Starting phenix.real_space_refine on Thu Mar 5 21:19:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4n_22668/03_2026/7k4n_22668.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4n_22668/03_2026/7k4n_22668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k4n_22668/03_2026/7k4n_22668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4n_22668/03_2026/7k4n_22668.map" model { file = "/net/cci-nas-00/data/ceres_data/7k4n_22668/03_2026/7k4n_22668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4n_22668/03_2026/7k4n_22668.cif" } resolution = 3.3 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= 0.044 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 120 5.16 5 C 16036 2.51 5 N 4351 2.21 5 O 4846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25353 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 17, 'ASN:plan1': 29, 'GLN:plan1': 9, 'PHE:plan': 8, 'ARG:plan': 10, 'TYR:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 437 Chain: "H" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 598 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 5, 'ARG:plan': 7, 'PHE:plan': 4, 'TRP:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 5, 'HIS:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 201 Chain: "L" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 504 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 3, 'ARG:plan': 6, 'TYR:plan': 6, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 167 Chain: "B" Number of atoms: 7026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7026 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 788 Unresolved non-hydrogen angles: 1010 Unresolved non-hydrogen dihedrals: 620 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 18, 'ASN:plan1': 29, 'GLN:plan1': 9, 'PHE:plan': 10, 'ARG:plan': 10, 'TYR:plan': 10, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 460 Chain: "C" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 598 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 5, 'ARG:plan': 7, 'PHE:plan': 4, 'TRP:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 5, 'HIS:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 201 Chain: "D" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 506 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 3, 'ARG:plan': 6, 'TYR:plan': 6, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 167 Chain: "E" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 17, 'ASN:plan1': 29, 'GLN:plan1': 9, 'PHE:plan': 8, 'ARG:plan': 10, 'TYR:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 437 Chain: "F" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 598 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 5, 'ARG:plan': 7, 'PHE:plan': 4, 'TRP:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 5, 'HIS:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 201 Chain: "G" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 513 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 3, 'ARG:plan': 5, 'TYR:plan': 6, 'TRP:plan': 2, 'PHE:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 159 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: 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "E" 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: 5.98, per 1000 atoms: 0.24 Number of scatterers: 25353 At special positions: 0 Unit cell: (129.15, 132.3, 219.45, 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 120 16.00 O 4846 8.00 N 4351 7.00 C 16036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.09 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.09 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.09 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.09 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 106 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.09 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.04 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.09 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.04 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 122 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 234 " " NAG A1310 " - " ASN A 331 " " NAG A1311 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 122 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B 709 " " NAG E1301 " - " ASN E 282 " " NAG E1302 " - " ASN E 603 " " NAG E1303 " - " ASN E 657 " " NAG E1304 " - " ASN E1074 " " NAG E1305 " - " ASN E 61 " " NAG E1306 " - " ASN E 616 " " NAG E1307 " - " ASN E 122 " " NAG E1308 " - " ASN E 165 " " NAG E1309 " - " ASN E 234 " " NAG E1310 " - " ASN E 331 " " NAG E1311 " - " ASN E 709 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 343 " " NAG N 1 " - " ASN A 801 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN E 717 " " NAG U 1 " - " ASN E1098 " " NAG V 1 " - " ASN E1134 " " NAG W 1 " - " ASN E 343 " " NAG X 1 " - " ASN E 801 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6798 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 63 sheets defined 23.2% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.217A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.248A 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 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.839A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.997A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.817A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.217A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.248A 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 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.839A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 967 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.997A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.817A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.217A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 390 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.247A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 753 Processing helix chain 'E' and resid 754 through 757 Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.839A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 945 through 967 Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.997A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1145 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.817A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.937A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.522A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.398A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.010A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.281A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.054A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.180A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.180A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.654A 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 702 removed outlier: 6.775A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.534A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.876A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.406A 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 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.525A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.646A pdb=" N GLU H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.646A pdb=" N GLU H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 101 through 102 Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.557A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.937A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.398A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.011A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.281A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.054A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE B 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.181A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.181A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.654A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.776A pdb=" N ALA B 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.535A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.876A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.524A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.646A pdb=" N GLU C 10 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.646A pdb=" N GLU C 10 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AE7, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.555A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 99 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 28 through 30 removed outlier: 7.938A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 48 through 55 removed outlier: 7.398A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.010A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN E 122 " --> pdb=" O ASN E 125 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL E 126 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR E 170 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.282A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.180A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.180A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AF8, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.654A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 711 through 715 removed outlier: 3.534A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 718 through 728 removed outlier: 5.877A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.407A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.525A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.646A pdb=" N GLU F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.646A pdb=" N GLU F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AG8, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AG9, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.557A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR G 99 " --> pdb=" O GLN G 91 " (cutoff:3.500A) 1260 hydrogen bonds defined for protein. 3366 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: 6.72 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6976 1.33 - 1.46: 7413 1.46 - 1.59: 11303 1.59 - 1.73: 6 1.73 - 1.86: 144 Bond restraints: 25842 Sorted by residual: bond pdb=" CB LEU E1145 " pdb=" CG LEU E1145 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CB LEU B1145 " pdb=" CG LEU B1145 " ideal model delta sigma weight residual 1.530 1.617 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" CB LEU A1145 " pdb=" CG LEU A1145 " ideal model delta sigma weight residual 1.530 1.617 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CB ASN B 914 " pdb=" CG ASN B 914 " ideal model delta sigma weight residual 1.516 1.423 0.093 2.50e-02 1.60e+03 1.39e+01 bond pdb=" CB ASN A 914 " pdb=" CG ASN A 914 " ideal model delta sigma weight residual 1.516 1.423 0.093 2.50e-02 1.60e+03 1.39e+01 ... (remaining 25837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 28487 1.62 - 3.24: 5709 3.24 - 4.85: 883 4.85 - 6.47: 299 6.47 - 8.09: 69 Bond angle restraints: 35447 Sorted by residual: angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 120.03 128.09 -8.06 9.90e-01 1.02e+00 6.63e+01 angle pdb=" C GLY F 8 " pdb=" N PRO F 9 " pdb=" CA PRO F 9 " ideal model delta sigma weight residual 120.03 128.05 -8.02 9.90e-01 1.02e+00 6.56e+01 angle pdb=" C GLY C 8 " pdb=" N PRO C 9 " pdb=" CA PRO C 9 " ideal model delta sigma weight residual 120.03 128.05 -8.02 9.90e-01 1.02e+00 6.56e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 125.33 -5.67 7.20e-01 1.93e+00 6.20e+01 angle pdb=" C LEU E 861 " pdb=" N PRO E 862 " pdb=" CA PRO E 862 " ideal model delta sigma weight residual 119.66 125.30 -5.64 7.20e-01 1.93e+00 6.13e+01 ... (remaining 35442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15509 17.58 - 35.16: 484 35.16 - 52.75: 47 52.75 - 70.33: 34 70.33 - 87.91: 18 Dihedral angle restraints: 16092 sinusoidal: 5569 harmonic: 10523 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -147.04 61.04 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS E 538 " pdb=" SG CYS E 538 " pdb=" SG CYS E 590 " pdb=" CB CYS E 590 " ideal model delta sinusoidal sigma weight residual -86.00 -147.02 61.02 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -147.01 61.01 1 1.00e+01 1.00e-02 4.95e+01 ... (remaining 16089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3108 0.078 - 0.156: 930 0.156 - 0.234: 185 0.234 - 0.312: 96 0.312 - 0.390: 75 Chirality restraints: 4394 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.18e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.02e+01 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.94e+01 ... (remaining 4391 not shown) Planarity restraints: 4693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1134 " 0.023 2.00e-02 2.50e+03 2.45e-02 7.52e+00 pdb=" CG ASN B1134 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN B1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B1134 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E1134 " 0.023 2.00e-02 2.50e+03 2.45e-02 7.50e+00 pdb=" CG ASN E1134 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN E1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E1134 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.023 2.00e-02 2.50e+03 2.45e-02 7.47e+00 pdb=" CG ASN A1134 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.030 2.00e-02 2.50e+03 ... (remaining 4690 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 11044 2.93 - 3.42: 22347 3.42 - 3.91: 40399 3.91 - 4.41: 44581 4.41 - 4.90: 75440 Nonbonded interactions: 193811 Sorted by model distance: nonbonded pdb=" OD2 ASP E 808 " pdb=" NZ LYS E 811 " model vdw 2.431 3.120 nonbonded pdb=" OD2 ASP A 808 " pdb=" NZ LYS A 811 " model vdw 2.431 3.120 nonbonded pdb=" OD2 ASP B 808 " pdb=" NZ LYS B 811 " model vdw 2.432 3.120 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.453 3.120 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.453 3.120 ... (remaining 193806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 374 or \ (resid 375 through 378 and (name N or name CA or name C or name O or name CB )) \ or resid 379 through 920 or (resid 921 and (name N or name CA or name C or name \ O or name CB )) or resid 922 through 1311)) selection = (chain 'B' and (resid 27 through 510 or (resid 511 through 512 and (name N or na \ me CA or name C or name O or name CB )) or resid 513 through 1311)) selection = (chain 'E' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 374 or \ (resid 375 through 378 and (name N or name CA or name C or name O or name CB )) \ or resid 379 through 920 or (resid 921 and (name N or name CA or name C or name \ O or name CB )) or resid 922 through 1311)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'D' and ((resid 2 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 104)) selection = (chain 'G' and (resid 2 through 60 or (resid 61 through 64 and (name N or name C \ A or name C or name O or name CB )) or resid 65 through 104)) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 8.490 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.710 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.014 0.101 25953 Z= 0.761 Angle : 1.428 8.089 35732 Z= 0.961 Chirality : 0.094 0.390 4394 Planarity : 0.005 0.041 4645 Dihedral : 9.342 87.908 9150 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 3588 helix: 0.56 (0.18), residues: 672 sheet: 1.10 (0.16), residues: 933 loop : 0.56 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 102 TYR 0.028 0.004 TYR B 495 PHE 0.021 0.003 PHE B 58 TRP 0.019 0.006 TRP B1102 HIS 0.005 0.002 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.01337 (25842) covalent geometry : angle 1.41236 (35447) SS BOND : bond 0.02184 ( 48) SS BOND : angle 2.78252 ( 96) hydrogen bonds : bond 0.15588 ( 1248) hydrogen bonds : angle 8.20705 ( 3366) link_BETA1-4 : bond 0.06769 ( 15) link_BETA1-4 : angle 3.83044 ( 45) link_NAG-ASN : bond 0.06719 ( 48) link_NAG-ASN : angle 2.28903 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.5886 (t80) cc_final: 0.5664 (t80) REVERT: A 423 TYR cc_start: 0.6877 (t80) cc_final: 0.6343 (t80) REVERT: A 734 THR cc_start: 0.8866 (m) cc_final: 0.8543 (p) REVERT: A 875 SER cc_start: 0.8675 (t) cc_final: 0.8199 (p) REVERT: B 61 ASN cc_start: 0.5844 (t0) cc_final: 0.5422 (p0) REVERT: B 734 THR cc_start: 0.8977 (m) cc_final: 0.8677 (p) REVERT: B 875 SER cc_start: 0.8674 (t) cc_final: 0.8207 (p) REVERT: E 61 ASN cc_start: 0.6185 (t0) cc_final: 0.5778 (p0) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.1709 time to fit residues: 95.3423 Evaluate side-chains 164 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.0370 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 957 GLN A1005 GLN A1010 GLN B 957 GLN B1005 GLN B1010 GLN E 762 GLN E 957 GLN E1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.151037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.104971 restraints weight = 46063.929| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.60 r_work: 0.3143 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 25953 Z= 0.163 Angle : 0.626 18.992 35732 Z= 0.324 Chirality : 0.047 0.268 4394 Planarity : 0.004 0.037 4645 Dihedral : 5.138 42.713 5118 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.83 % Allowed : 6.58 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.14), residues: 3588 helix: 2.06 (0.19), residues: 645 sheet: 1.26 (0.16), residues: 957 loop : 0.44 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 237 TYR 0.018 0.001 TYR A 265 PHE 0.024 0.002 PHE E 133 TRP 0.011 0.001 TRP A 104 HIS 0.003 0.001 HIS E 655 Details of bonding type rmsd covalent geometry : bond 0.00361 (25842) covalent geometry : angle 0.57919 (35447) SS BOND : bond 0.00213 ( 48) SS BOND : angle 2.50094 ( 96) hydrogen bonds : bond 0.04614 ( 1248) hydrogen bonds : angle 6.12562 ( 3366) link_BETA1-4 : bond 0.00576 ( 15) link_BETA1-4 : angle 2.36889 ( 45) link_NAG-ASN : bond 0.00486 ( 48) link_NAG-ASN : angle 2.96414 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 342 PHE cc_start: 0.7928 (m-80) cc_final: 0.7621 (m-10) REVERT: A 734 THR cc_start: 0.9205 (m) cc_final: 0.8903 (p) REVERT: B 61 ASN cc_start: 0.6917 (t0) cc_final: 0.6123 (p0) REVERT: B 734 THR cc_start: 0.9250 (m) cc_final: 0.8959 (p) REVERT: B 875 SER cc_start: 0.9231 (t) cc_final: 0.8874 (p) REVERT: B 904 TYR cc_start: 0.8583 (m-10) cc_final: 0.8143 (m-10) REVERT: E 61 ASN cc_start: 0.6558 (t0) cc_final: 0.6166 (p0) REVERT: E 342 PHE cc_start: 0.8100 (m-80) cc_final: 0.7547 (m-80) REVERT: E 380 TYR cc_start: 0.6836 (m-80) cc_final: 0.6635 (m-10) REVERT: E 423 TYR cc_start: 0.5810 (t80) cc_final: 0.5428 (t80) REVERT: E 875 SER cc_start: 0.9139 (t) cc_final: 0.8839 (p) outliers start: 16 outliers final: 10 residues processed: 204 average time/residue: 0.1421 time to fit residues: 48.5318 Evaluate side-chains 154 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 723 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 255 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 354 optimal weight: 40.0000 chunk 153 optimal weight: 0.0020 chunk 353 optimal weight: 40.0000 chunk 341 optimal weight: 40.0000 chunk 319 optimal weight: 0.4980 chunk 177 optimal weight: 0.9980 chunk 105 optimal weight: 40.0000 chunk 127 optimal weight: 2.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 957 GLN A1071 GLN B 901 GLN B1071 GLN E 957 GLN E1071 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.148318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.101562 restraints weight = 45943.032| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.50 r_work: 0.3084 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 25953 Z= 0.202 Angle : 0.574 18.499 35732 Z= 0.295 Chirality : 0.047 0.204 4394 Planarity : 0.004 0.037 4645 Dihedral : 4.490 36.321 5118 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.55 % Allowed : 7.98 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.14), residues: 3588 helix: 2.21 (0.20), residues: 645 sheet: 0.97 (0.16), residues: 972 loop : 0.35 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 905 TYR 0.018 0.001 TYR A 380 PHE 0.016 0.002 PHE A 86 TRP 0.012 0.002 TRP B 886 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00467 (25842) covalent geometry : angle 0.54161 (35447) SS BOND : bond 0.00202 ( 48) SS BOND : angle 1.54728 ( 96) hydrogen bonds : bond 0.04085 ( 1248) hydrogen bonds : angle 5.66082 ( 3366) link_BETA1-4 : bond 0.00532 ( 15) link_BETA1-4 : angle 1.90280 ( 45) link_NAG-ASN : bond 0.00603 ( 48) link_NAG-ASN : angle 2.61957 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8113 (t80) REVERT: A 734 THR cc_start: 0.9237 (m) cc_final: 0.8899 (p) REVERT: B 61 ASN cc_start: 0.6674 (t0) cc_final: 0.5994 (p0) REVERT: B 306 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: B 423 TYR cc_start: 0.7108 (t80) cc_final: 0.6730 (t80) REVERT: B 734 THR cc_start: 0.9277 (m) cc_final: 0.8893 (p) REVERT: B 875 SER cc_start: 0.9244 (t) cc_final: 0.8898 (p) REVERT: E 61 ASN cc_start: 0.6770 (t0) cc_final: 0.6339 (p0) REVERT: E 306 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7740 (t80) REVERT: E 423 TYR cc_start: 0.5882 (t80) cc_final: 0.5629 (t80) REVERT: E 900 MET cc_start: 0.8975 (mtp) cc_final: 0.8724 (mtp) outliers start: 30 outliers final: 14 residues processed: 172 average time/residue: 0.1387 time to fit residues: 41.1659 Evaluate side-chains 147 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 161 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 197 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 344 optimal weight: 6.9990 chunk 245 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 314 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 957 GLN B 957 GLN E 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.147630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.108493 restraints weight = 45842.115| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.23 r_work: 0.3141 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25953 Z= 0.195 Angle : 0.554 15.661 35732 Z= 0.280 Chirality : 0.046 0.196 4394 Planarity : 0.004 0.055 4645 Dihedral : 4.255 33.257 5118 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.81 % Allowed : 9.12 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.14), residues: 3588 helix: 2.15 (0.20), residues: 666 sheet: 0.68 (0.16), residues: 990 loop : 0.28 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.016 0.001 TYR E 365 PHE 0.021 0.002 PHE A 377 TRP 0.011 0.001 TRP B 886 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00458 (25842) covalent geometry : angle 0.52334 (35447) SS BOND : bond 0.00145 ( 48) SS BOND : angle 1.39098 ( 96) hydrogen bonds : bond 0.03847 ( 1248) hydrogen bonds : angle 5.57597 ( 3366) link_BETA1-4 : bond 0.00489 ( 15) link_BETA1-4 : angle 1.81927 ( 45) link_NAG-ASN : bond 0.00456 ( 48) link_NAG-ASN : angle 2.50808 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8092 (t80) REVERT: A 377 PHE cc_start: 0.6490 (t80) cc_final: 0.6249 (t80) REVERT: B 61 ASN cc_start: 0.6642 (t0) cc_final: 0.5956 (p0) REVERT: B 306 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8164 (t80) REVERT: E 61 ASN cc_start: 0.6798 (t0) cc_final: 0.6331 (p0) REVERT: E 102 ARG cc_start: 0.6918 (ptp90) cc_final: 0.6280 (ptt90) REVERT: E 306 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7818 (t80) REVERT: E 423 TYR cc_start: 0.6062 (t80) cc_final: 0.5814 (t80) REVERT: E 900 MET cc_start: 0.8859 (mtp) cc_final: 0.8624 (mtp) outliers start: 35 outliers final: 21 residues processed: 163 average time/residue: 0.1247 time to fit residues: 35.7343 Evaluate side-chains 149 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 170 optimal weight: 0.5980 chunk 256 optimal weight: 7.9990 chunk 354 optimal weight: 30.0000 chunk 172 optimal weight: 1.9990 chunk 232 optimal weight: 40.0000 chunk 342 optimal weight: 0.0770 chunk 9 optimal weight: 6.9990 chunk 359 optimal weight: 40.0000 chunk 162 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 907 ASN A 957 GLN B 540 ASN E 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.145692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105735 restraints weight = 45754.420| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.21 r_work: 0.3104 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 25953 Z= 0.270 Angle : 0.606 14.335 35732 Z= 0.305 Chirality : 0.048 0.191 4394 Planarity : 0.004 0.041 4645 Dihedral : 4.524 33.737 5118 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.28 % Allowed : 9.12 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3588 helix: 2.06 (0.20), residues: 648 sheet: 0.55 (0.16), residues: 963 loop : 0.14 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 905 TYR 0.016 0.002 TYR E 380 PHE 0.018 0.002 PHE E 898 TRP 0.013 0.002 TRP A 886 HIS 0.007 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00638 (25842) covalent geometry : angle 0.57791 (35447) SS BOND : bond 0.00542 ( 48) SS BOND : angle 1.27491 ( 96) hydrogen bonds : bond 0.04141 ( 1248) hydrogen bonds : angle 5.57028 ( 3366) link_BETA1-4 : bond 0.00456 ( 15) link_BETA1-4 : angle 1.79619 ( 45) link_NAG-ASN : bond 0.00484 ( 48) link_NAG-ASN : angle 2.62938 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7018 (ptp90) cc_final: 0.6477 (ptt90) REVERT: A 306 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.7970 (t80) REVERT: B 61 ASN cc_start: 0.6587 (t0) cc_final: 0.6038 (p0) REVERT: B 306 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8097 (t80) REVERT: E 61 ASN cc_start: 0.6898 (t0) cc_final: 0.6294 (p0) REVERT: E 102 ARG cc_start: 0.7045 (ptp90) cc_final: 0.6291 (ptt90) REVERT: E 306 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7750 (t80) REVERT: E 423 TYR cc_start: 0.6359 (t80) cc_final: 0.6034 (t80) REVERT: E 900 MET cc_start: 0.8916 (mtp) cc_final: 0.8703 (mtp) outliers start: 44 outliers final: 30 residues processed: 167 average time/residue: 0.1352 time to fit residues: 39.3341 Evaluate side-chains 153 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 902 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 272 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 345 optimal weight: 5.9990 chunk 131 optimal weight: 0.0870 chunk 303 optimal weight: 0.6980 chunk 154 optimal weight: 20.0000 chunk 169 optimal weight: 0.0060 chunk 200 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 306 optimal weight: 0.7980 chunk 357 optimal weight: 0.7980 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN E 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.147423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.100393 restraints weight = 45918.099| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.49 r_work: 0.3065 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25953 Z= 0.127 Angle : 0.511 13.345 35732 Z= 0.257 Chirality : 0.045 0.184 4394 Planarity : 0.004 0.040 4645 Dihedral : 4.047 30.763 5118 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.92 % Allowed : 9.43 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.14), residues: 3588 helix: 2.38 (0.20), residues: 648 sheet: 0.67 (0.16), residues: 978 loop : 0.19 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.013 0.001 TYR B1067 PHE 0.021 0.001 PHE A 377 TRP 0.006 0.001 TRP A 353 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00287 (25842) covalent geometry : angle 0.48456 (35447) SS BOND : bond 0.00216 ( 48) SS BOND : angle 1.13173 ( 96) hydrogen bonds : bond 0.03477 ( 1248) hydrogen bonds : angle 5.35780 ( 3366) link_BETA1-4 : bond 0.00495 ( 15) link_BETA1-4 : angle 1.54419 ( 45) link_NAG-ASN : bond 0.00354 ( 48) link_NAG-ASN : angle 2.31122 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.781 Fit side-chains REVERT: A 102 ARG cc_start: 0.6909 (ptp90) cc_final: 0.6336 (ptt90) REVERT: A 306 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8051 (t80) REVERT: A 377 PHE cc_start: 0.6422 (t80) cc_final: 0.6130 (t80) REVERT: B 61 ASN cc_start: 0.6549 (t0) cc_final: 0.5972 (p0) REVERT: B 287 ASP cc_start: 0.8635 (t0) cc_final: 0.8256 (t0) REVERT: B 306 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.7819 (t80) REVERT: E 61 ASN cc_start: 0.6778 (t0) cc_final: 0.6218 (p0) REVERT: E 306 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7783 (t80) REVERT: E 423 TYR cc_start: 0.6346 (t80) cc_final: 0.5982 (t80) outliers start: 37 outliers final: 25 residues processed: 155 average time/residue: 0.1384 time to fit residues: 37.2835 Evaluate side-chains 142 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 218 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 113 optimal weight: 40.0000 chunk 105 optimal weight: 40.0000 chunk 84 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 355 optimal weight: 40.0000 chunk 182 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 344 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.143486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.103616 restraints weight = 45923.431| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.12 r_work: 0.3075 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.107 25953 Z= 0.427 Angle : 0.727 12.568 35732 Z= 0.362 Chirality : 0.052 0.223 4394 Planarity : 0.005 0.051 4645 Dihedral : 5.046 40.107 5118 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.44 % Allowed : 9.90 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3588 helix: 1.31 (0.20), residues: 684 sheet: 0.41 (0.17), residues: 933 loop : -0.14 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E1014 TYR 0.017 0.002 TYR E1067 PHE 0.023 0.003 PHE A 220 TRP 0.014 0.002 TRP E 353 HIS 0.009 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.01018 (25842) covalent geometry : angle 0.69606 (35447) SS BOND : bond 0.00291 ( 48) SS BOND : angle 1.68927 ( 96) hydrogen bonds : bond 0.04740 ( 1248) hydrogen bonds : angle 5.75512 ( 3366) link_BETA1-4 : bond 0.00352 ( 15) link_BETA1-4 : angle 1.90557 ( 45) link_NAG-ASN : bond 0.00673 ( 48) link_NAG-ASN : angle 2.98486 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7111 (ptp90) cc_final: 0.6539 (ptt90) REVERT: A 306 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7858 (t80) REVERT: B 61 ASN cc_start: 0.6709 (t0) cc_final: 0.6166 (p0) REVERT: B 306 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.7967 (t80) REVERT: B 904 TYR cc_start: 0.8453 (m-10) cc_final: 0.8122 (m-10) REVERT: E 61 ASN cc_start: 0.6969 (t0) cc_final: 0.6487 (p0) REVERT: E 306 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7757 (t80) REVERT: E 423 TYR cc_start: 0.6669 (t80) cc_final: 0.6277 (t80) outliers start: 47 outliers final: 40 residues processed: 169 average time/residue: 0.1337 time to fit residues: 39.7484 Evaluate side-chains 166 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 33 optimal weight: 20.0000 chunk 271 optimal weight: 0.0570 chunk 56 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 330 optimal weight: 0.0970 chunk 140 optimal weight: 0.6980 chunk 270 optimal weight: 0.9990 chunk 315 optimal weight: 0.5980 chunk 216 optimal weight: 0.6980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.146911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.101775 restraints weight = 45593.392| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.11 r_work: 0.3084 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25953 Z= 0.125 Angle : 0.524 11.923 35732 Z= 0.263 Chirality : 0.045 0.192 4394 Planarity : 0.004 0.040 4645 Dihedral : 4.175 27.041 5118 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.50 % Allowed : 11.14 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.14), residues: 3588 helix: 2.06 (0.20), residues: 666 sheet: 0.65 (0.17), residues: 885 loop : 0.07 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 328 TYR 0.014 0.001 TYR B1067 PHE 0.026 0.001 PHE A 377 TRP 0.007 0.001 TRP E 436 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00285 (25842) covalent geometry : angle 0.49762 (35447) SS BOND : bond 0.00157 ( 48) SS BOND : angle 1.08727 ( 96) hydrogen bonds : bond 0.03488 ( 1248) hydrogen bonds : angle 5.37338 ( 3366) link_BETA1-4 : bond 0.00524 ( 15) link_BETA1-4 : angle 1.48212 ( 45) link_NAG-ASN : bond 0.00370 ( 48) link_NAG-ASN : angle 2.40410 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6949 (ptp90) cc_final: 0.6355 (ptt90) REVERT: A 306 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7872 (t80) REVERT: A 377 PHE cc_start: 0.6503 (t80) cc_final: 0.6204 (t80) REVERT: B 61 ASN cc_start: 0.6552 (t0) cc_final: 0.6042 (p0) REVERT: B 306 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8119 (t80) REVERT: E 61 ASN cc_start: 0.6780 (t0) cc_final: 0.6358 (p0) REVERT: E 306 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.7786 (t80) REVERT: E 423 TYR cc_start: 0.6617 (t80) cc_final: 0.6133 (t80) outliers start: 29 outliers final: 21 residues processed: 149 average time/residue: 0.1393 time to fit residues: 36.1812 Evaluate side-chains 143 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 153 optimal weight: 0.0050 chunk 98 optimal weight: 4.9990 chunk 301 optimal weight: 0.6980 chunk 249 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 211 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 279 optimal weight: 20.0000 chunk 223 optimal weight: 20.0000 chunk 286 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.146243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109758 restraints weight = 45844.019| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.34 r_work: 0.3122 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25953 Z= 0.184 Angle : 0.545 11.371 35732 Z= 0.272 Chirality : 0.045 0.231 4394 Planarity : 0.004 0.037 4645 Dihedral : 4.155 26.196 5118 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.81 % Allowed : 11.14 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3588 helix: 2.03 (0.20), residues: 666 sheet: 0.48 (0.16), residues: 960 loop : 0.05 (0.15), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 905 TYR 0.014 0.001 TYR B1067 PHE 0.021 0.002 PHE A 377 TRP 0.007 0.001 TRP E 353 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00434 (25842) covalent geometry : angle 0.51698 (35447) SS BOND : bond 0.00167 ( 48) SS BOND : angle 1.37021 ( 96) hydrogen bonds : bond 0.03626 ( 1248) hydrogen bonds : angle 5.34116 ( 3366) link_BETA1-4 : bond 0.00406 ( 15) link_BETA1-4 : angle 1.48098 ( 45) link_NAG-ASN : bond 0.00351 ( 48) link_NAG-ASN : angle 2.42014 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7046 (ptp90) cc_final: 0.6483 (ptt90) REVERT: A 306 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7890 (t80) REVERT: B 61 ASN cc_start: 0.6545 (t0) cc_final: 0.6006 (p0) REVERT: B 306 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8120 (t80) REVERT: E 61 ASN cc_start: 0.6835 (t0) cc_final: 0.6404 (p0) REVERT: E 306 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.7817 (t80) REVERT: E 423 TYR cc_start: 0.6669 (t80) cc_final: 0.6232 (t80) REVERT: E 580 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8316 (mt0) outliers start: 35 outliers final: 28 residues processed: 150 average time/residue: 0.1356 time to fit residues: 35.5906 Evaluate side-chains 151 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 580 GLN Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 239 optimal weight: 0.0030 chunk 148 optimal weight: 5.9990 chunk 217 optimal weight: 0.0980 chunk 247 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 317 optimal weight: 0.1980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.147471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.108209 restraints weight = 45594.052| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.09 r_work: 0.3168 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25953 Z= 0.119 Angle : 0.495 10.788 35732 Z= 0.250 Chirality : 0.044 0.182 4394 Planarity : 0.004 0.042 4645 Dihedral : 3.828 26.352 5118 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.55 % Allowed : 11.30 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3588 helix: 2.28 (0.20), residues: 666 sheet: 0.56 (0.16), residues: 966 loop : 0.12 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 237 TYR 0.014 0.001 TYR E1067 PHE 0.024 0.001 PHE A 377 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00276 (25842) covalent geometry : angle 0.47159 (35447) SS BOND : bond 0.00178 ( 48) SS BOND : angle 1.08795 ( 96) hydrogen bonds : bond 0.03216 ( 1248) hydrogen bonds : angle 5.17339 ( 3366) link_BETA1-4 : bond 0.00482 ( 15) link_BETA1-4 : angle 1.31063 ( 45) link_NAG-ASN : bond 0.00304 ( 48) link_NAG-ASN : angle 2.19988 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6898 (ptp90) cc_final: 0.6303 (ptt90) REVERT: A 306 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7890 (t80) REVERT: A 377 PHE cc_start: 0.6393 (t80) cc_final: 0.6135 (t80) REVERT: B 61 ASN cc_start: 0.6490 (t0) cc_final: 0.5959 (p0) REVERT: B 306 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8147 (t80) REVERT: B 875 SER cc_start: 0.9131 (t) cc_final: 0.8801 (p) REVERT: B 1029 MET cc_start: 0.8833 (tpp) cc_final: 0.8395 (ttm) REVERT: E 61 ASN cc_start: 0.6773 (t0) cc_final: 0.6202 (p0) REVERT: E 306 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7771 (t80) REVERT: E 423 TYR cc_start: 0.6636 (t80) cc_final: 0.6190 (t80) REVERT: E 820 ASP cc_start: 0.8423 (t0) cc_final: 0.8183 (t0) outliers start: 30 outliers final: 22 residues processed: 153 average time/residue: 0.1331 time to fit residues: 35.6108 Evaluate side-chains 145 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 250 optimal weight: 5.9990 chunk 223 optimal weight: 20.0000 chunk 313 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 334 optimal weight: 0.9990 chunk 317 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 347 optimal weight: 50.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A 907 ASN E 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.143932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105946 restraints weight = 45905.956| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.24 r_work: 0.3076 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 25953 Z= 0.380 Angle : 0.679 10.700 35732 Z= 0.338 Chirality : 0.050 0.204 4394 Planarity : 0.005 0.045 4645 Dihedral : 4.727 33.489 5118 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.07 % Allowed : 11.04 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3588 helix: 1.63 (0.20), residues: 666 sheet: 0.31 (0.16), residues: 1005 loop : -0.15 (0.15), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 905 TYR 0.019 0.002 TYR E1067 PHE 0.026 0.003 PHE E 86 TRP 0.015 0.002 TRP B 353 HIS 0.007 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00907 (25842) covalent geometry : angle 0.65101 (35447) SS BOND : bond 0.00245 ( 48) SS BOND : angle 1.66612 ( 96) hydrogen bonds : bond 0.04424 ( 1248) hydrogen bonds : angle 5.56001 ( 3366) link_BETA1-4 : bond 0.00320 ( 15) link_BETA1-4 : angle 1.62777 ( 45) link_NAG-ASN : bond 0.00529 ( 48) link_NAG-ASN : angle 2.73169 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7322.14 seconds wall clock time: 125 minutes 8.51 seconds (7508.51 seconds total)