Starting phenix.real_space_refine on Sat Mar 7 00:59:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cws_30486/03_2026/7cws_30486.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cws_30486/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7cws_30486/03_2026/7cws_30486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cws_30486/03_2026/7cws_30486.map" model { file = "/net/cci-nas-00/data/ceres_data/7cws_30486/03_2026/7cws_30486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cws_30486/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 18 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.69, per 1000 atoms: 0.21 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: 3.27 Conformation dependent library (CDL) restraints added in 1.7 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: 1.86 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: 9.83 Time building geometry restraints manager: 4.19 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: 21555 16.86 - 33.71: 866 33.71 - 50.57: 192 50.57 - 67.43: 43 67.43 - 84.28: 27 Dihedral angle restraints: 22683 sinusoidal: 9348 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 22680 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 34.650 Find NCS groups from input model: 0.930 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: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5394 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 : 10.377 84.285 13995 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 covalent geometry : bond 0.00844 (37220) covalent geometry : angle 1.12940 (50629) SS BOND : bond 0.01359 ( 48) SS BOND : angle 1.81535 ( 96) hydrogen bonds : bond 0.29150 ( 1146) hydrogen bonds : angle 11.22414 ( 3066) link_BETA1-4 : bond 0.00738 ( 15) link_BETA1-4 : angle 3.22162 ( 45) link_NAG-ASN : bond 0.10121 ( 30) link_NAG-ASN : angle 4.93100 ( 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 : 1.342 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: 0.2296 time to fit residues: 139.7733 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 : 1.297 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN C 6 GLN C 53 ASN D 99 GLN E 6 GLN F 6 GLN ** 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 O 935 GLN ** O1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1010 GLN Q 121 ASN Q 122 ASN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 GLN R 317 ASN R 437 ASN R 655 HIS ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 913 GLN R1010 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.123174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.095638 restraints weight = 159861.301| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 4.39 r_work: 0.3695 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37313 Z= 0.184 Angle : 0.760 16.031 50860 Z= 0.396 Chirality : 0.050 0.730 5829 Planarity : 0.005 0.051 6461 Dihedral : 7.785 59.046 5897 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.29 % Favored : 95.53 % Rotamer: Outliers : 1.13 % Allowed : 6.49 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.41 (0.11), residues: 4542 helix: -0.99 (0.18), residues: 660 sheet: -1.68 (0.14), residues: 1134 loop : -1.75 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 815 TYR 0.028 0.002 TYR G 50 PHE 0.033 0.002 PHE N 109 TRP 0.024 0.002 TRP N 112 HIS 0.009 0.002 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00392 (37220) covalent geometry : angle 0.74401 (50629) SS BOND : bond 0.00363 ( 48) SS BOND : angle 1.10970 ( 96) hydrogen bonds : bond 0.05534 ( 1146) hydrogen bonds : angle 7.80764 ( 3066) link_BETA1-4 : bond 0.00879 ( 15) link_BETA1-4 : angle 2.29165 ( 45) link_NAG-ASN : bond 0.00581 ( 30) link_NAG-ASN : angle 3.32313 ( 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 224 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 179 time to evaluate : 1.300 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: H 103 LEU cc_start: 0.0014 (tp) cc_final: -0.0553 (mp) REVERT: O 518 LEU cc_start: 0.4296 (mt) cc_final: 0.3695 (pt) REVERT: O 869 MET cc_start: 0.8388 (mtt) cc_final: 0.8165 (mmm) outliers start: 45 outliers final: 16 residues processed: 218 average time/residue: 0.2258 time to fit residues: 80.8951 Evaluate side-chains 141 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I residue 76 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 342 optimal weight: 0.9980 chunk 79 optimal weight: 40.0000 chunk 155 optimal weight: 20.0000 chunk 361 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 355 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 386 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 128 optimal weight: 50.0000 chunk 264 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN E 39 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 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 234 ASN R 658 ASN ** R 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 935 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.117426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.087672 restraints weight = 159488.416| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 4.38 r_work: 0.3538 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3437 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= 0.296 Angle : 0.784 19.116 50860 Z= 0.401 Chirality : 0.050 0.652 5829 Planarity : 0.005 0.070 6461 Dihedral : 7.069 59.496 5896 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.02 % Favored : 94.80 % Rotamer: Outliers : 2.04 % Allowed : 7.67 % Favored : 90.30 % 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: -2.04 (0.12), residues: 4542 helix: -0.30 (0.19), residues: 651 sheet: -1.42 (0.15), residues: 1071 loop : -1.62 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 68 TYR 0.026 0.002 TYR E 94 PHE 0.034 0.003 PHE O 220 TRP 0.024 0.002 TRP N 112 HIS 0.010 0.002 HIS R1088 Details of bonding type rmsd covalent geometry : bond 0.00641 (37220) covalent geometry : angle 0.76508 (50629) SS BOND : bond 0.00581 ( 48) SS BOND : angle 1.24673 ( 96) hydrogen bonds : bond 0.04957 ( 1146) hydrogen bonds : angle 7.18497 ( 3066) link_BETA1-4 : bond 0.00645 ( 15) link_BETA1-4 : angle 2.66005 ( 45) link_NAG-ASN : bond 0.00966 ( 30) link_NAG-ASN : angle 3.59391 ( 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 229 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 148 time to evaluate : 1.247 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: L 82 MET cc_start: 0.5197 (ttt) cc_final: 0.3903 (ptm) REVERT: H 103 LEU cc_start: 0.0578 (tp) cc_final: -0.0264 (mp) REVERT: I 39 GLN cc_start: 0.4623 (tt0) cc_final: 0.3592 (tm-30) REVERT: N 82 MET cc_start: 0.5417 (ttt) cc_final: 0.4278 (ptm) REVERT: K 33 TYR cc_start: 0.6398 (m-10) cc_final: 0.6162 (m-80) REVERT: P 47 GLU cc_start: 0.7881 (tp30) cc_final: 0.7649 (tp30) REVERT: P 82 MET cc_start: 0.5109 (ttm) cc_final: 0.4196 (ptm) REVERT: O 357 ARG cc_start: -0.0638 (OUTLIER) cc_final: -0.1261 (ttm170) REVERT: O 869 MET cc_start: 0.8584 (mtt) cc_final: 0.8379 (mmm) REVERT: Q 675 GLN cc_start: 0.8357 (pt0) cc_final: 0.8090 (pp30) REVERT: Q 869 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8235 (mtt) REVERT: Q 906 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8635 (m-80) REVERT: Q 1029 MET cc_start: 0.8701 (mmm) cc_final: 0.8320 (tpp) REVERT: Q 1089 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: R 697 MET cc_start: 0.8252 (ttt) cc_final: 0.7771 (ptm) REVERT: R 906 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8564 (m-80) REVERT: R 983 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7782 (mtp85) REVERT: R 1019 ARG cc_start: 0.8092 (tpt90) cc_final: 0.7577 (tpm170) outliers start: 81 outliers final: 36 residues processed: 217 average time/residue: 0.2168 time to fit residues: 79.0166 Evaluate side-chains 154 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 P residue 49 MET 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 O residue 1130 ILE 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 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: 0.9990 chunk 275 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 127 optimal weight: 40.0000 chunk 411 optimal weight: 1.9990 chunk 50 optimal weight: 50.0000 chunk 341 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN E 6 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN I 6 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** M 53 ASN O 506 GLN O 762 GLN O 955 ASN ** Q 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 506 GLN Q 540 ASN ** Q 762 GLN ** 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 506 GLN R 540 ASN R 658 ASN R 762 GLN ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.127389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.097936 restraints weight = 155187.335| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 4.30 r_work: 0.3603 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3845 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= 0.151 Angle : 0.640 15.783 50860 Z= 0.324 Chirality : 0.046 0.611 5829 Planarity : 0.004 0.074 6461 Dihedral : 6.336 57.523 5896 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.87 % Favored : 94.94 % Rotamer: Outliers : 1.96 % Allowed : 8.57 % Favored : 89.47 % 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: -1.68 (0.12), residues: 4542 helix: 0.28 (0.20), residues: 678 sheet: -1.18 (0.15), residues: 1056 loop : -1.48 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 20 TYR 0.016 0.002 TYR I 94 PHE 0.020 0.002 PHE N 109 TRP 0.021 0.001 TRP L 112 HIS 0.004 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00326 (37220) covalent geometry : angle 0.62349 (50629) SS BOND : bond 0.00266 ( 48) SS BOND : angle 0.82069 ( 96) hydrogen bonds : bond 0.03947 ( 1146) hydrogen bonds : angle 6.55637 ( 3066) link_BETA1-4 : bond 0.00633 ( 15) link_BETA1-4 : angle 2.50431 ( 45) link_NAG-ASN : bond 0.00509 ( 30) link_NAG-ASN : angle 3.01516 ( 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 215 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 137 time to evaluate : 1.110 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: 0.5332 (tp40) cc_final: 0.4886 (tp40) REVERT: L 47 GLU cc_start: 0.7899 (tp30) cc_final: 0.7662 (tp30) REVERT: L 82 MET cc_start: 0.5367 (ttt) cc_final: 0.4069 (ptm) REVERT: E 106 VAL cc_start: 0.2484 (OUTLIER) cc_final: 0.2282 (m) REVERT: H 103 LEU cc_start: 0.0649 (tp) cc_final: -0.0185 (mp) REVERT: I 107 MET cc_start: 0.0129 (mtt) cc_final: -0.0229 (mtm) REVERT: N 82 MET cc_start: 0.5840 (ttt) cc_final: 0.4573 (ptm) REVERT: P 82 MET cc_start: 0.5482 (ttm) cc_final: 0.4491 (ptm) REVERT: O 357 ARG cc_start: -0.0637 (OUTLIER) cc_final: -0.1263 (ttm170) REVERT: O 906 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8535 (m-80) REVERT: Q 1029 MET cc_start: 0.8730 (mmm) cc_final: 0.8440 (tpp) REVERT: R 675 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7770 (pp30) REVERT: R 906 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: R 983 ARG cc_start: 0.7947 (ttp-170) cc_final: 0.7632 (mtp85) REVERT: R 1019 ARG cc_start: 0.8227 (tpt90) cc_final: 0.7634 (tpm170) outliers start: 78 outliers final: 43 residues processed: 202 average time/residue: 0.2195 time to fit residues: 73.4846 Evaluate side-chains 158 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 110 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 D residue 51 SER Chi-restraints excluded: chain E residue 81 MET 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 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 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 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 866 THR Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 1130 ILE Chi-restraints excluded: chain O residue 1136 THR 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 306 PHE 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 1089 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: 0.7980 chunk 34 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 431 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 443 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** 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 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN Q 121 ASN Q 506 GLN ** Q 762 GLN ** 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 234 ASN R 658 ASN ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.127559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.097778 restraints weight = 154984.976| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 4.19 r_work: 0.3599 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37313 Z= 0.160 Angle : 0.627 14.982 50860 Z= 0.316 Chirality : 0.045 0.646 5829 Planarity : 0.004 0.071 6461 Dihedral : 5.919 58.325 5896 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.22 % Favored : 94.58 % Rotamer: Outliers : 2.01 % Allowed : 9.13 % Favored : 88.86 % 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: -1.49 (0.12), residues: 4542 helix: 0.73 (0.20), residues: 651 sheet: -0.98 (0.16), residues: 1014 loop : -1.46 (0.11), residues: 2877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O1039 TYR 0.017 0.001 TYR C 50 PHE 0.016 0.002 PHE N 109 TRP 0.016 0.001 TRP N 112 HIS 0.006 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00345 (37220) covalent geometry : angle 0.61026 (50629) SS BOND : bond 0.00247 ( 48) SS BOND : angle 0.68905 ( 96) hydrogen bonds : bond 0.03827 ( 1146) hydrogen bonds : angle 6.30259 ( 3066) link_BETA1-4 : bond 0.00541 ( 15) link_BETA1-4 : angle 2.43679 ( 45) link_NAG-ASN : bond 0.00579 ( 30) link_NAG-ASN : angle 3.06105 ( 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 210 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 130 time to evaluate : 1.425 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: 0.4665 (tp40) cc_final: 0.2688 (pt0) REVERT: L 110 ASP cc_start: 0.3025 (OUTLIER) cc_final: 0.2700 (p0) REVERT: D 46 LEU cc_start: 0.1583 (OUTLIER) cc_final: 0.0982 (mt) REVERT: H 103 LEU cc_start: 0.0689 (tp) cc_final: -0.0228 (mp) REVERT: N 49 MET cc_start: 0.6580 (OUTLIER) cc_final: 0.6112 (ptt) REVERT: N 60 MET cc_start: 0.4477 (tmm) cc_final: 0.4265 (tmm) REVERT: N 82 MET cc_start: 0.6009 (ttt) cc_final: 0.4802 (ptm) REVERT: P 60 MET cc_start: 0.3800 (ttt) cc_final: 0.3283 (tmm) REVERT: P 82 MET cc_start: 0.5744 (ttm) cc_final: 0.4521 (ptm) REVERT: O 357 ARG cc_start: -0.0351 (OUTLIER) cc_final: -0.0937 (ttm170) REVERT: O 906 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: O 1029 MET cc_start: 0.8832 (mmm) cc_final: 0.8545 (tpp) REVERT: O 1144 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: Q 906 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: Q 1029 MET cc_start: 0.8622 (mmm) cc_final: 0.8373 (tpp) REVERT: Q 1089 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8002 (m-10) REVERT: R 128 ILE cc_start: 0.8088 (mm) cc_final: 0.7734 (mm) REVERT: R 902 MET cc_start: 0.8298 (mmm) cc_final: 0.8015 (mmt) REVERT: R 906 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: R 983 ARG cc_start: 0.8017 (ttp-170) cc_final: 0.7674 (mtp85) REVERT: R 1019 ARG cc_start: 0.8302 (tpt90) cc_final: 0.7891 (tpm170) outliers start: 80 outliers final: 47 residues processed: 196 average time/residue: 0.2197 time to fit residues: 72.3040 Evaluate side-chains 169 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 113 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 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 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 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 92 THR Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 108 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 866 THR 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 1104 VAL Chi-restraints excluded: chain O residue 1130 ILE Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain O residue 1144 GLU Chi-restraints excluded: chain Q residue 69 HIS 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 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 286 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 101 optimal weight: 0.2980 chunk 171 optimal weight: 0.0370 chunk 190 optimal weight: 2.9990 chunk 263 optimal weight: 20.0000 chunk 354 optimal weight: 20.0000 chunk 81 optimal weight: 40.0000 chunk 399 optimal weight: 0.8980 chunk 199 optimal weight: 7.9990 chunk 329 optimal weight: 9.9990 chunk 217 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN 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 Q 30 ASN Q 506 GLN ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 901 GLN R 506 GLN R 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.122486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.094351 restraints weight = 157576.111| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.86 r_work: 0.3729 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 37313 Z= 0.110 Angle : 0.597 14.340 50860 Z= 0.300 Chirality : 0.045 0.605 5829 Planarity : 0.004 0.070 6461 Dihedral : 5.502 57.581 5896 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.84 % Favored : 94.96 % Rotamer: Outliers : 1.78 % Allowed : 9.83 % Favored : 88.39 % 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 (0.21), residues: 663 sheet: -0.75 (0.16), residues: 1032 loop : -1.42 (0.11), residues: 2847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 68 TYR 0.025 0.001 TYR R 200 PHE 0.027 0.001 PHE Q1095 TRP 0.014 0.001 TRP N 112 HIS 0.007 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00236 (37220) covalent geometry : angle 0.57862 (50629) SS BOND : bond 0.00293 ( 48) SS BOND : angle 1.47344 ( 96) hydrogen bonds : bond 0.03548 ( 1146) hydrogen bonds : angle 5.97550 ( 3066) link_BETA1-4 : bond 0.00607 ( 15) link_BETA1-4 : angle 2.36267 ( 45) link_NAG-ASN : bond 0.00493 ( 30) link_NAG-ASN : angle 2.84906 ( 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 196 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 125 time to evaluate : 1.138 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: 0.4310 (tp40) cc_final: 0.2868 (pt0) REVERT: D 46 LEU cc_start: 0.1731 (OUTLIER) cc_final: 0.0937 (mt) REVERT: E 73 ASP cc_start: 0.3125 (t0) cc_final: 0.2490 (m-30) REVERT: H 103 LEU cc_start: 0.0384 (tp) cc_final: -0.0437 (mp) REVERT: N 60 MET cc_start: 0.4320 (tmm) cc_final: 0.4066 (tmm) REVERT: N 82 MET cc_start: 0.5954 (ttt) cc_final: 0.4768 (ptm) REVERT: P 3 GLN cc_start: 0.4608 (tp40) cc_final: 0.3384 (pp30) REVERT: P 60 MET cc_start: 0.3510 (OUTLIER) cc_final: 0.3203 (tmm) REVERT: P 82 MET cc_start: 0.5595 (ttm) cc_final: 0.4495 (ptm) REVERT: O 357 ARG cc_start: -0.0819 (OUTLIER) cc_final: -0.1321 (ttm170) REVERT: Q 906 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: Q 1029 MET cc_start: 0.8367 (mmm) cc_final: 0.8111 (tpp) REVERT: R 675 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7824 (pp30) REVERT: R 983 ARG cc_start: 0.7777 (ttp-170) cc_final: 0.7543 (mtp85) REVERT: R 1019 ARG cc_start: 0.7894 (tpt90) cc_final: 0.7641 (tpm170) outliers start: 71 outliers final: 42 residues processed: 180 average time/residue: 0.2193 time to fit residues: 65.7896 Evaluate side-chains 158 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 111 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 E residue 81 MET 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 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 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 973 ILE Chi-restraints excluded: chain O residue 1104 VAL Chi-restraints excluded: chain O residue 1130 ILE Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 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 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 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: 0.0980 chunk 91 optimal weight: 50.0000 chunk 440 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 347 optimal weight: 0.9980 chunk 427 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** M 53 ASN O 30 ASN O 49 HIS ** O 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.128188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.098703 restraints weight = 156665.232| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 4.01 r_work: 0.3643 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 37313 Z= 0.135 Angle : 0.598 13.703 50860 Z= 0.300 Chirality : 0.045 0.586 5829 Planarity : 0.004 0.066 6461 Dihedral : 5.341 57.961 5896 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.24 % Favored : 94.58 % Rotamer: Outliers : 1.73 % Allowed : 10.21 % Favored : 88.06 % 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: -1.30 (0.12), residues: 4542 helix: 1.08 (0.21), residues: 663 sheet: -0.78 (0.15), residues: 1059 loop : -1.43 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q1107 TYR 0.022 0.001 TYR O 200 PHE 0.025 0.001 PHE O 133 TRP 0.015 0.001 TRP N 112 HIS 0.007 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00295 (37220) covalent geometry : angle 0.58041 (50629) SS BOND : bond 0.00207 ( 48) SS BOND : angle 1.21887 ( 96) hydrogen bonds : bond 0.03533 ( 1146) hydrogen bonds : angle 5.86761 ( 3066) link_BETA1-4 : bond 0.00503 ( 15) link_BETA1-4 : angle 2.36566 ( 45) link_NAG-ASN : bond 0.00502 ( 30) link_NAG-ASN : angle 2.87345 ( 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 187 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 118 time to evaluate : 1.311 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: 0.4359 (tp40) cc_final: 0.2992 (pt0) REVERT: L 60 MET cc_start: 0.4602 (OUTLIER) cc_final: 0.4188 (tmm) REVERT: D 46 LEU cc_start: 0.1714 (OUTLIER) cc_final: 0.0902 (mt) REVERT: E 73 ASP cc_start: 0.3250 (t0) cc_final: 0.2604 (m-30) REVERT: H 103 LEU cc_start: 0.0544 (tp) cc_final: -0.0334 (mp) REVERT: N 60 MET cc_start: 0.4256 (tmm) cc_final: 0.4023 (tmm) REVERT: N 82 MET cc_start: 0.6230 (ttt) cc_final: 0.5065 (ptm) REVERT: P 60 MET cc_start: 0.3290 (OUTLIER) cc_final: 0.3069 (tmm) REVERT: P 82 MET cc_start: 0.5743 (ttm) cc_final: 0.4658 (ptm) REVERT: O 357 ARG cc_start: -0.0501 (OUTLIER) cc_final: -0.0969 (ttm170) REVERT: O 906 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: Q 906 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: Q 1029 MET cc_start: 0.8610 (mmm) cc_final: 0.8368 (tpp) REVERT: R 906 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: R 983 ARG cc_start: 0.7880 (ttp-170) cc_final: 0.7530 (mtp85) outliers start: 69 outliers final: 48 residues processed: 175 average time/residue: 0.2115 time to fit residues: 62.5217 Evaluate side-chains 165 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 110 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 60 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 F residue 12 VAL Chi-restraints excluded: chain F residue 54 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 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 30 ASN Chi-restraints excluded: chain O residue 108 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 1032 CYS Chi-restraints excluded: chain O residue 1104 VAL Chi-restraints excluded: chain O residue 1130 ILE 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 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 276 LEU Chi-restraints excluded: chain R residue 286 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 44 optimal weight: 4.9990 chunk 277 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 172 optimal weight: 7.9990 chunk 360 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 18 optimal weight: 50.0000 chunk 159 optimal weight: 7.9990 chunk 422 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN O 30 ASN ** O 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 779 GLN ** O 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN ** Q 762 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.117356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.088447 restraints weight = 156477.934| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 4.22 r_work: 0.3541 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 37313 Z= 0.249 Angle : 0.671 15.080 50860 Z= 0.340 Chirality : 0.047 0.568 5829 Planarity : 0.004 0.066 6461 Dihedral : 5.589 59.114 5896 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.97 % Favored : 93.88 % Rotamer: Outliers : 1.94 % Allowed : 10.23 % Favored : 87.83 % 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: -1.57 (0.12), residues: 4542 helix: 0.91 (0.21), residues: 651 sheet: -1.02 (0.15), residues: 1086 loop : -1.58 (0.11), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R1019 TYR 0.018 0.002 TYR Q 756 PHE 0.022 0.002 PHE O 643 TRP 0.018 0.001 TRP N 112 HIS 0.008 0.001 HIS O1088 Details of bonding type rmsd covalent geometry : bond 0.00536 (37220) covalent geometry : angle 0.65206 (50629) SS BOND : bond 0.00253 ( 48) SS BOND : angle 1.34491 ( 96) hydrogen bonds : bond 0.04046 ( 1146) hydrogen bonds : angle 6.11194 ( 3066) link_BETA1-4 : bond 0.00483 ( 15) link_BETA1-4 : angle 2.43714 ( 45) link_NAG-ASN : bond 0.00816 ( 30) link_NAG-ASN : angle 3.17485 ( 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 193 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 116 time to evaluate : 1.235 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: L 82 MET cc_start: 0.5234 (ttm) cc_final: 0.4392 (ptm) REVERT: E 73 ASP cc_start: 0.3321 (t0) cc_final: 0.2595 (m-30) REVERT: F 36 GLN cc_start: 0.4447 (OUTLIER) cc_final: 0.4053 (pt0) REVERT: H 103 LEU cc_start: 0.0864 (tp) cc_final: -0.0186 (mp) REVERT: N 82 MET cc_start: 0.6087 (ttt) cc_final: 0.5027 (ptm) REVERT: P 3 GLN cc_start: 0.4105 (tp40) cc_final: 0.2780 (pp30) REVERT: P 60 MET cc_start: 0.3588 (OUTLIER) cc_final: 0.3247 (tmm) REVERT: O 357 ARG cc_start: -0.0218 (OUTLIER) cc_final: -0.0705 (ttm170) REVERT: O 906 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: Q 906 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: Q 1029 MET cc_start: 0.8856 (mmm) cc_final: 0.8588 (tpp) REVERT: Q 1089 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8048 (m-10) REVERT: R 902 MET cc_start: 0.8503 (mmt) cc_final: 0.8217 (mmm) REVERT: R 906 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: R 983 ARG cc_start: 0.8198 (ttp-170) cc_final: 0.7904 (mtp85) outliers start: 77 outliers final: 54 residues processed: 181 average time/residue: 0.1981 time to fit residues: 61.8492 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 : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain C residue 3 VAL 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 12 VAL Chi-restraints excluded: chain F residue 36 GLN 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 I residue 117 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 108 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 1104 VAL Chi-restraints excluded: chain O residue 1130 ILE 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 382 VAL Chi-restraints excluded: chain Q residue 611 LEU Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain Q residue 794 ILE 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 213 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 306 PHE Chi-restraints excluded: chain R residue 546 LEU 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 976 VAL 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=1.50 ------------------------------------------------------------------------------- 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: 6.9990 chunk 279 optimal weight: 6.9990 chunk 320 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 217 optimal weight: 1.9990 chunk 178 optimal weight: 50.0000 chunk 137 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** F 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN O 30 ASN O 641 ASN Q 30 ASN ** Q 762 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 = 0.4520 r_free = 0.4520 target = 0.117396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.088896 restraints weight = 155938.372| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 4.38 r_work: 0.3577 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37313 Z= 0.194 Angle : 0.628 13.803 50860 Z= 0.317 Chirality : 0.045 0.552 5829 Planarity : 0.004 0.060 6461 Dihedral : 5.500 58.853 5896 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.64 % Favored : 94.21 % Rotamer: Outliers : 1.71 % Allowed : 10.53 % Favored : 87.76 % 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: -1.52 (0.12), residues: 4542 helix: 0.92 (0.20), residues: 660 sheet: -1.00 (0.15), residues: 1095 loop : -1.54 (0.11), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R1019 TYR 0.018 0.002 TYR O1067 PHE 0.027 0.002 PHE O 133 TRP 0.016 0.001 TRP N 112 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00419 (37220) covalent geometry : angle 0.60982 (50629) SS BOND : bond 0.00215 ( 48) SS BOND : angle 1.36406 ( 96) hydrogen bonds : bond 0.03744 ( 1146) hydrogen bonds : angle 6.00968 ( 3066) link_BETA1-4 : bond 0.00536 ( 15) link_BETA1-4 : angle 2.36894 ( 45) link_NAG-ASN : bond 0.00623 ( 30) link_NAG-ASN : angle 2.94619 ( 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 181 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 113 time to evaluate : 1.314 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: L 82 MET cc_start: 0.5224 (ttm) cc_final: 0.4328 (ptm) REVERT: E 73 ASP cc_start: 0.3264 (t0) cc_final: 0.2370 (m-30) REVERT: F 36 GLN cc_start: 0.4419 (OUTLIER) cc_final: 0.4113 (pt0) REVERT: H 103 LEU cc_start: 0.1111 (tp) cc_final: 0.0036 (mp) REVERT: N 82 MET cc_start: 0.6099 (ttt) cc_final: 0.4994 (ptm) REVERT: P 60 MET cc_start: 0.3468 (OUTLIER) cc_final: 0.3140 (tmm) REVERT: P 82 MET cc_start: 0.5369 (ttm) cc_final: 0.4341 (ptm) REVERT: O 357 ARG cc_start: -0.0356 (OUTLIER) cc_final: -0.0804 (ttm170) REVERT: O 906 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: Q 906 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8546 (m-80) REVERT: Q 1029 MET cc_start: 0.8695 (mmm) cc_final: 0.8405 (tpp) REVERT: R 906 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: R 983 ARG cc_start: 0.8006 (ttp-170) cc_final: 0.7673 (mtp85) outliers start: 68 outliers final: 57 residues processed: 168 average time/residue: 0.2106 time to fit residues: 60.4910 Evaluate side-chains 174 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 111 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 3 VAL 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 F residue 84 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 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 92 THR Chi-restraints excluded: chain K residue 3 VAL 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 M residue 3 VAL Chi-restraints excluded: chain O residue 30 ASN Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 200 TYR 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 1130 ILE 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 377 PHE 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 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 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 1081 ILE 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: 1.9990 chunk 152 optimal weight: 4.9990 chunk 300 optimal weight: 2.9990 chunk 112 optimal weight: 30.0000 chunk 27 optimal weight: 0.0980 chunk 316 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 136 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 347 optimal weight: 8.9990 chunk 338 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN C 53 ASN ** F 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 30 ASN ** O 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 ASN ** 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 = 0.4540 r_free = 0.4540 target = 0.118144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.089722 restraints weight = 156787.851| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 4.23 r_work: 0.3606 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 37313 Z= 0.116 Angle : 0.597 14.627 50860 Z= 0.300 Chirality : 0.045 0.543 5829 Planarity : 0.004 0.056 6461 Dihedral : 5.277 58.904 5896 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.13 % Favored : 94.72 % Rotamer: Outliers : 1.53 % Allowed : 10.71 % Favored : 87.76 % 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: -1.28 (0.12), residues: 4542 helix: 1.17 (0.21), residues: 660 sheet: -0.78 (0.16), residues: 1071 loop : -1.43 (0.12), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R1019 TYR 0.021 0.001 TYR M 50 PHE 0.016 0.001 PHE R 133 TRP 0.016 0.001 TRP N 112 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00257 (37220) covalent geometry : angle 0.57741 (50629) SS BOND : bond 0.00220 ( 48) SS BOND : angle 1.85145 ( 96) hydrogen bonds : bond 0.03509 ( 1146) hydrogen bonds : angle 5.83083 ( 3066) link_BETA1-4 : bond 0.00520 ( 15) link_BETA1-4 : angle 2.31534 ( 45) link_NAG-ASN : bond 0.00447 ( 30) link_NAG-ASN : angle 2.73436 ( 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 177 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 116 time to evaluate : 1.301 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: L 82 MET cc_start: 0.5237 (ttm) cc_final: 0.4349 (ptm) REVERT: E 73 ASP cc_start: 0.3255 (t0) cc_final: 0.2494 (m-30) REVERT: H 103 LEU cc_start: 0.1040 (tp) cc_final: -0.0030 (mp) REVERT: N 82 MET cc_start: 0.6106 (ttt) cc_final: 0.4977 (ptm) REVERT: P 60 MET cc_start: 0.3484 (OUTLIER) cc_final: 0.3117 (tmm) REVERT: P 82 MET cc_start: 0.5350 (ttm) cc_final: 0.4413 (ptm) REVERT: O 357 ARG cc_start: -0.0408 (OUTLIER) cc_final: -0.0803 (ttm170) REVERT: O 906 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8507 (m-80) REVERT: Q 906 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8429 (m-80) REVERT: Q 1029 MET cc_start: 0.8592 (mmm) cc_final: 0.8343 (tpp) REVERT: R 128 ILE cc_start: 0.8182 (mm) cc_final: 0.7695 (mp) REVERT: R 906 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: R 983 ARG cc_start: 0.8050 (ttp-170) cc_final: 0.7688 (mtp85) outliers start: 61 outliers final: 48 residues processed: 166 average time/residue: 0.2083 time to fit residues: 58.6031 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 : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain F residue 84 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 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 K residue 3 VAL 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 30 ASN Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 200 TYR 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 1104 VAL Chi-restraints excluded: chain O residue 1130 ILE 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 377 PHE 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 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 306 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 13 optimal weight: 40.0000 chunk 134 optimal weight: 7.9990 chunk 259 optimal weight: 0.0470 chunk 207 optimal weight: 3.9990 chunk 335 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 236 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 421 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 237 optimal weight: 0.0030 overall best weight: 0.5490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN C 53 ASN F 6 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 30 ASN ** O 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 564 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 = 0.4578 r_free = 0.4578 target = 0.122295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.093188 restraints weight = 155973.812| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.51 r_work: 0.3676 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 37313 Z= 0.107 Angle : 0.585 12.932 50860 Z= 0.293 Chirality : 0.044 0.534 5829 Planarity : 0.004 0.054 6461 Dihedral : 5.067 58.585 5896 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.33 % Favored : 94.52 % Rotamer: Outliers : 1.38 % Allowed : 10.83 % Favored : 87.78 % 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: -1.17 (0.12), residues: 4542 helix: 1.26 (0.21), residues: 669 sheet: -0.70 (0.15), residues: 1104 loop : -1.37 (0.12), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R1019 TYR 0.018 0.001 TYR M 50 PHE 0.028 0.001 PHE O 133 TRP 0.017 0.001 TRP N 112 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00231 (37220) covalent geometry : angle 0.56653 (50629) SS BOND : bond 0.00207 ( 48) SS BOND : angle 1.65445 ( 96) hydrogen bonds : bond 0.03378 ( 1146) hydrogen bonds : angle 5.68479 ( 3066) link_BETA1-4 : bond 0.00607 ( 15) link_BETA1-4 : angle 2.25158 ( 45) link_NAG-ASN : bond 0.00433 ( 30) link_NAG-ASN : angle 2.67012 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10431.60 seconds wall clock time: 178 minutes 57.33 seconds (10737.33 seconds total)