Starting phenix.real_space_refine on Mon Aug 25 07:39:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c44_45174/08_2025/9c44_45174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c44_45174/08_2025/9c44_45174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c44_45174/08_2025/9c44_45174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c44_45174/08_2025/9c44_45174_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c44_45174/08_2025/9c44_45174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c44_45174/08_2025/9c44_45174.map" } resolution = 2.6 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= 0.003 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16707 2.51 5 N 4515 2.21 5 O 4998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26337 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7030 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 300} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 1056 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 881 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 14, 'ASN:plan1': 23, 'ARG:plan': 15, 'HIS:plan': 4, 'PHE:plan': 15, 'ASP:plan': 29, 'GLU:plan': 20, 'TYR:plan': 18, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 639 Chain: "H" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 847 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "L" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 625 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'TRP:plan': 2, 'GLN:plan1': 5, 'ASP:plan': 7, 'ARG:plan': 2, 'PHE:plan': 5, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 7030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7030 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 300} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 1056 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 881 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 14, 'ASN:plan1': 23, 'ARG:plan': 15, 'HIS:plan': 4, 'PHE:plan': 15, 'ASP:plan': 29, 'GLU:plan': 20, 'TYR:plan': 18, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 639 Chain: "E" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 847 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 625 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'TRP:plan': 2, 'GLN:plan1': 5, 'ASP:plan': 7, 'ARG:plan': 2, 'PHE:plan': 5, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "C" Number of atoms: 7030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7030 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 300} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 1056 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 881 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 14, 'ASN:plan1': 23, 'ARG:plan': 15, 'HIS:plan': 4, 'PHE:plan': 15, 'ASP:plan': 29, 'GLU:plan': 20, 'TYR:plan': 18, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 639 Chain: "F" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 847 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 625 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'TRP:plan': 2, 'GLN:plan1': 5, 'ASP:plan': 7, 'ARG:plan': 2, 'PHE:plan': 5, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.32, per 1000 atoms: 0.20 Number of scatterers: 26337 At special positions: 0 Unit cell: (152.583, 155.955, 178.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4998 8.00 N 4515 7.00 C 16707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.13 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.13 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.13 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 331 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 331 " " NAG I 1 " - " ASN A 122 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN B 122 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN C 122 " " NAG S 1 " - " ASN C 234 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 808.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7020 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 63 sheets defined 23.2% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.924A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.765A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.822A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.173A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.500A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.507A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.732A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.089A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.924A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.765A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.822A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.173A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.500A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.507A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.732A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.090A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.924A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.765A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.822A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.173A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.500A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.507A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.732A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.088A pdb=" N ILE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.810A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.525A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.290A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 153 through 155 removed outlier: 6.325A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.933A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.208A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.381A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.606A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.670A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.722A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.722A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.663A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.644A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.827A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.715A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.715A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.810A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.526A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.290A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 153 through 155 removed outlier: 6.325A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.934A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.381A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.606A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.722A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.722A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.663A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.644A pdb=" N MET E 34 " --> pdb=" O PHE E 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.827A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 67 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.715A pdb=" N LEU D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.715A pdb=" N LEU D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.525A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.290A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 153 through 155 removed outlier: 6.325A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.933A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.381A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.606A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.310A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.663A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.644A pdb=" N MET F 34 " --> pdb=" O PHE F 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AG7, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.828A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER G 67 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.715A pdb=" N LEU G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU G 33 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.715A pdb=" N LEU G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) 1363 hydrogen bonds defined for protein. 3594 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: 5.47 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4897 1.32 - 1.45: 6675 1.45 - 1.57: 15146 1.57 - 1.70: 18 1.70 - 1.82: 144 Bond restraints: 26880 Sorted by residual: bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.93e+00 ... (remaining 26875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 31879 1.62 - 3.24: 4132 3.24 - 4.86: 463 4.86 - 6.48: 267 6.48 - 8.10: 177 Bond angle restraints: 36918 Sorted by residual: angle pdb=" C LEU B 861 " pdb=" N PRO B 862 " pdb=" CA PRO B 862 " ideal model delta sigma weight residual 119.66 126.45 -6.79 7.20e-01 1.93e+00 8.89e+01 angle pdb=" C LEU C 861 " pdb=" N PRO C 862 " pdb=" CA PRO C 862 " ideal model delta sigma weight residual 119.66 126.43 -6.77 7.20e-01 1.93e+00 8.84e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.43 -6.77 7.20e-01 1.93e+00 8.84e+01 angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 126.35 -6.69 7.20e-01 1.93e+00 8.64e+01 angle pdb=" C THR B 791 " pdb=" N PRO B 792 " pdb=" CA PRO B 792 " ideal model delta sigma weight residual 119.66 126.32 -6.66 7.20e-01 1.93e+00 8.56e+01 ... (remaining 36913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 16156 21.34 - 42.67: 275 42.67 - 64.01: 84 64.01 - 85.35: 36 85.35 - 106.68: 24 Dihedral angle restraints: 16575 sinusoidal: 5688 harmonic: 10887 Sorted by residual: dihedral pdb=" CD ARG C 319 " pdb=" NE ARG C 319 " pdb=" CZ ARG C 319 " pdb=" NH1 ARG C 319 " ideal model delta sinusoidal sigma weight residual 0.00 79.96 -79.96 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CD ARG A 319 " pdb=" NE ARG A 319 " pdb=" CZ ARG A 319 " pdb=" NH1 ARG A 319 " ideal model delta sinusoidal sigma weight residual 0.00 79.94 -79.94 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CD ARG B 319 " pdb=" NE ARG B 319 " pdb=" CZ ARG B 319 " pdb=" NH1 ARG B 319 " ideal model delta sinusoidal sigma weight residual 0.00 79.89 -79.89 1 1.00e+01 1.00e-02 7.92e+01 ... (remaining 16572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3532 0.077 - 0.154: 792 0.154 - 0.231: 155 0.231 - 0.308: 21 0.308 - 0.386: 48 Chirality restraints: 4548 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.00e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.98e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.79e+01 ... (remaining 4545 not shown) Planarity restraints: 4875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 319 " -1.081 9.50e-02 1.11e+02 4.85e-01 1.42e+02 pdb=" NE ARG B 319 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 319 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 319 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 319 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 319 " -1.081 9.50e-02 1.11e+02 4.85e-01 1.42e+02 pdb=" NE ARG A 319 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 319 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 319 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 319 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 319 " -1.081 9.50e-02 1.11e+02 4.84e-01 1.42e+02 pdb=" NE ARG C 319 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 319 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 319 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG C 319 " -0.019 2.00e-02 2.50e+03 ... (remaining 4872 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 12580 2.96 - 3.45: 23178 3.45 - 3.93: 42694 3.93 - 4.42: 47307 4.42 - 4.90: 79387 Nonbonded interactions: 205146 Sorted by model distance: nonbonded pdb=" NZ LYS B 557 " pdb=" OD1 ASP B 586 " model vdw 2.477 3.120 nonbonded pdb=" NZ LYS A 557 " pdb=" OD1 ASP A 586 " model vdw 2.477 3.120 nonbonded pdb=" NZ LYS C 557 " pdb=" OD1 ASP C 586 " model vdw 2.477 3.120 nonbonded pdb=" O GLU C1092 " pdb=" NH1 ARG C1107 " model vdw 2.534 3.120 nonbonded pdb=" O GLU B1092 " pdb=" NH1 ARG B1107 " model vdw 2.534 3.120 ... (remaining 205141 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'O' selection = chain 'S' } 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: 7.770 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: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.470 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 0.010 0.102 26985 Z= 0.563 Angle : 1.305 8.096 37188 Z= 0.868 Chirality : 0.076 0.386 4548 Planarity : 0.013 0.485 4830 Dihedral : 11.220 106.685 9420 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.29 % Allowed : 0.88 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.13), residues: 3708 helix: 0.27 (0.18), residues: 699 sheet: 0.95 (0.15), residues: 1101 loop : 0.40 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.035 0.005 TYR C1067 PHE 0.022 0.004 PHE C 898 TRP 0.018 0.005 TRP A 886 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00987 (26880) covalent geometry : angle 1.28299 (36918) SS BOND : bond 0.02770 ( 45) SS BOND : angle 3.16006 ( 90) hydrogen bonds : bond 0.16921 ( 1291) hydrogen bonds : angle 8.33800 ( 3594) link_BETA1-4 : bond 0.03703 ( 15) link_BETA1-4 : angle 3.54297 ( 45) link_NAG-ASN : bond 0.01232 ( 45) link_NAG-ASN : angle 2.81165 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 323 time to evaluate : 0.670 Fit side-chains REVERT: A 633 TRP cc_start: 0.7500 (OUTLIER) cc_final: 0.6729 (m100) REVERT: A 773 GLU cc_start: 0.7778 (tt0) cc_final: 0.7568 (tt0) REVERT: B 633 TRP cc_start: 0.7539 (OUTLIER) cc_final: 0.6748 (m100) REVERT: B 773 GLU cc_start: 0.7770 (tt0) cc_final: 0.7539 (tt0) REVERT: C 319 ARG cc_start: 0.7081 (mtp85) cc_final: 0.6857 (mtp180) outliers start: 6 outliers final: 2 residues processed: 329 average time/residue: 0.5632 time to fit residues: 214.6966 Evaluate side-chains 226 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 633 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 50.0000 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A 655 HIS A 658 ASN A 751 ASN A 913 GLN A1002 GLN A1005 GLN A1010 GLN A1113 GLN H 77 ASN B 658 ASN B 784 GLN B 907 ASN B 913 GLN B1002 GLN B1005 GLN B1113 GLN E 77 ASN C 317 ASN C 613 GLN C 658 ASN C 907 ASN C 913 GLN C 957 GLN C 978 ASN C1005 GLN C1010 GLN C1011 GLN C1113 GLN F 77 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.222754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.174778 restraints weight = 26406.600| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 4.83 r_work: 0.3350 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26985 Z= 0.151 Angle : 0.567 6.955 37188 Z= 0.303 Chirality : 0.046 0.153 4548 Planarity : 0.005 0.100 4830 Dihedral : 6.293 70.631 5207 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.71 % Allowed : 5.90 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.14), residues: 3708 helix: 1.71 (0.20), residues: 675 sheet: 1.24 (0.16), residues: 1035 loop : 0.61 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 52 TYR 0.026 0.002 TYR C1067 PHE 0.015 0.002 PHE A 898 TRP 0.012 0.002 TRP B 886 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00341 (26880) covalent geometry : angle 0.54526 (36918) SS BOND : bond 0.00234 ( 45) SS BOND : angle 1.22517 ( 90) hydrogen bonds : bond 0.05428 ( 1291) hydrogen bonds : angle 6.20533 ( 3594) link_BETA1-4 : bond 0.00386 ( 15) link_BETA1-4 : angle 1.75937 ( 45) link_NAG-ASN : bond 0.00335 ( 45) link_NAG-ASN : angle 2.28931 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.790 Fit side-chains REVERT: A 633 TRP cc_start: 0.7688 (OUTLIER) cc_final: 0.7124 (m100) REVERT: A 750 SER cc_start: 0.8457 (t) cc_final: 0.8011 (m) REVERT: A 751 ASN cc_start: 0.8501 (m-40) cc_final: 0.8207 (m110) REVERT: A 773 GLU cc_start: 0.8529 (tt0) cc_final: 0.8218 (tt0) REVERT: B 633 TRP cc_start: 0.7736 (OUTLIER) cc_final: 0.7164 (m100) REVERT: B 773 GLU cc_start: 0.8503 (tt0) cc_final: 0.8226 (tt0) REVERT: B 1010 GLN cc_start: 0.8504 (pt0) cc_final: 0.8159 (mm-40) REVERT: C 314 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: F 52 ARG cc_start: 0.8604 (mtp180) cc_final: 0.8275 (mtp85) REVERT: F 95 TYR cc_start: 0.6773 (m-80) cc_final: 0.6399 (m-80) outliers start: 35 outliers final: 12 residues processed: 236 average time/residue: 0.4971 time to fit residues: 139.2604 Evaluate side-chains 225 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 633 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 284 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 318 optimal weight: 0.0170 chunk 97 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 chunk 323 optimal weight: 0.5980 chunk 137 optimal weight: 9.9990 chunk 366 optimal weight: 6.9990 chunk 358 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 613 GLN A 658 ASN A 784 GLN A 804 GLN A 957 GLN A1002 GLN A1005 GLN A1010 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 784 GLN B1002 GLN B1005 GLN B1113 GLN E 77 ASN C 317 ASN C 658 ASN C 751 ASN C 804 GLN C 957 GLN C1002 GLN C1005 GLN C1010 GLN F 77 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.220593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.171293 restraints weight = 26150.761| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 4.87 r_work: 0.3288 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 26985 Z= 0.194 Angle : 0.587 9.030 37188 Z= 0.309 Chirality : 0.048 0.297 4548 Planarity : 0.004 0.040 4830 Dihedral : 5.149 57.940 5207 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.00 % Allowed : 5.95 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.14), residues: 3708 helix: 1.98 (0.21), residues: 636 sheet: 1.19 (0.16), residues: 1035 loop : 0.45 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 319 TYR 0.026 0.002 TYR C1067 PHE 0.025 0.002 PHE B 898 TRP 0.012 0.002 TRP A 886 HIS 0.005 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00468 (26880) covalent geometry : angle 0.56306 (36918) SS BOND : bond 0.00277 ( 45) SS BOND : angle 1.61324 ( 90) hydrogen bonds : bond 0.05658 ( 1291) hydrogen bonds : angle 5.89965 ( 3594) link_BETA1-4 : bond 0.00392 ( 15) link_BETA1-4 : angle 1.66931 ( 45) link_NAG-ASN : bond 0.00346 ( 45) link_NAG-ASN : angle 2.36423 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.850 Fit side-chains REVERT: A 314 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: A 633 TRP cc_start: 0.7675 (OUTLIER) cc_final: 0.6883 (m100) REVERT: A 751 ASN cc_start: 0.8512 (m-40) cc_final: 0.8256 (m110) REVERT: A 773 GLU cc_start: 0.8649 (tt0) cc_final: 0.8444 (tt0) REVERT: A 935 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: B 298 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: B 633 TRP cc_start: 0.7718 (OUTLIER) cc_final: 0.6901 (m100) REVERT: B 773 GLU cc_start: 0.8629 (tt0) cc_final: 0.8266 (tt0) REVERT: B 1010 GLN cc_start: 0.8568 (pt0) cc_final: 0.8157 (mm-40) REVERT: C 191 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7612 (mt-10) REVERT: C 314 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: C 750 SER cc_start: 0.8292 (t) cc_final: 0.7819 (m) REVERT: C 790 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8364 (mmmt) REVERT: F 95 TYR cc_start: 0.7097 (m-80) cc_final: 0.6723 (m-80) outliers start: 41 outliers final: 12 residues processed: 250 average time/residue: 0.5041 time to fit residues: 149.5207 Evaluate side-chains 231 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 343 optimal weight: 0.5980 chunk 264 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 357 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 658 ASN A1002 GLN A1010 GLN B 196 ASN B 540 ASN B 658 ASN B 751 ASN B 784 GLN B 804 GLN B 949 GLN B1005 GLN C 196 ASN C 658 ASN C 751 ASN C1002 GLN C1005 GLN C1010 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.221638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.174060 restraints weight = 26056.180| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 4.69 r_work: 0.3363 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26985 Z= 0.136 Angle : 0.517 5.780 37188 Z= 0.271 Chirality : 0.045 0.151 4548 Planarity : 0.004 0.038 4830 Dihedral : 4.381 57.498 5205 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.80 % Allowed : 6.24 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.14), residues: 3708 helix: 2.12 (0.21), residues: 639 sheet: 1.10 (0.16), residues: 1059 loop : 0.47 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.022 0.001 TYR C1067 PHE 0.018 0.001 PHE A 898 TRP 0.007 0.001 TRP B1102 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00314 (26880) covalent geometry : angle 0.49913 (36918) SS BOND : bond 0.00180 ( 45) SS BOND : angle 1.07005 ( 90) hydrogen bonds : bond 0.04785 ( 1291) hydrogen bonds : angle 5.62337 ( 3594) link_BETA1-4 : bond 0.00390 ( 15) link_BETA1-4 : angle 1.45567 ( 45) link_NAG-ASN : bond 0.00269 ( 45) link_NAG-ASN : angle 2.02656 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: A 633 TRP cc_start: 0.7775 (OUTLIER) cc_final: 0.6952 (m100) REVERT: A 773 GLU cc_start: 0.8488 (tt0) cc_final: 0.8122 (tt0) REVERT: B 633 TRP cc_start: 0.7753 (OUTLIER) cc_final: 0.6919 (m100) REVERT: B 773 GLU cc_start: 0.8585 (tt0) cc_final: 0.8164 (tt0) REVERT: B 1010 GLN cc_start: 0.8525 (pt0) cc_final: 0.8154 (mm-40) REVERT: C 28 TYR cc_start: 0.8776 (m-80) cc_final: 0.8505 (m-80) REVERT: C 750 SER cc_start: 0.8420 (t) cc_final: 0.7968 (m) REVERT: C 790 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8328 (mmmt) REVERT: F 34 MET cc_start: 0.7733 (mmm) cc_final: 0.7515 (mmt) REVERT: F 95 TYR cc_start: 0.7083 (m-80) cc_final: 0.6718 (m-80) outliers start: 37 outliers final: 12 residues processed: 236 average time/residue: 0.5071 time to fit residues: 141.7220 Evaluate side-chains 222 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 40.0000 chunk 78 optimal weight: 0.9990 chunk 243 optimal weight: 20.0000 chunk 198 optimal weight: 1.9990 chunk 364 optimal weight: 50.0000 chunk 159 optimal weight: 50.0000 chunk 46 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A1002 GLN A1010 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 658 ASN B 751 ASN B 907 ASN B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 751 ASN C1002 GLN C1005 GLN C1010 GLN F 77 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.220671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.174043 restraints weight = 26017.661| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 4.63 r_work: 0.3301 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 26985 Z= 0.193 Angle : 0.567 7.370 37188 Z= 0.297 Chirality : 0.047 0.155 4548 Planarity : 0.004 0.039 4830 Dihedral : 4.352 57.152 5205 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.71 % Allowed : 7.12 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.14), residues: 3708 helix: 1.93 (0.21), residues: 642 sheet: 1.12 (0.16), residues: 1047 loop : 0.29 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.026 0.002 TYR C1067 PHE 0.024 0.002 PHE A 898 TRP 0.014 0.002 TRP B 104 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00464 (26880) covalent geometry : angle 0.54892 (36918) SS BOND : bond 0.00327 ( 45) SS BOND : angle 1.32560 ( 90) hydrogen bonds : bond 0.05409 ( 1291) hydrogen bonds : angle 5.65083 ( 3594) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 1.33920 ( 45) link_NAG-ASN : bond 0.00292 ( 45) link_NAG-ASN : angle 2.10299 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 ASP cc_start: 0.7376 (p0) cc_final: 0.7136 (p0) REVERT: A 633 TRP cc_start: 0.7699 (OUTLIER) cc_final: 0.6956 (m100) REVERT: A 773 GLU cc_start: 0.8609 (tt0) cc_final: 0.8361 (tt0) REVERT: A 935 GLN cc_start: 0.7552 (tt0) cc_final: 0.7317 (tt0) REVERT: B 298 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: B 633 TRP cc_start: 0.7786 (OUTLIER) cc_final: 0.6881 (m100) REVERT: B 773 GLU cc_start: 0.8689 (tt0) cc_final: 0.8234 (tt0) REVERT: B 1010 GLN cc_start: 0.8577 (pt0) cc_final: 0.8173 (mm-40) REVERT: C 750 SER cc_start: 0.8380 (t) cc_final: 0.7893 (m) REVERT: C 790 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8348 (mmmt) REVERT: F 34 MET cc_start: 0.7832 (mmm) cc_final: 0.7531 (mmt) REVERT: F 95 TYR cc_start: 0.7331 (m-80) cc_final: 0.6968 (m-80) outliers start: 35 outliers final: 15 residues processed: 244 average time/residue: 0.4756 time to fit residues: 138.6073 Evaluate side-chains 228 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 124 optimal weight: 30.0000 chunk 267 optimal weight: 0.6980 chunk 167 optimal weight: 10.0000 chunk 291 optimal weight: 20.0000 chunk 27 optimal weight: 0.6980 chunk 161 optimal weight: 50.0000 chunk 357 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 210 optimal weight: 0.5980 chunk 252 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A1010 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 613 GLN B 658 ASN B 751 ASN B 957 GLN B1005 GLN E 77 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 751 ASN C 907 ASN C1002 GLN C1005 GLN C1010 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.221318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.172793 restraints weight = 25964.118| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 4.82 r_work: 0.3330 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26985 Z= 0.134 Angle : 0.509 6.010 37188 Z= 0.266 Chirality : 0.045 0.150 4548 Planarity : 0.004 0.037 4830 Dihedral : 4.068 56.815 5203 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.32 % Allowed : 7.80 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.14), residues: 3708 helix: 2.02 (0.21), residues: 663 sheet: 1.11 (0.15), residues: 1053 loop : 0.26 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1014 TYR 0.022 0.001 TYR C1067 PHE 0.018 0.001 PHE B 898 TRP 0.014 0.001 TRP A 64 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00310 (26880) covalent geometry : angle 0.49289 (36918) SS BOND : bond 0.00263 ( 45) SS BOND : angle 1.04898 ( 90) hydrogen bonds : bond 0.04589 ( 1291) hydrogen bonds : angle 5.43190 ( 3594) link_BETA1-4 : bond 0.00360 ( 15) link_BETA1-4 : angle 1.21884 ( 45) link_NAG-ASN : bond 0.00249 ( 45) link_NAG-ASN : angle 1.89810 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 773 GLU cc_start: 0.8534 (tt0) cc_final: 0.8096 (tt0) REVERT: A 935 GLN cc_start: 0.7509 (tt0) cc_final: 0.7276 (tt0) REVERT: B 576 VAL cc_start: 0.8174 (t) cc_final: 0.7972 (p) REVERT: B 633 TRP cc_start: 0.7744 (OUTLIER) cc_final: 0.6822 (m100) REVERT: B 773 GLU cc_start: 0.8598 (tt0) cc_final: 0.8166 (tt0) REVERT: B 1010 GLN cc_start: 0.8543 (pt0) cc_final: 0.8153 (mm-40) REVERT: C 750 SER cc_start: 0.8352 (t) cc_final: 0.7904 (m) REVERT: C 790 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8324 (mmmt) REVERT: F 34 MET cc_start: 0.7753 (mmm) cc_final: 0.7483 (mmt) REVERT: F 95 TYR cc_start: 0.7271 (m-80) cc_final: 0.6964 (m-80) outliers start: 27 outliers final: 14 residues processed: 227 average time/residue: 0.4817 time to fit residues: 131.5723 Evaluate side-chains 215 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 98 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 306 optimal weight: 0.6980 chunk 213 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 196 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 354 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A1002 GLN A1010 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 658 ASN B 751 ASN B1005 GLN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 751 ASN C1002 GLN C1005 GLN C1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.220545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.172515 restraints weight = 25909.987| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 4.86 r_work: 0.3275 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26985 Z= 0.186 Angle : 0.558 7.783 37188 Z= 0.291 Chirality : 0.047 0.155 4548 Planarity : 0.004 0.038 4830 Dihedral : 4.120 56.720 5201 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.46 % Allowed : 8.28 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.14), residues: 3708 helix: 1.86 (0.21), residues: 663 sheet: 1.13 (0.16), residues: 1032 loop : 0.14 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1014 TYR 0.026 0.002 TYR C1067 PHE 0.024 0.002 PHE A 898 TRP 0.013 0.002 TRP C 64 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00447 (26880) covalent geometry : angle 0.54077 (36918) SS BOND : bond 0.00344 ( 45) SS BOND : angle 1.27191 ( 90) hydrogen bonds : bond 0.05236 ( 1291) hydrogen bonds : angle 5.52151 ( 3594) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 1.25689 ( 45) link_NAG-ASN : bond 0.00260 ( 45) link_NAG-ASN : angle 2.05800 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.8670 (tt0) cc_final: 0.8398 (tt0) REVERT: A 935 GLN cc_start: 0.7607 (tt0) cc_final: 0.7366 (tt0) REVERT: B 633 TRP cc_start: 0.7737 (OUTLIER) cc_final: 0.6717 (m100) REVERT: B 773 GLU cc_start: 0.8695 (tt0) cc_final: 0.8240 (tt0) REVERT: B 1010 GLN cc_start: 0.8618 (pt0) cc_final: 0.8166 (mm-40) REVERT: C 750 SER cc_start: 0.8327 (t) cc_final: 0.7870 (m) REVERT: C 790 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8356 (mmmt) REVERT: F 34 MET cc_start: 0.7796 (mmm) cc_final: 0.7539 (mmt) REVERT: F 95 TYR cc_start: 0.7365 (m-80) cc_final: 0.7025 (m-80) outliers start: 30 outliers final: 20 residues processed: 238 average time/residue: 0.4917 time to fit residues: 139.8571 Evaluate side-chains 228 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 192 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 346 optimal weight: 1.9990 chunk 364 optimal weight: 50.0000 chunk 325 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 355 optimal weight: 0.0270 chunk 147 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 121 optimal weight: 30.0000 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 658 ASN A 675 GLN A1010 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 613 GLN B 658 ASN B 751 ASN B 957 GLN B1005 GLN E 77 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C1002 GLN C1005 GLN C1010 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.221788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.176313 restraints weight = 26135.735| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 4.54 r_work: 0.3360 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26985 Z= 0.119 Angle : 0.503 7.237 37188 Z= 0.262 Chirality : 0.045 0.152 4548 Planarity : 0.004 0.037 4830 Dihedral : 3.930 56.367 5201 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.12 % Allowed : 8.48 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.14), residues: 3708 helix: 2.07 (0.21), residues: 663 sheet: 1.11 (0.16), residues: 1017 loop : 0.18 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1014 TYR 0.021 0.001 TYR C1067 PHE 0.017 0.001 PHE C 65 TRP 0.015 0.001 TRP C 64 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00270 (26880) covalent geometry : angle 0.48759 (36918) SS BOND : bond 0.00220 ( 45) SS BOND : angle 1.03866 ( 90) hydrogen bonds : bond 0.04475 ( 1291) hydrogen bonds : angle 5.36214 ( 3594) link_BETA1-4 : bond 0.00381 ( 15) link_BETA1-4 : angle 1.20796 ( 45) link_NAG-ASN : bond 0.00232 ( 45) link_NAG-ASN : angle 1.89221 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.8540 (tt0) cc_final: 0.8099 (tt0) REVERT: B 773 GLU cc_start: 0.8598 (tt0) cc_final: 0.8165 (tt0) REVERT: B 1010 GLN cc_start: 0.8527 (pt0) cc_final: 0.8134 (mm-40) REVERT: C 750 SER cc_start: 0.8349 (t) cc_final: 0.7938 (m) REVERT: C 790 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8330 (mmmt) REVERT: F 34 MET cc_start: 0.7819 (mmm) cc_final: 0.7542 (mmt) outliers start: 23 outliers final: 15 residues processed: 223 average time/residue: 0.4682 time to fit residues: 125.1098 Evaluate side-chains 223 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 157 optimal weight: 50.0000 chunk 335 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 370 optimal weight: 3.9990 chunk 198 optimal weight: 0.0010 chunk 205 optimal weight: 2.9990 overall best weight: 2.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 957 GLN A1002 GLN A1010 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 751 ASN B 957 GLN B1005 GLN E 77 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C1002 GLN C1005 GLN C1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.226308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.183277 restraints weight = 27241.395| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.00 r_work: 0.3904 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 26985 Z= 0.309 Angle : 0.672 8.163 37188 Z= 0.350 Chirality : 0.052 0.200 4548 Planarity : 0.005 0.039 4830 Dihedral : 4.552 34.208 5199 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.51 % Allowed : 8.24 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.13), residues: 3708 helix: 1.69 (0.21), residues: 645 sheet: 1.01 (0.15), residues: 1071 loop : -0.01 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1039 TYR 0.028 0.002 TYR C1067 PHE 0.035 0.003 PHE A 898 TRP 0.020 0.003 TRP A 104 HIS 0.008 0.002 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00757 (26880) covalent geometry : angle 0.65245 (36918) SS BOND : bond 0.00538 ( 45) SS BOND : angle 1.74189 ( 90) hydrogen bonds : bond 0.06375 ( 1291) hydrogen bonds : angle 5.76053 ( 3594) link_BETA1-4 : bond 0.00395 ( 15) link_BETA1-4 : angle 1.43576 ( 45) link_NAG-ASN : bond 0.00335 ( 45) link_NAG-ASN : angle 2.32161 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 773 GLU cc_start: 0.8412 (tt0) cc_final: 0.7988 (tt0) REVERT: C 750 SER cc_start: 0.8478 (t) cc_final: 0.8111 (m) REVERT: C 790 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8174 (mmmt) outliers start: 31 outliers final: 18 residues processed: 243 average time/residue: 0.4945 time to fit residues: 143.1046 Evaluate side-chains 237 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 151 optimal weight: 0.6980 chunk 370 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 280 optimal weight: 30.0000 chunk 350 optimal weight: 9.9990 chunk 257 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 329 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 357 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 613 GLN A 658 ASN A1002 GLN H 77 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 613 GLN B 658 ASN B 957 GLN B1002 GLN B1005 GLN E 77 ASN C 658 ASN C1002 GLN C1005 GLN C1010 GLN F 77 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.227630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.186592 restraints weight = 27125.502| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.92 r_work: 0.3918 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26985 Z= 0.181 Angle : 0.571 12.852 37188 Z= 0.296 Chirality : 0.047 0.155 4548 Planarity : 0.004 0.039 4830 Dihedral : 4.265 33.089 5199 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.51 % Allowed : 9.02 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.14), residues: 3708 helix: 1.87 (0.21), residues: 645 sheet: 1.04 (0.16), residues: 1014 loop : 0.05 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.023 0.002 TYR C1067 PHE 0.023 0.002 PHE B 898 TRP 0.022 0.002 TRP A 64 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00433 (26880) covalent geometry : angle 0.54857 (36918) SS BOND : bond 0.00339 ( 45) SS BOND : angle 1.32368 ( 90) hydrogen bonds : bond 0.05220 ( 1291) hydrogen bonds : angle 5.54931 ( 3594) link_BETA1-4 : bond 0.00374 ( 15) link_BETA1-4 : angle 1.28505 ( 45) link_NAG-ASN : bond 0.00272 ( 45) link_NAG-ASN : angle 2.43859 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 633 TRP cc_start: 0.7772 (OUTLIER) cc_final: 0.7044 (m100) REVERT: A 1002 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: B 298 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: B 773 GLU cc_start: 0.8369 (tt0) cc_final: 0.7935 (tt0) REVERT: B 1014 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8522 (ttp-170) REVERT: C 750 SER cc_start: 0.8387 (t) cc_final: 0.8053 (m) REVERT: C 790 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8163 (mmmt) outliers start: 31 outliers final: 16 residues processed: 225 average time/residue: 0.5197 time to fit residues: 138.4868 Evaluate side-chains 225 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 231 optimal weight: 0.7980 chunk 226 optimal weight: 8.9990 chunk 238 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 chunk 219 optimal weight: 0.7980 chunk 317 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 264 optimal weight: 0.1980 chunk 180 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 201 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 613 GLN A 658 ASN A 675 GLN A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 613 GLN B 658 ASN B 957 GLN B1002 GLN B1005 GLN E 77 ASN C 658 ASN C1002 GLN C1005 GLN C1010 GLN F 77 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.228361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.187299 restraints weight = 27098.019| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.93 r_work: 0.3948 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26985 Z= 0.150 Angle : 0.537 8.419 37188 Z= 0.279 Chirality : 0.046 0.151 4548 Planarity : 0.004 0.038 4830 Dihedral : 4.109 30.997 5199 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.27 % Allowed : 9.31 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.14), residues: 3708 helix: 2.05 (0.21), residues: 645 sheet: 1.06 (0.16), residues: 1017 loop : 0.12 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 319 TYR 0.022 0.001 TYR C1067 PHE 0.019 0.002 PHE B 898 TRP 0.021 0.002 TRP A 64 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00353 (26880) covalent geometry : angle 0.51721 (36918) SS BOND : bond 0.00270 ( 45) SS BOND : angle 1.22051 ( 90) hydrogen bonds : bond 0.04826 ( 1291) hydrogen bonds : angle 5.44243 ( 3594) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 1.24341 ( 45) link_NAG-ASN : bond 0.00254 ( 45) link_NAG-ASN : angle 2.16740 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9276.35 seconds wall clock time: 157 minutes 59.93 seconds (9479.93 seconds total)