --> pdb=" O LEU R 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER R 205 " --> pdb=" O GLU R 224 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU R 224 " --> pdb=" O SER R 205 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS R 207 " --> pdb=" O ALA R 222 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA R 222 " --> pdb=" O HIS R 207 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL R 36 " --> pdb=" O LEU R 223 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'R' and resid 48 through 55 removed outlier: 7.192A pdb=" N THR R 274 " --> pdb=" O ASP R 290 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP R 290 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU R 276 " --> pdb=" O ALA R 288 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA R 288 " --> pdb=" O LEU R 276 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LYS R 278 " --> pdb=" O THR R 286 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 69 through 70 Processing sheet with id=AI3, first strand: chain 'R' and resid 84 through 85 Processing sheet with id=AI4, first strand: chain 'R' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE R 101 " --> pdb=" O ALA R 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA R 243 " --> pdb=" O ILE R 101 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY R 103 " --> pdb=" O LEU R 241 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'R' and resid 116 through 120 removed outlier: 6.403A pdb=" N GLU R 132 " --> pdb=" O CYS R 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS R 166 " --> pdb=" O GLU R 132 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN R 134 " --> pdb=" O ASN R 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN R 164 " --> pdb=" O GLN R 134 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 311 through 319 removed outlier: 3.841A pdb=" N VAL R 595 " --> pdb=" O THR R 315 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN R 317 " --> pdb=" O GLY R 593 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY R 593 " --> pdb=" O ASN R 317 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY R 594 " --> pdb=" O GLN R 613 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'R' and resid 325 through 328 removed outlier: 3.685A pdb=" N THR R 553 " --> pdb=" O ASP R 586 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'R' and resid 357 through 358 removed outlier: 4.178A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 Processing sheet with id=AJ1, first strand: chain 'R' and resid 378 through 379 Processing sheet with id=AJ2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AJ3, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AJ4, first strand: chain 'R' and resid 654 through 655 removed outlier: 6.389A pdb=" N GLU R 654 " --> pdb=" O ALA R 694 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR R 696 " --> pdb=" O GLU R 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE R 670 " --> pdb=" O ILE R 666 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'R' and resid 711 through 715 removed outlier: 3.848A pdb=" N ILE R 714 " --> pdb=" O LYS R1073 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR R1076 " --> pdb=" O SER R1097 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA R1078 " --> pdb=" O PHE R1095 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE R1095 " --> pdb=" O ALA R1078 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'R' and resid 718 through 728 removed outlier: 7.169A pdb=" N GLY R1059 " --> pdb=" O SER R1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER R1055 " --> pdb=" O GLY R1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL R1061 " --> pdb=" O PRO R1053 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU R1063 " --> pdb=" O SER R1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER R1051 " --> pdb=" O LEU R1063 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL R1065 " --> pdb=" O LEU R1049 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'R' and resid 734 through 736 Processing sheet with id=AJ8, first strand: chain 'R' and resid 1120 through 1123 removed outlier: 3.769A pdb=" N ALA R1087 " --> pdb=" O SER R1123 " (cutoff:3.500A) 1165 hydrogen bonds defined for protein. 3066 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: 9.20 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8577 1.33 - 1.45: 9733 1.45 - 1.58: 18697 1.58 - 1.71: 0 1.71 - 1.83: 213 Bond restraints: 37220 Sorted by residual: bond pdb=" N CYS O 336 " pdb=" CA CYS O 336 " ideal model delta sigma weight residual 1.457 1.521 -0.064 1.41e-02 5.03e+03 2.08e+01 bond pdb=" CA SER O 60 " pdb=" CB SER O 60 " ideal model delta sigma weight residual 1.533 1.476 0.058 1.51e-02 4.39e+03 1.45e+01 bond pdb=" N THR O 588 " pdb=" CA THR O 588 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.80e-03 1.04e+04 1.42e+01 bond pdb=" N LEU O 24 " pdb=" CA LEU O 24 " ideal model delta sigma weight residual 1.455 1.490 -0.035 9.60e-03 1.09e+04 1.35e+01 bond pdb=" C1 NAG Z 1 " pdb=" O5 NAG Z 1 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 37215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 48743 2.75 - 5.51: 1726 5.51 - 8.26: 135 8.26 - 11.02: 17 11.02 - 13.77: 8 Bond angle restraints: 50629 Sorted by residual: angle pdb=" N ILE O 100 " pdb=" CA ILE O 100 " pdb=" C ILE O 100 " ideal model delta sigma weight residual 113.20 102.84 10.36 9.60e-01 1.09e+00 1.16e+02 angle pdb=" N ILE R 100 " pdb=" CA ILE R 100 " pdb=" C ILE R 100 " ideal model delta sigma weight residual 113.20 102.87 10.33 9.60e-01 1.09e+00 1.16e+02 angle pdb=" C TYR D 95 " pdb=" CA TYR D 95 " pdb=" CB TYR D 95 " ideal model delta sigma weight residual 110.67 124.25 -13.58 1.52e+00 4.33e-01 7.99e+01 angle pdb=" N CYS Q 301 " pdb=" CA CYS Q 301 " pdb=" C CYS Q 301 " ideal model delta sigma weight residual 113.23 102.37 10.86 1.24e+00 6.50e-01 7.67e+01 angle pdb=" N LYS O 386 " pdb=" CA LYS O 386 " pdb=" C LYS O 386 " ideal model delta sigma weight residual 113.38 103.29 10.09 1.23e+00 6.61e-01 6.73e+01 ... (remaining 50624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 20733 16.86 - 33.71: 790 33.71 - 50.57: 133 50.57 - 67.43: 34 67.43 - 84.28: 27 Dihedral angle restraints: 21717 sinusoidal: 8382 harmonic: 13335 Sorted by residual: dihedral pdb=" CB CYS Q1082 " pdb=" SG CYS Q1082 " pdb=" SG CYS Q1126 " pdb=" CB CYS Q1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.99 72.99 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS R1082 " pdb=" SG CYS R1082 " pdb=" SG CYS R1126 " pdb=" CB CYS R1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.92 72.92 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS O1082 " pdb=" SG CYS O1082 " pdb=" SG CYS O1126 " pdb=" CB CYS O1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.28 72.28 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 21714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 5810 0.315 - 0.631: 17 0.631 - 0.946: 0 0.946 - 1.261: 0 1.261 - 1.577: 2 Chirality restraints: 5829 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN O 234 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.82 -1.58 2.00e-01 2.50e+01 6.21e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN Q 234 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.00 -1.40 2.00e-01 2.50e+01 4.89e+01 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.10e+01 ... (remaining 5826 not shown) Planarity restraints: 6491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " -0.333 2.00e-02 2.50e+03 2.81e-01 9.88e+02 pdb=" C7 NAG d 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " 0.489 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " 0.262 2.00e-02 2.50e+03 2.23e-01 6.24e+02 pdb=" C7 NAG T 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " -0.373 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN O 234 " 0.019 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" CG ASN O 234 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN O 234 " -0.119 2.00e-02 2.50e+03 pdb=" ND2 ASN O 234 " 0.192 2.00e-02 2.50e+03 pdb=" C1 NAG A 1 " -0.121 2.00e-02 2.50e+03 ... (remaining 6488 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 28 2.15 - 2.84: 12432 2.84 - 3.52: 52267 3.52 - 4.21: 89359 4.21 - 4.90: 149155 Nonbonded interactions: 303241 Sorted by model distance: nonbonded pdb=" CD2 LEU R 48 " pdb=" CE2 PHE R 306 " model vdw 1.462 3.760 nonbonded pdb=" OD1 ASP L 110 " pdb=" CD PRO L 111 " model vdw 1.753 3.440 nonbonded pdb=" CD1 LEU Q 48 " pdb=" O LYS Q 304 " model vdw 1.804 3.460 nonbonded pdb=" OE2 GLU Q 324 " pdb=" CG2 VAL Q 534 " model vdw 1.847 3.460 nonbonded pdb=" CG2 THR O 63 " pdb=" CZ PHE O 65 " model vdw 1.853 3.760 ... (remaining 303236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'J' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = (chain 'O' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 345 or (resid 346 and (name N or n \ ame CA or name C or name O or name CB )) or resid 347 through 1205)) selection = (chain 'Q' and (resid 14 through 345 or (resid 346 and (name N or name CA or nam \ e C or name O or name CB )) or resid 347 through 698 or (resid 699 and (name N o \ r name CA or name C or name O or name CB )) or resid 700 through 1305)) selection = (chain 'R' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 698 or (resid 699 and (name N or n \ ame CA or name C or name O or name CB )) or resid 700 through 1205)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 33.870 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.120 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 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 : 0.009 0.393 37313 Z= 0.505 Angle : 1.152 25.668 50860 Z= 0.716 Chirality : 0.074 1.577 5829 Planarity : 0.008 0.281 6461 Dihedral : 10.031 84.285 13029 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 32.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.83 % Favored : 92.98 % Rotamer: Outliers : 0.20 % Allowed : 1.99 % Favored : 97.81 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.39 (0.10), residues: 4542 helix: -3.27 (0.14), residues: 642 sheet: -1.84 (0.13), residues: 1089 loop : -2.23 (0.10), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 815 TYR 0.034 0.003 TYR G 50 PHE 0.046 0.003 PHE Q 347 TRP 0.031 0.003 TRP O 353 HIS 0.012 0.002 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.48 (37220) covalent geometry : angle 1.12940 / 0.71 (50629) SS BOND : bond 0.01359 / 0.69 ( 48) SS BOND : angle 1.81535 / 1.37 ( 96) hydrogen bonds : bond 0.29150 / 19.23 ( 1146) hydrogen bonds : angle 11.22414 / 7.69 ( 3066) link_BETA1-4 : bond 0.00738 / 0.37 ( 15) link_BETA1-4 : angle 3.22162 / 2.03 ( 45) link_NAG-ASN : bond 0.10121 / 6.40 ( 30) link_NAG-ASN : angle 4.93100 / 3.20 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 372 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 973 ILE cc_start: 0.7616 (pt) cc_final: 0.7167 (pt) REVERT: R 1139 ASP cc_start: 0.5357 (t0) cc_final: 0.5036 (t0) outliers start: 8 outliers final: 1 residues processed: 380 average time/residue: 0.2326 time to fit residues: 142.2437 Evaluate side-chains 153 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 126 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 0.4980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN C 6 GLN C 53 ASN D 99 GLN E 6 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 GLN F 37 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN H 91 ASN H 99 GLN I 6 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN K 6 GLN ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN M 6 GLN O 61 ASN O 146 HIS O 148 ASN O 271 GLN O 282 ASN O 317 ASN O 354 ASN O 437 ASN O 655 HIS ** O 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 913 GLN ** O1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1010 GLN Q 121 ASN Q 122 ASN Q 317 ASN Q 354 ASN Q 437 ASN ** Q 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 606 ASN Q 655 HIS ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 913 GLN Q1002 GLN Q1010 GLN ** R 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 ASN R 234 ASN R 271 GLN R 317 ASN R 437 ASN R 655 HIS ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1010 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.123248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.094864 restraints weight = 160409.283| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.88 r_work: 0.3758 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37313 Z= 0.183 Angle : 0.759 16.100 50860 Z= 0.395 Chirality : 0.049 0.639 5829 Planarity : 0.005 0.055 6461 Dihedral : 6.522 35.229 4931 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.12 % Favored : 95.71 % Rotamer: Outliers : 1.21 % Allowed : 6.23 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.35 (0.11), residues: 4542 helix: -0.90 (0.18), residues: 660 sheet: -1.64 (0.14), residues: 1134 loop : -1.72 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R1019 TYR 0.027 0.002 TYR G 50 PHE 0.033 0.002 PHE N 109 TRP 0.023 0.002 TRP N 112 HIS 0.009 0.002 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (37220) covalent geometry : angle 0.74469 / 0.39 (50629) SS BOND : bond 0.00353 / 0.20 ( 48) SS BOND : angle 1.08958 / 0.76 ( 96) hydrogen bonds : bond 0.05337 / 3.49 ( 1146) hydrogen bonds : angle 7.70296 / 5.28 ( 3066) link_BETA1-4 : bond 0.00975 / 0.44 ( 15) link_BETA1-4 : angle 2.15025 / 1.41 ( 45) link_NAG-ASN : bond 0.00656 / 0.45 ( 30) link_NAG-ASN : angle 3.21880 / 2.13 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 103 LEU cc_start: 0.0007 (tp) cc_final: -0.0548 (mp) REVERT: P 82 MET cc_start: 0.4736 (ttt) cc_final: 0.3891 (ptm) REVERT: O 287 ASP cc_start: 0.7449 (m-30) cc_final: 0.7246 (m-30) REVERT: O 518 LEU cc_start: 0.4250 (mt) cc_final: 0.3663 (pt) REVERT: O 869 MET cc_start: 0.8300 (mtt) cc_final: 0.8071 (mmm) outliers start: 48 outliers final: 19 residues processed: 225 average time/residue: 0.2361 time to fit residues: 86.7312 Evaluate side-chains 147 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 976 VAL Chi-restraints excluded: chain Q residue 69 HIS Chi-restraints excluded: chain Q residue 611 LEU Chi-restraints excluded: chain Q residue 976 VAL Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 611 LEU Chi-restraints excluded: chain R residue 976 VAL Chi-restraints excluded: chain R residue 1089 PHE Chi-restraints excluded: chain R residue 1114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 342 optimal weight: 2.9990 chunk 79 optimal weight: 40.0000 chunk 155 optimal weight: 20.0000 chunk 361 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 355 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 386 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 128 optimal weight: 50.0000 chunk 264 optimal weight: 2.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN E 39 GLN F 6 GLN F 10 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN O 115 GLN O 354 ASN O 506 GLN O 564 GLN O 641 ASN ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 779 GLN O 901 GLN O 957 GLN Q 115 GLN Q 121 ASN Q 271 GLN Q 354 ASN Q 506 GLN ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 935 GLN Q 957 GLN ** R 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 ASN R 658 ASN ** R 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 935 GLN R1005 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.126740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.096289 restraints weight = 158246.039| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 4.28 r_work: 0.3548 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 37313 Z= 0.293 Angle : 0.771 18.977 50860 Z= 0.395 Chirality : 0.049 0.566 5829 Planarity : 0.005 0.072 6461 Dihedral : 6.104 36.465 4930 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.95 % Favored : 94.85 % Rotamer: Outliers : 1.94 % Allowed : 7.69 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -2.02 (0.12), residues: 4542 helix: -0.36 (0.19), residues: 669 sheet: -1.44 (0.15), residues: 1083 loop : -1.57 (0.11), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 577 TYR 0.026 0.002 TYR E 94 PHE 0.031 0.003 PHE O 220 TRP 0.028 0.002 TRP N 112 HIS 0.009 0.002 HIS R1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.29 (37220) covalent geometry : angle 0.75393 / 0.39 (50629) SS BOND : bond 0.00826 / 0.36 ( 48) SS BOND : angle 1.17807 / 0.78 ( 96) hydrogen bonds : bond 0.04982 / 3.28 ( 1146) hydrogen bonds : angle 7.15638 / 4.93 ( 3066) link_BETA1-4 : bond 0.00422 / 0.27 ( 15) link_BETA1-4 : angle 2.39520 / 1.57 ( 45) link_NAG-ASN : bond 0.00958 / 0.61 ( 30) link_NAG-ASN : angle 3.49031 / 2.28 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 150 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 82 MET cc_start: 0.5292 (ttt) cc_final: 0.4013 (ptm) REVERT: H 103 LEU cc_start: 0.0527 (tp) cc_final: -0.0331 (mp) REVERT: I 39 GLN cc_start: 0.4675 (tt0) cc_final: 0.3567 (tm-30) REVERT: N 82 MET cc_start: 0.5138 (ttt) cc_final: 0.4074 (ptm) REVERT: K 33 TYR cc_start: 0.6439 (m-10) cc_final: 0.6211 (m-80) REVERT: O 357 ARG cc_start: -0.0746 (OUTLIER) cc_final: -0.1357 (ttm170) REVERT: O 869 MET cc_start: 0.8611 (mtt) cc_final: 0.8410 (mmm) REVERT: O 906 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: Q 675 GLN cc_start: 0.8388 (pt0) cc_final: 0.8105 (pp30) REVERT: Q 869 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8181 (mtt) REVERT: Q 906 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8597 (m-80) REVERT: Q 1029 MET cc_start: 0.8736 (mmm) cc_final: 0.8342 (tpp) REVERT: Q 1089 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: R 307 THR cc_start: 0.7826 (m) cc_final: 0.7622 (t) REVERT: R 697 MET cc_start: 0.8232 (ttt) cc_final: 0.7756 (ptm) REVERT: R 906 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: R 1019 ARG cc_start: 0.8109 (tpt90) cc_final: 0.7585 (tpm170) outliers start: 77 outliers final: 35 residues processed: 214 average time/residue: 0.2257 time to fit residues: 80.2081 Evaluate side-chains 159 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 357 ARG Chi-restraints excluded: chain O residue 620 VAL Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 740 MET Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 976 VAL Chi-restraints excluded: chain O residue 1089 PHE Chi-restraints excluded: chain O residue 1094 VAL Chi-restraints excluded: chain Q residue 69 HIS Chi-restraints excluded: chain Q residue 200 TYR Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 611 LEU Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain Q residue 869 MET Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain Q residue 976 VAL Chi-restraints excluded: chain Q residue 1089 PHE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 976 VAL Chi-restraints excluded: chain R residue 1089 PHE Chi-restraints excluded: chain R residue 1114 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 423 optimal weight: 2.9990 chunk 275 optimal weight: 0.0670 chunk 242 optimal weight: 0.0670 chunk 74 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 127 optimal weight: 40.0000 chunk 411 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 341 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN D 88 GLN E 6 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN G 6 GLN I 6 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN O 506 GLN O 935 GLN O 955 ASN Q 30 ASN Q 506 GLN Q 540 ASN Q 762 GLN ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 234 ASN R 540 ASN R 658 ASN R 762 GLN R 901 GLN ** R 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.122560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.094067 restraints weight = 156785.370| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.85 r_work: 0.3768 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 37313 Z= 0.114 Angle : 0.620 14.805 50860 Z= 0.313 Chirality : 0.045 0.520 5829 Planarity : 0.004 0.075 6461 Dihedral : 5.446 27.186 4930 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.69 % Favored : 95.11 % Rotamer: Outliers : 1.91 % Allowed : 8.35 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.55 (0.12), residues: 4542 helix: 0.48 (0.20), residues: 675 sheet: -1.17 (0.15), residues: 1077 loop : -1.37 (0.11), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q1019 TYR 0.016 0.001 TYR I 94 PHE 0.019 0.001 PHE N 109 TRP 0.017 0.001 TRP N 112 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (37220) covalent geometry : angle 0.60530 / 0.31 (50629) SS BOND : bond 0.00261 / 0.15 ( 48) SS BOND : angle 0.78235 / 0.53 ( 96) hydrogen bonds : bond 0.03833 / 2.53 ( 1146) hydrogen bonds : angle 6.46977 / 4.48 ( 3066) link_BETA1-4 : bond 0.00544 / 0.25 ( 15) link_BETA1-4 : angle 2.26336 / 1.50 ( 45) link_NAG-ASN : bond 0.00531 / 0.33 ( 30) link_NAG-ASN : angle 2.79284 / 1.87 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 135 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 82 MET cc_start: 0.5311 (ttt) cc_final: 0.4066 (ptm) REVERT: C 51 ASP cc_start: 0.5473 (m-30) cc_final: 0.3877 (t70) REVERT: E 106 VAL cc_start: 0.2300 (OUTLIER) cc_final: 0.2071 (m) REVERT: H 103 LEU cc_start: 0.0684 (tp) cc_final: -0.0156 (mp) REVERT: N 82 MET cc_start: 0.5501 (ttt) cc_final: 0.4335 (ptm) REVERT: O 357 ARG cc_start: -0.0364 (OUTLIER) cc_final: -0.0990 (ttm170) REVERT: Q 1029 MET cc_start: 0.8426 (mmm) cc_final: 0.8130 (tpp) REVERT: R 902 MET cc_start: 0.8200 (mmm) cc_final: 0.7971 (mmt) REVERT: R 906 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: R 1002 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8305 (tm-30) REVERT: R 1019 ARG cc_start: 0.7877 (tpt90) cc_final: 0.7471 (tpm170) outliers start: 76 outliers final: 42 residues processed: 201 average time/residue: 0.2305 time to fit residues: 76.5699 Evaluate side-chains 163 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 357 ARG Chi-restraints excluded: chain O residue 620 VAL Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 866 THR Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 1094 VAL Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain Q residue 30 ASN Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 69 HIS Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 611 LEU Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 611 LEU Chi-restraints excluded: chain R residue 675 GLN Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 1114 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 307 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 125 optimal weight: 40.0000 chunk 155 optimal weight: 20.0000 chunk 431 optimal weight: 6.9990 chunk 257 optimal weight: 0.0870 chunk 32 optimal weight: 10.0000 chunk 443 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 3 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN O 506 GLN O 762 GLN Q 121 ASN ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 564 GLN R 658 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.121905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.093144 restraints weight = 156328.655| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.96 r_work: 0.3717 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37313 Z= 0.132 Angle : 0.603 14.791 50860 Z= 0.303 Chirality : 0.044 0.483 5829 Planarity : 0.004 0.073 6461 Dihedral : 5.185 25.099 4930 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.76 % Favored : 95.05 % Rotamer: Outliers : 1.86 % Allowed : 8.95 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.39 (0.12), residues: 4542 helix: 0.77 (0.20), residues: 672 sheet: -1.02 (0.15), residues: 1038 loop : -1.34 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O1039 TYR 0.014 0.001 TYR E 50 PHE 0.019 0.001 PHE L 65 TRP 0.017 0.001 TRP L 112 HIS 0.006 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (37220) covalent geometry : angle 0.58854 / 0.30 (50629) SS BOND : bond 0.00243 / 0.14 ( 48) SS BOND : angle 0.72144 / 0.48 ( 96) hydrogen bonds : bond 0.03711 / 2.45 ( 1146) hydrogen bonds : angle 6.17928 / 4.28 ( 3066) link_BETA1-4 : bond 0.00693 / 0.29 ( 15) link_BETA1-4 : angle 2.17325 / 1.44 ( 45) link_NAG-ASN : bond 0.00514 / 0.32 ( 30) link_NAG-ASN : angle 2.77181 / 1.86 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 135 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.4932 (tp-100) cc_final: 0.3031 (pt0) REVERT: L 82 MET cc_start: 0.5441 (ttt) cc_final: 0.4214 (ptm) REVERT: L 110 ASP cc_start: 0.2764 (OUTLIER) cc_final: 0.2508 (p0) REVERT: D 46 LEU cc_start: 0.1574 (OUTLIER) cc_final: 0.0810 (mt) REVERT: H 103 LEU cc_start: 0.0639 (tp) cc_final: -0.0205 (mp) REVERT: N 49 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6356 (ptt) REVERT: N 82 MET cc_start: 0.5501 (ttt) cc_final: 0.4224 (ptm) REVERT: P 60 MET cc_start: 0.3781 (OUTLIER) cc_final: 0.3315 (tmm) REVERT: P 82 MET cc_start: 0.5022 (ttm) cc_final: 0.4235 (ptm) REVERT: O 357 ARG cc_start: -0.0634 (OUTLIER) cc_final: -0.1169 (ttm170) REVERT: O 869 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8201 (mmm) REVERT: O 906 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: O 1019 ARG cc_start: 0.8089 (tpt90) cc_final: 0.7861 (tpm170) REVERT: O 1029 MET cc_start: 0.8677 (mmm) cc_final: 0.8373 (tpp) REVERT: Q 906 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: Q 1029 MET cc_start: 0.8483 (mmm) cc_final: 0.8230 (tpp) REVERT: R 128 ILE cc_start: 0.7820 (mm) cc_final: 0.7437 (mm) REVERT: R 906 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: R 1019 ARG cc_start: 0.7903 (tpt90) cc_final: 0.7462 (tpm170) outliers start: 74 outliers final: 44 residues processed: 195 average time/residue: 0.2086 time to fit residues: 68.3798 Evaluate side-chains 165 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 110 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 357 ARG Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 866 THR Chi-restraints excluded: chain O residue 869 MET Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 976 VAL Chi-restraints excluded: chain O residue 987 VAL Chi-restraints excluded: chain O residue 1104 VAL Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain Q residue 869 MET Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 577 ARG Chi-restraints excluded: chain R residue 611 LEU Chi-restraints excluded: chain R residue 740 MET Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 1089 PHE Chi-restraints excluded: chain R residue 1114 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 101 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 263 optimal weight: 20.0000 chunk 354 optimal weight: 20.0000 chunk 81 optimal weight: 40.0000 chunk 399 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 329 optimal weight: 0.0570 chunk 217 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN F 10 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN O 506 GLN Q 30 ASN Q 121 ASN ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.121962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.093407 restraints weight = 157631.608| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.93 r_work: 0.3654 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 37313 Z= 0.131 Angle : 0.594 14.543 50860 Z= 0.298 Chirality : 0.044 0.440 5829 Planarity : 0.004 0.070 6461 Dihedral : 5.003 22.577 4930 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.58 % Favored : 95.22 % Rotamer: Outliers : 2.06 % Allowed : 9.40 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.32 (0.12), residues: 4542 helix: 0.87 (0.20), residues: 684 sheet: -0.91 (0.15), residues: 1062 loop : -1.35 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 68 TYR 0.023 0.001 TYR C 50 PHE 0.016 0.001 PHE R 133 TRP 0.033 0.001 TRP L 112 HIS 0.007 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (37220) covalent geometry : angle 0.57977 / 0.30 (50629) SS BOND : bond 0.00500 / 0.19 ( 48) SS BOND : angle 1.17370 / 0.92 ( 96) hydrogen bonds : bond 0.03606 / 2.37 ( 1146) hydrogen bonds : angle 5.96180 / 4.12 ( 3066) link_BETA1-4 : bond 0.00594 / 0.23 ( 15) link_BETA1-4 : angle 2.11207 / 1.40 ( 45) link_NAG-ASN : bond 0.00495 / 0.31 ( 30) link_NAG-ASN : angle 2.61756 / 1.76 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 121 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.4854 (tp-100) cc_final: 0.3194 (pt0) REVERT: D 46 LEU cc_start: 0.1552 (OUTLIER) cc_final: 0.0817 (mt) REVERT: E 73 ASP cc_start: 0.3211 (t0) cc_final: 0.2551 (m-30) REVERT: F 10 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7067 (mp10) REVERT: H 103 LEU cc_start: 0.0393 (tp) cc_final: -0.0473 (mp) REVERT: N 49 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6323 (ptt) REVERT: N 82 MET cc_start: 0.5807 (ttt) cc_final: 0.4494 (ptm) REVERT: P 60 MET cc_start: 0.3579 (OUTLIER) cc_final: 0.3302 (tmm) REVERT: P 82 MET cc_start: 0.5287 (ttm) cc_final: 0.4292 (ptm) REVERT: O 357 ARG cc_start: -0.0400 (OUTLIER) cc_final: -0.0948 (ttm170) REVERT: O 906 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: O 1019 ARG cc_start: 0.8330 (tpt90) cc_final: 0.7931 (tpm170) REVERT: Q 906 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: Q 1029 MET cc_start: 0.8564 (mmm) cc_final: 0.8313 (tpp) REVERT: R 321 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7825 (mp10) REVERT: R 902 MET cc_start: 0.8262 (mmm) cc_final: 0.7951 (mmt) REVERT: R 906 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: R 1019 ARG cc_start: 0.8194 (tpt90) cc_final: 0.7729 (tpm170) outliers start: 82 outliers final: 46 residues processed: 189 average time/residue: 0.2113 time to fit residues: 67.0641 Evaluate side-chains 165 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 111 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain F residue 10 GLN Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 357 ARG Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 866 THR Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 1104 VAL Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain Q residue 30 ASN Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain Q residue 869 MET Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 577 ARG Chi-restraints excluded: chain R residue 611 LEU Chi-restraints excluded: chain R residue 740 MET Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 1032 CYS Chi-restraints excluded: chain R residue 1089 PHE Chi-restraints excluded: chain R residue 1114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 440 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 295 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 210 optimal weight: 0.9990 chunk 347 optimal weight: 6.9990 chunk 427 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN F 10 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN Q 121 ASN ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 ASN ** 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 = 0.4529 r_free = 0.4529 target = 0.118016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.089204 restraints weight = 157846.772| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 4.38 r_work: 0.3558 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 37313 Z= 0.214 Angle : 0.640 16.016 50860 Z= 0.322 Chirality : 0.045 0.413 5829 Planarity : 0.004 0.065 6461 Dihedral : 5.102 24.173 4930 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.57 % Favored : 94.25 % Rotamer: Outliers : 1.84 % Allowed : 9.75 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.43 (0.12), residues: 4542 helix: 0.81 (0.20), residues: 666 sheet: -0.93 (0.15), residues: 1053 loop : -1.44 (0.11), residues: 2823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 68 TYR 0.020 0.002 TYR G 95 PHE 0.027 0.002 PHE O 133 TRP 0.023 0.001 TRP P 112 HIS 0.006 0.001 HIS Q1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (37220) covalent geometry : angle 0.62450 / 0.32 (50629) SS BOND : bond 0.00239 / 0.13 ( 48) SS BOND : angle 1.27779 / 1.01 ( 96) hydrogen bonds : bond 0.03854 / 2.55 ( 1146) hydrogen bonds : angle 6.04594 / 4.19 ( 3066) link_BETA1-4 : bond 0.00400 / 0.20 ( 15) link_BETA1-4 : angle 2.15768 / 1.42 ( 45) link_NAG-ASN : bond 0.00686 / 0.44 ( 30) link_NAG-ASN : angle 2.79609 / 1.86 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 126 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.4887 (tp-100) cc_final: 0.3224 (pt0) REVERT: L 82 MET cc_start: 0.5222 (ttm) cc_final: 0.4202 (ptm) REVERT: D 46 LEU cc_start: 0.1644 (OUTLIER) cc_final: 0.0830 (mt) REVERT: E 73 ASP cc_start: 0.3220 (t0) cc_final: 0.2604 (m-30) REVERT: F 36 GLN cc_start: 0.4262 (OUTLIER) cc_final: 0.3924 (pt0) REVERT: H 103 LEU cc_start: 0.0354 (tp) cc_final: -0.0515 (mp) REVERT: I 39 GLN cc_start: 0.3124 (tt0) cc_final: 0.2869 (pp30) REVERT: N 49 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6476 (ptt) REVERT: N 82 MET cc_start: 0.5845 (ttt) cc_final: 0.4552 (ptm) REVERT: P 60 MET cc_start: 0.3680 (OUTLIER) cc_final: 0.3373 (tmm) REVERT: P 82 MET cc_start: 0.5263 (ttm) cc_final: 0.4319 (ptm) REVERT: O 200 TYR cc_start: 0.7475 (m-80) cc_final: 0.7186 (m-80) REVERT: O 357 ARG cc_start: -0.0366 (OUTLIER) cc_final: -0.0864 (ttm170) REVERT: Q 906 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: Q 1029 MET cc_start: 0.8679 (mmm) cc_final: 0.8430 (tpp) REVERT: Q 1089 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7971 (m-10) REVERT: R 906 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8540 (m-80) REVERT: R 1019 ARG cc_start: 0.8186 (tpt90) cc_final: 0.7806 (tpm170) outliers start: 73 outliers final: 45 residues processed: 189 average time/residue: 0.2154 time to fit residues: 68.3913 Evaluate side-chains 164 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 111 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 357 ARG Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 976 VAL Chi-restraints excluded: chain O residue 1032 CYS Chi-restraints excluded: chain O residue 1094 VAL Chi-restraints excluded: chain O residue 1104 VAL Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 611 LEU Chi-restraints excluded: chain Q residue 794 ILE Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain Q residue 1089 PHE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 577 ARG Chi-restraints excluded: chain R residue 740 MET Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 1032 CYS Chi-restraints excluded: chain R residue 1089 PHE Chi-restraints excluded: chain R residue 1114 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 44 optimal weight: 8.9990 chunk 277 optimal weight: 20.0000 chunk 176 optimal weight: 0.6980 chunk 172 optimal weight: 10.0000 chunk 360 optimal weight: 20.0000 chunk 240 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 422 optimal weight: 0.9980 chunk 294 optimal weight: 0.5980 chunk 174 optimal weight: 20.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN F 10 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 641 ASN Q 30 ASN Q 121 ASN ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.118229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.089864 restraints weight = 155914.986| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 4.17 r_work: 0.3613 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37313 Z= 0.135 Angle : 0.594 14.069 50860 Z= 0.298 Chirality : 0.044 0.410 5829 Planarity : 0.004 0.064 6461 Dihedral : 4.925 23.856 4930 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.11 % Favored : 94.74 % Rotamer: Outliers : 1.63 % Allowed : 9.90 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.31 (0.12), residues: 4542 helix: 0.98 (0.20), residues: 675 sheet: -0.91 (0.15), residues: 1089 loop : -1.36 (0.12), residues: 2778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 68 TYR 0.021 0.001 TYR C 50 PHE 0.023 0.001 PHE R 133 TRP 0.040 0.001 TRP P 112 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (37220) covalent geometry : angle 0.57936 / 0.29 (50629) SS BOND : bond 0.00243 / 0.13 ( 48) SS BOND : angle 1.24405 / 0.82 ( 96) hydrogen bonds : bond 0.03520 / 2.32 ( 1146) hydrogen bonds : angle 5.84671 / 4.06 ( 3066) link_BETA1-4 : bond 0.00490 / 0.20 ( 15) link_BETA1-4 : angle 2.08526 / 1.38 ( 45) link_NAG-ASN : bond 0.00487 / 0.31 ( 30) link_NAG-ASN : angle 2.56917 / 1.76 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 118 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 60 MET cc_start: 0.5285 (ptm) cc_final: 0.4378 (tmm) REVERT: L 82 MET cc_start: 0.5293 (ttm) cc_final: 0.4008 (ptm) REVERT: E 73 ASP cc_start: 0.3235 (t0) cc_final: 0.2620 (m-30) REVERT: H 103 LEU cc_start: 0.0545 (tp) cc_final: -0.0449 (mp) REVERT: N 49 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.6457 (ptt) REVERT: N 82 MET cc_start: 0.5921 (ttt) cc_final: 0.4608 (ptm) REVERT: P 3 GLN cc_start: 0.4716 (tp40) cc_final: 0.3351 (pp30) REVERT: P 60 MET cc_start: 0.3750 (OUTLIER) cc_final: 0.3412 (tmm) REVERT: P 82 MET cc_start: 0.5290 (ttm) cc_final: 0.4290 (ptm) REVERT: O 200 TYR cc_start: 0.7789 (m-80) cc_final: 0.7461 (m-80) REVERT: O 357 ARG cc_start: -0.0424 (OUTLIER) cc_final: -0.0886 (ttm170) REVERT: O 906 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8519 (m-80) REVERT: Q 906 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: Q 1029 MET cc_start: 0.8626 (mmm) cc_final: 0.8381 (tpp) REVERT: R 902 MET cc_start: 0.8308 (mmm) cc_final: 0.7994 (mmt) REVERT: R 906 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8423 (m-80) REVERT: R 1019 ARG cc_start: 0.8264 (tpt90) cc_final: 0.7818 (tpm170) outliers start: 65 outliers final: 45 residues processed: 173 average time/residue: 0.2290 time to fit residues: 66.4770 Evaluate side-chains 164 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 113 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain F residue 10 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 357 ARG Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 987 VAL Chi-restraints excluded: chain O residue 1104 VAL Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain Q residue 69 HIS Chi-restraints excluded: chain Q residue 200 TYR Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 740 MET Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 1032 CYS Chi-restraints excluded: chain R residue 1081 ILE Chi-restraints excluded: chain R residue 1089 PHE Chi-restraints excluded: chain R residue 1114 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 19 optimal weight: 50.0000 chunk 139 optimal weight: 10.0000 chunk 107 optimal weight: 50.0000 chunk 279 optimal weight: 6.9990 chunk 320 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 217 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN F 10 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN H 99 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN Q 30 ASN Q 121 ASN Q 414 GLN Q 501 ASN ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN R 501 ASN R 658 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.117014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.088206 restraints weight = 155855.571| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 4.11 r_work: 0.3515 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 37313 Z= 0.302 Angle : 0.722 16.431 50860 Z= 0.367 Chirality : 0.048 0.396 5829 Planarity : 0.005 0.060 6461 Dihedral : 5.331 29.133 4930 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.30 % Favored : 93.55 % Rotamer: Outliers : 1.91 % Allowed : 9.75 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.65 (0.12), residues: 4542 helix: 0.58 (0.20), residues: 657 sheet: -1.10 (0.15), residues: 1101 loop : -1.56 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q1091 TYR 0.024 0.002 TYR Q 756 PHE 0.038 0.002 PHE F 9 TRP 0.022 0.002 TRP L 112 HIS 0.012 0.002 HIS O1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.30 (37220) covalent geometry : angle 0.70524 / 0.36 (50629) SS BOND : bond 0.00320 / 0.18 ( 48) SS BOND : angle 1.66463 / 1.02 ( 96) hydrogen bonds : bond 0.04196 / 2.77 ( 1146) hydrogen bonds : angle 6.25176 / 4.34 ( 3066) link_BETA1-4 : bond 0.00586 / 0.25 ( 15) link_BETA1-4 : angle 2.22401 / 1.46 ( 45) link_NAG-ASN : bond 0.01014 / 0.63 ( 30) link_NAG-ASN : angle 3.09250 / 2.07 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 121 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 60 MET cc_start: 0.5543 (ptm) cc_final: 0.4609 (tmm) REVERT: L 82 MET cc_start: 0.5324 (ttm) cc_final: 0.4022 (ptm) REVERT: E 73 ASP cc_start: 0.3340 (t0) cc_final: 0.2405 (m-30) REVERT: H 103 LEU cc_start: 0.0943 (tp) cc_final: -0.0149 (mp) REVERT: N 49 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6495 (ptt) REVERT: N 82 MET cc_start: 0.5896 (ttt) cc_final: 0.4669 (ptm) REVERT: P 3 GLN cc_start: 0.4353 (tp40) cc_final: 0.2972 (pp30) REVERT: P 60 MET cc_start: 0.3927 (OUTLIER) cc_final: 0.3537 (tmm) REVERT: P 82 MET cc_start: 0.5368 (ttm) cc_final: 0.4544 (ptm) REVERT: O 357 ARG cc_start: -0.0376 (OUTLIER) cc_final: -0.0848 (ttm170) REVERT: O 902 MET cc_start: 0.8417 (mmm) cc_final: 0.8214 (mmm) REVERT: O 1029 MET cc_start: 0.8839 (mmm) cc_final: 0.8610 (tpp) REVERT: Q 906 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8627 (m-80) REVERT: Q 1029 MET cc_start: 0.8782 (mmm) cc_final: 0.8492 (tpp) REVERT: Q 1089 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8024 (m-10) REVERT: R 902 MET cc_start: 0.8532 (mmm) cc_final: 0.8207 (mmt) REVERT: R 906 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8529 (m-80) outliers start: 76 outliers final: 55 residues processed: 185 average time/residue: 0.2223 time to fit residues: 69.9012 Evaluate side-chains 169 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 108 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 357 ARG Chi-restraints excluded: chain O residue 501 ASN Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 976 VAL Chi-restraints excluded: chain O residue 987 VAL Chi-restraints excluded: chain O residue 1032 CYS Chi-restraints excluded: chain O residue 1094 VAL Chi-restraints excluded: chain O residue 1104 VAL Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain Q residue 30 ASN Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 312 ILE Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 611 LEU Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain Q residue 976 VAL Chi-restraints excluded: chain Q residue 1039 ARG Chi-restraints excluded: chain Q residue 1089 PHE Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 740 MET Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 1032 CYS Chi-restraints excluded: chain R residue 1089 PHE Chi-restraints excluded: chain R residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 193 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 300 optimal weight: 0.9990 chunk 112 optimal weight: 0.0970 chunk 27 optimal weight: 0.0970 chunk 316 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 347 optimal weight: 5.9990 chunk 338 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 7 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN ** Q 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN ** R 913 GLN ** 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 = 0.4568 r_free = 0.4568 target = 0.127913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.098917 restraints weight = 155699.841| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 4.00 r_work: 0.3613 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 37313 Z= 0.113 Angle : 0.598 12.445 50860 Z= 0.302 Chirality : 0.044 0.396 5829 Planarity : 0.004 0.057 6461 Dihedral : 4.914 22.507 4930 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.95 % Favored : 94.89 % Rotamer: Outliers : 1.13 % Allowed : 10.66 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.31 (0.12), residues: 4542 helix: 0.96 (0.20), residues: 675 sheet: -0.87 (0.15), residues: 1098 loop : -1.37 (0.12), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 68 TYR 0.020 0.001 TYR C 50 PHE 0.016 0.001 PHE R 133 TRP 0.032 0.001 TRP L 112 HIS 0.005 0.001 HIS Q1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (37220) covalent geometry : angle 0.58581 / 0.30 (50629) SS BOND : bond 0.00220 / 0.12 ( 48) SS BOND : angle 1.09627 / 0.70 ( 96) hydrogen bonds : bond 0.03498 / 2.30 ( 1146) hydrogen bonds : angle 5.80165 / 4.04 ( 3066) link_BETA1-4 : bond 0.00672 / 0.28 ( 15) link_BETA1-4 : angle 2.07252 / 1.37 ( 45) link_NAG-ASN : bond 0.00448 / 0.28 ( 30) link_NAG-ASN : angle 2.41031 / 1.63 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 60 MET cc_start: 0.5499 (ptm) cc_final: 0.4442 (tmm) REVERT: L 82 MET cc_start: 0.5241 (ttm) cc_final: 0.4215 (ptm) REVERT: E 73 ASP cc_start: 0.3257 (t0) cc_final: 0.2505 (m-30) REVERT: H 103 LEU cc_start: 0.0938 (tp) cc_final: -0.0092 (mp) REVERT: N 49 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6330 (ptt) REVERT: N 82 MET cc_start: 0.5931 (ttt) cc_final: 0.4671 (ptm) REVERT: P 60 MET cc_start: 0.3241 (OUTLIER) cc_final: 0.3010 (tmm) REVERT: P 82 MET cc_start: 0.5324 (ttm) cc_final: 0.4511 (ptm) REVERT: O 357 ARG cc_start: -0.0309 (OUTLIER) cc_final: -0.0712 (ttm170) REVERT: O 906 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8460 (m-80) REVERT: Q 900 MET cc_start: 0.8560 (tpp) cc_final: 0.8333 (mpp) REVERT: Q 906 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8501 (m-80) REVERT: Q 1029 MET cc_start: 0.8591 (mmm) cc_final: 0.8347 (tpp) REVERT: R 128 ILE cc_start: 0.8100 (mm) cc_final: 0.7621 (mp) REVERT: R 902 MET cc_start: 0.8201 (mmm) cc_final: 0.7920 (mmt) REVERT: R 906 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8290 (m-80) outliers start: 45 outliers final: 37 residues processed: 153 average time/residue: 0.2069 time to fit residues: 53.9149 Evaluate side-chains 153 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 357 ARG Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 987 VAL Chi-restraints excluded: chain O residue 1104 VAL Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain Q residue 30 ASN Chi-restraints excluded: chain Q residue 69 HIS Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 501 ASN Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 740 MET Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 1032 CYS Chi-restraints excluded: chain R residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 13 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 259 optimal weight: 0.3980 chunk 207 optimal weight: 3.9990 chunk 335 optimal weight: 2.9990 chunk 7 optimal weight: 40.0000 chunk 236 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 421 optimal weight: 0.5980 chunk 202 optimal weight: 5.9990 chunk 237 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN H 36 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.122079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.093634 restraints weight = 156074.573| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 4.00 r_work: 0.3609 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37313 Z= 0.118 Angle : 0.585 11.759 50860 Z= 0.293 Chirality : 0.044 0.382 5829 Planarity : 0.004 0.057 6461 Dihedral : 4.769 21.814 4930 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.39 % Rotamer: Outliers : 1.21 % Allowed : 10.66 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.18 (0.12), residues: 4542 helix: 1.12 (0.20), residues: 681 sheet: -0.75 (0.15), residues: 1095 loop : -1.32 (0.12), residues: 2766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 68 TYR 0.019 0.001 TYR Q 200 PHE 0.027 0.001 PHE O 133 TRP 0.026 0.001 TRP L 112 HIS 0.004 0.001 HIS Q1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (37220) covalent geometry : angle 0.57230 / 0.29 (50629) SS BOND : bond 0.00212 / 0.11 ( 48) SS BOND : angle 1.06071 / 0.66 ( 96) hydrogen bonds : bond 0.03432 / 2.26 ( 1146) hydrogen bonds : angle 5.66376 / 3.94 ( 3066) link_BETA1-4 : bond 0.00507 / 0.21 ( 15) link_BETA1-4 : angle 2.01392 / 1.34 ( 45) link_NAG-ASN : bond 0.00459 / 0.29 ( 30) link_NAG-ASN : angle 2.44312 / 1.65 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10120.26 seconds wall clock time: 174 minutes 15.27 seconds (10455.27 seconds total)