Starting phenix.real_space_refine on Sun May 25 02:28:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c44_45174/05_2025/9c44_45174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c44_45174/05_2025/9c44_45174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c44_45174/05_2025/9c44_45174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c44_45174/05_2025/9c44_45174.map" model { file = "/net/cci-nas-00/data/ceres_data/9c44_45174/05_2025/9c44_45174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c44_45174/05_2025/9c44_45174_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16707 2.51 5 N 4515 2.21 5 O 4998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 1.77s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26337 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7030 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 300} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 1056 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 881 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 15, 'TYR:plan': 18, 'ASN:plan1': 23, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 15, 'GLU:plan': 20, 'ASP:plan': 29} Unresolved non-hydrogen planarities: 639 Chain: "H" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 847 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "L" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 625 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 7030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7030 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 300} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 1056 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 881 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 15, 'TYR:plan': 18, 'ASN:plan1': 23, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 15, 'GLU:plan': 20, 'ASP:plan': 29} Unresolved non-hydrogen planarities: 639 Chain: "E" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 847 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 625 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "C" Number of atoms: 7030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7030 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 300} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 1056 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 881 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 15, 'TYR:plan': 18, 'ASN:plan1': 23, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 15, 'GLU:plan': 20, 'ASP:plan': 29} Unresolved non-hydrogen planarities: 639 Chain: "F" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 847 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 625 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 16.48, per 1000 atoms: 0.63 Number of scatterers: 26337 At special positions: 0 Unit cell: (152.583, 155.955, 178.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4998 8.00 N 4515 7.00 C 16707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.13 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.13 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.13 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 331 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 331 " " NAG I 1 " - " ASN A 122 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN B 122 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN C 122 " " NAG S 1 " - " ASN C 234 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " Time building additional restraints: 6.43 Conformation dependent library (CDL) restraints added in 3.5 seconds 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7020 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 63 sheets defined 23.2% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.96 Creating SS restraints... Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.924A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.765A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.822A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.173A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.500A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.507A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.732A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.089A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.924A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.765A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.822A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.173A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.500A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.507A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.732A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.090A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.924A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.765A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.822A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.173A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.500A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.507A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.732A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.088A pdb=" N ILE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.810A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.525A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.290A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 153 through 155 removed outlier: 6.325A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.933A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.208A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.381A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.606A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.670A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.722A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.722A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.663A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.644A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.827A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.715A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.715A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.810A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.526A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.290A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 153 through 155 removed outlier: 6.325A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.934A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.381A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.606A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.722A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.722A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.663A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.644A pdb=" N MET E 34 " --> pdb=" O PHE E 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.827A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 67 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.715A pdb=" N LEU D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.715A pdb=" N LEU D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.525A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.290A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 153 through 155 removed outlier: 6.325A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.933A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.381A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.606A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.310A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.663A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.644A pdb=" N MET F 34 " --> pdb=" O PHE F 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AG7, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.828A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER G 67 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.715A pdb=" N LEU G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU G 33 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.715A pdb=" N LEU G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) 1363 hydrogen bonds defined for protein. 3594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.61 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4897 1.32 - 1.45: 6675 1.45 - 1.57: 15146 1.57 - 1.70: 18 1.70 - 1.82: 144 Bond restraints: 26880 Sorted by residual: bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.93e+00 ... (remaining 26875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 31879 1.62 - 3.24: 4132 3.24 - 4.86: 463 4.86 - 6.48: 267 6.48 - 8.10: 177 Bond angle restraints: 36918 Sorted by residual: angle pdb=" C LEU B 861 " pdb=" N PRO B 862 " pdb=" CA PRO B 862 " ideal model delta sigma weight residual 119.66 126.45 -6.79 7.20e-01 1.93e+00 8.89e+01 angle pdb=" C LEU C 861 " pdb=" N PRO C 862 " pdb=" CA PRO C 862 " ideal model delta sigma weight residual 119.66 126.43 -6.77 7.20e-01 1.93e+00 8.84e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.43 -6.77 7.20e-01 1.93e+00 8.84e+01 angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 126.35 -6.69 7.20e-01 1.93e+00 8.64e+01 angle pdb=" C THR B 791 " pdb=" N PRO B 792 " pdb=" CA PRO B 792 " ideal model delta sigma weight residual 119.66 126.32 -6.66 7.20e-01 1.93e+00 8.56e+01 ... (remaining 36913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 16156 21.34 - 42.67: 275 42.67 - 64.01: 84 64.01 - 85.35: 36 85.35 - 106.68: 24 Dihedral angle restraints: 16575 sinusoidal: 5688 harmonic: 10887 Sorted by residual: dihedral pdb=" CD ARG C 319 " pdb=" NE ARG C 319 " pdb=" CZ ARG C 319 " pdb=" NH1 ARG C 319 " ideal model delta sinusoidal sigma weight residual 0.00 79.96 -79.96 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CD ARG A 319 " pdb=" NE ARG A 319 " pdb=" CZ ARG A 319 " pdb=" NH1 ARG A 319 " ideal model delta sinusoidal sigma weight residual 0.00 79.94 -79.94 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CD ARG B 319 " pdb=" NE ARG B 319 " pdb=" CZ ARG B 319 " pdb=" NH1 ARG B 319 " ideal model delta sinusoidal sigma weight residual 0.00 79.89 -79.89 1 1.00e+01 1.00e-02 7.92e+01 ... (remaining 16572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3532 0.077 - 0.154: 792 0.154 - 0.231: 155 0.231 - 0.308: 21 0.308 - 0.386: 48 Chirality restraints: 4548 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.00e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.98e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.79e+01 ... (remaining 4545 not shown) Planarity restraints: 4875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 319 " -1.081 9.50e-02 1.11e+02 4.85e-01 1.42e+02 pdb=" NE ARG B 319 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 319 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 319 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 319 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 319 " -1.081 9.50e-02 1.11e+02 4.85e-01 1.42e+02 pdb=" NE ARG A 319 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 319 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 319 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 319 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 319 " -1.081 9.50e-02 1.11e+02 4.84e-01 1.42e+02 pdb=" NE ARG C 319 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 319 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 319 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG C 319 " -0.019 2.00e-02 2.50e+03 ... (remaining 4872 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 12580 2.96 - 3.45: 23178 3.45 - 3.93: 42694 3.93 - 4.42: 47307 4.42 - 4.90: 79387 Nonbonded interactions: 205146 Sorted by model distance: nonbonded pdb=" NZ LYS B 557 " pdb=" OD1 ASP B 586 " model vdw 2.477 3.120 nonbonded pdb=" NZ LYS A 557 " pdb=" OD1 ASP A 586 " model vdw 2.477 3.120 nonbonded pdb=" NZ LYS C 557 " pdb=" OD1 ASP C 586 " model vdw 2.477 3.120 nonbonded pdb=" O GLU C1092 " pdb=" NH1 ARG C1107 " model vdw 2.534 3.120 nonbonded pdb=" O GLU B1092 " pdb=" NH1 ARG B1107 " model vdw 2.534 3.120 ... (remaining 205141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'O' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.520 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: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 64.560 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.170 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.102 26985 Z= 0.563 Angle : 1.305 8.096 37188 Z= 0.868 Chirality : 0.076 0.386 4548 Planarity : 0.013 0.485 4830 Dihedral : 11.220 106.685 9420 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.29 % Allowed : 0.88 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.13), residues: 3708 helix: 0.27 (0.18), residues: 699 sheet: 0.95 (0.15), residues: 1101 loop : 0.40 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.005 TRP A 886 HIS 0.004 0.001 HIS C 655 PHE 0.022 0.004 PHE C 898 TYR 0.035 0.005 TYR C1067 ARG 0.004 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01232 ( 45) link_NAG-ASN : angle 2.81165 ( 135) link_BETA1-4 : bond 0.03703 ( 15) link_BETA1-4 : angle 3.54297 ( 45) hydrogen bonds : bond 0.16921 ( 1291) hydrogen bonds : angle 8.33800 ( 3594) SS BOND : bond 0.02770 ( 45) SS BOND : angle 3.16006 ( 90) covalent geometry : bond 0.00987 (26880) covalent geometry : angle 1.28299 (36918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 323 time to evaluate : 2.527 Fit side-chains REVERT: A 633 TRP cc_start: 0.7500 (OUTLIER) cc_final: 0.6728 (m100) REVERT: A 773 GLU cc_start: 0.7778 (tt0) cc_final: 0.7568 (tt0) REVERT: B 633 TRP cc_start: 0.7539 (OUTLIER) cc_final: 0.6748 (m100) REVERT: B 773 GLU cc_start: 0.7770 (tt0) cc_final: 0.7539 (tt0) REVERT: C 319 ARG cc_start: 0.7081 (mtp85) cc_final: 0.6857 (mtp180) outliers start: 6 outliers final: 2 residues processed: 329 average time/residue: 1.4086 time to fit residues: 535.2175 Evaluate side-chains 226 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 633 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.9990 chunk 281 optimal weight: 50.0000 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 291 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 217 optimal weight: 0.4980 chunk 337 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 641 ASN A 655 HIS A 658 ASN A 751 ASN A 907 ASN A 913 GLN A1002 GLN A1005 GLN A1010 GLN A1113 GLN H 77 ASN B 658 ASN B 784 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN B1113 GLN E 77 ASN C 317 ASN C 613 GLN C 658 ASN C 907 ASN C 913 GLN C 957 GLN C 978 ASN C1005 GLN C1010 GLN C1011 GLN C1113 GLN F 77 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.222937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.174051 restraints weight = 26277.208| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 5.03 r_work: 0.3326 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26985 Z= 0.141 Angle : 0.563 7.262 37188 Z= 0.299 Chirality : 0.046 0.160 4548 Planarity : 0.005 0.098 4830 Dihedral : 6.269 70.401 5207 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.66 % Allowed : 5.90 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.14), residues: 3708 helix: 1.75 (0.20), residues: 675 sheet: 1.25 (0.16), residues: 1041 loop : 0.64 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 886 HIS 0.004 0.001 HIS B1088 PHE 0.014 0.002 PHE A 898 TYR 0.025 0.002 TYR C1067 ARG 0.005 0.001 ARG E 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 45) link_NAG-ASN : angle 2.27680 ( 135) link_BETA1-4 : bond 0.00387 ( 15) link_BETA1-4 : angle 1.75538 ( 45) hydrogen bonds : bond 0.05254 ( 1291) hydrogen bonds : angle 6.18892 ( 3594) SS BOND : bond 0.00327 ( 45) SS BOND : angle 1.14426 ( 90) covalent geometry : bond 0.00318 (26880) covalent geometry : angle 0.54145 (36918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 2.531 Fit side-chains REVERT: A 633 TRP cc_start: 0.7640 (OUTLIER) cc_final: 0.7074 (m100) REVERT: A 750 SER cc_start: 0.8432 (t) cc_final: 0.7988 (m) REVERT: A 751 ASN cc_start: 0.8518 (m-40) cc_final: 0.8219 (m110) REVERT: A 773 GLU cc_start: 0.8529 (tt0) cc_final: 0.8216 (tt0) REVERT: B 633 TRP cc_start: 0.7690 (OUTLIER) cc_final: 0.7222 (m100) REVERT: B 773 GLU cc_start: 0.8502 (tt0) cc_final: 0.8226 (tt0) REVERT: B 1010 GLN cc_start: 0.8505 (pt0) cc_final: 0.8156 (mm-40) REVERT: C 196 ASN cc_start: 0.8268 (t0) cc_final: 0.8006 (t0) REVERT: C 314 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8423 (tt0) REVERT: F 52 ARG cc_start: 0.8592 (mtp180) cc_final: 0.8255 (mtp85) REVERT: F 95 TYR cc_start: 0.6745 (m-80) cc_final: 0.6381 (m-80) outliers start: 34 outliers final: 12 residues processed: 237 average time/residue: 1.0733 time to fit residues: 304.9435 Evaluate side-chains 224 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 633 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 2.9990 chunk 274 optimal weight: 0.0370 chunk 59 optimal weight: 2.9990 chunk 367 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 194 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 163 optimal weight: 40.0000 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 613 GLN A 658 ASN A 784 GLN A 804 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN A1010 GLN B 613 GLN B 641 ASN B 751 ASN B 784 GLN B 804 GLN B 907 ASN B 913 GLN B1002 GLN B1005 GLN B1113 GLN E 77 ASN C 317 ASN C 641 ASN C 658 ASN C 751 ASN C 804 GLN C 957 GLN C1002 GLN C1005 GLN C1010 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.221425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.174170 restraints weight = 26010.772| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 4.61 r_work: 0.3233 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26985 Z= 0.167 Angle : 0.545 6.418 37188 Z= 0.289 Chirality : 0.046 0.153 4548 Planarity : 0.004 0.043 4830 Dihedral : 4.876 57.586 5207 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.80 % Allowed : 5.85 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.14), residues: 3708 helix: 2.12 (0.21), residues: 636 sheet: 1.20 (0.16), residues: 1038 loop : 0.51 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 886 HIS 0.005 0.001 HIS B 625 PHE 0.022 0.002 PHE B 898 TYR 0.025 0.002 TYR C1067 ARG 0.008 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 45) link_NAG-ASN : angle 2.06397 ( 135) link_BETA1-4 : bond 0.00449 ( 15) link_BETA1-4 : angle 1.60902 ( 45) hydrogen bonds : bond 0.05279 ( 1291) hydrogen bonds : angle 5.79810 ( 3594) SS BOND : bond 0.00766 ( 45) SS BOND : angle 1.07069 ( 90) covalent geometry : bond 0.00392 (26880) covalent geometry : angle 0.52655 (36918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 2.516 Fit side-chains REVERT: A 314 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: A 633 TRP cc_start: 0.7425 (OUTLIER) cc_final: 0.6618 (m100) REVERT: A 751 ASN cc_start: 0.8495 (m-40) cc_final: 0.8204 (m110) REVERT: A 773 GLU cc_start: 0.8467 (tt0) cc_final: 0.8090 (tt0) REVERT: A 935 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: B 196 ASN cc_start: 0.8250 (t0) cc_final: 0.8030 (m-40) REVERT: B 633 TRP cc_start: 0.7461 (OUTLIER) cc_final: 0.6631 (m100) REVERT: B 773 GLU cc_start: 0.8457 (tt0) cc_final: 0.8081 (tt0) REVERT: B 1010 GLN cc_start: 0.8460 (pt0) cc_final: 0.8077 (mm-40) REVERT: C 191 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7484 (mt-10) REVERT: C 314 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: C 790 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8293 (mmmt) REVERT: F 34 MET cc_start: 0.7700 (mmm) cc_final: 0.7409 (mmt) REVERT: F 95 TYR cc_start: 0.7110 (m-80) cc_final: 0.6762 (m-80) outliers start: 37 outliers final: 11 residues processed: 248 average time/residue: 1.1287 time to fit residues: 333.8648 Evaluate side-chains 234 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 4 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 165 optimal weight: 30.0000 chunk 5 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 313 optimal weight: 2.9990 chunk 160 optimal weight: 50.0000 chunk 44 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 613 GLN A 658 ASN A 957 GLN A1010 GLN B 658 ASN B 751 ASN B 784 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 658 ASN C 751 ASN C1002 GLN C1005 GLN C1010 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.220589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.173604 restraints weight = 26133.458| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 4.68 r_work: 0.3292 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 26985 Z= 0.209 Angle : 0.586 7.317 37188 Z= 0.308 Chirality : 0.048 0.158 4548 Planarity : 0.004 0.041 4830 Dihedral : 4.507 57.469 5205 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.10 % Allowed : 6.29 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.14), residues: 3708 helix: 1.85 (0.21), residues: 642 sheet: 1.12 (0.16), residues: 1047 loop : 0.33 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B1102 HIS 0.005 0.002 HIS B1088 PHE 0.026 0.002 PHE A 898 TYR 0.027 0.002 TYR C1067 ARG 0.005 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 45) link_NAG-ASN : angle 2.14283 ( 135) link_BETA1-4 : bond 0.00403 ( 15) link_BETA1-4 : angle 1.47796 ( 45) hydrogen bonds : bond 0.05617 ( 1291) hydrogen bonds : angle 5.76099 ( 3594) SS BOND : bond 0.00364 ( 45) SS BOND : angle 1.41646 ( 90) covalent geometry : bond 0.00507 (26880) covalent geometry : angle 0.56688 (36918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 2.631 Fit side-chains revert: symmetry clash REVERT: A 294 ASP cc_start: 0.7446 (p0) cc_final: 0.7221 (p0) REVERT: A 633 TRP cc_start: 0.7724 (OUTLIER) cc_final: 0.6984 (m100) REVERT: A 773 GLU cc_start: 0.8630 (tt0) cc_final: 0.8383 (tt0) REVERT: B 298 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: B 633 TRP cc_start: 0.7767 (OUTLIER) cc_final: 0.6824 (m100) REVERT: B 773 GLU cc_start: 0.8706 (tt0) cc_final: 0.8252 (tt0) REVERT: B 1038 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8243 (mptt) REVERT: C 314 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: C 750 SER cc_start: 0.8448 (t) cc_final: 0.7962 (m) REVERT: C 790 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8347 (mmmt) REVERT: F 34 MET cc_start: 0.7849 (mmm) cc_final: 0.7574 (mmt) REVERT: F 95 TYR cc_start: 0.7295 (m-80) cc_final: 0.6945 (m-80) outliers start: 43 outliers final: 14 residues processed: 242 average time/residue: 1.1933 time to fit residues: 342.6915 Evaluate side-chains 228 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 80 optimal weight: 0.9980 chunk 268 optimal weight: 5.9990 chunk 284 optimal weight: 50.0000 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 249 optimal weight: 0.0170 chunk 294 optimal weight: 6.9990 chunk 280 optimal weight: 40.0000 chunk 19 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 338 optimal weight: 0.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 613 GLN A 641 ASN A 658 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 613 GLN B 658 ASN B 751 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B1005 GLN B1011 GLN E 77 ASN C 196 ASN C 658 ASN C1002 GLN C1005 GLN C1010 GLN F 77 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.221965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.174291 restraints weight = 26150.447| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 4.88 r_work: 0.3334 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26985 Z= 0.126 Angle : 0.502 5.975 37188 Z= 0.263 Chirality : 0.045 0.151 4548 Planarity : 0.004 0.038 4830 Dihedral : 4.052 56.977 5203 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.56 % Allowed : 7.16 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.14), residues: 3708 helix: 2.14 (0.21), residues: 642 sheet: 1.16 (0.16), residues: 1044 loop : 0.33 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.004 0.001 HIS B1088 PHE 0.017 0.001 PHE B 898 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 45) link_NAG-ASN : angle 1.86714 ( 135) link_BETA1-4 : bond 0.00384 ( 15) link_BETA1-4 : angle 1.25199 ( 45) hydrogen bonds : bond 0.04541 ( 1291) hydrogen bonds : angle 5.46981 ( 3594) SS BOND : bond 0.00250 ( 45) SS BOND : angle 1.02137 ( 90) covalent geometry : bond 0.00289 (26880) covalent geometry : angle 0.48663 (36918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8778 (m-80) cc_final: 0.8557 (m-80) REVERT: A 633 TRP cc_start: 0.7697 (OUTLIER) cc_final: 0.6899 (m100) REVERT: A 773 GLU cc_start: 0.8536 (tt0) cc_final: 0.8108 (tt0) REVERT: A 935 GLN cc_start: 0.7466 (tt0) cc_final: 0.7243 (tt0) REVERT: B 633 TRP cc_start: 0.7735 (OUTLIER) cc_final: 0.6793 (m100) REVERT: B 773 GLU cc_start: 0.8583 (tt0) cc_final: 0.8155 (tt0) REVERT: B 1010 GLN cc_start: 0.8605 (pt0) cc_final: 0.8169 (mm-40) REVERT: C 576 VAL cc_start: 0.8186 (t) cc_final: 0.7893 (p) REVERT: C 750 SER cc_start: 0.8348 (t) cc_final: 0.7888 (m) REVERT: C 790 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8316 (mmmt) REVERT: F 34 MET cc_start: 0.7797 (mmm) cc_final: 0.7455 (mmt) REVERT: F 95 TYR cc_start: 0.7224 (m-80) cc_final: 0.6917 (m-80) outliers start: 32 outliers final: 11 residues processed: 239 average time/residue: 1.1134 time to fit residues: 317.9362 Evaluate side-chains 222 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 230 optimal weight: 3.9990 chunk 282 optimal weight: 50.0000 chunk 248 optimal weight: 30.0000 chunk 119 optimal weight: 0.0030 chunk 36 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 349 optimal weight: 0.2980 chunk 6 optimal weight: 0.3980 chunk 330 optimal weight: 8.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 580 GLN A 613 GLN A 658 ASN A 779 GLN A 907 ASN A1002 GLN A1010 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 613 GLN B 658 ASN B 751 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1113 GLN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 658 ASN C 751 ASN C 907 ASN C1002 GLN C1005 GLN C1010 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.221369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.173398 restraints weight = 26007.084| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 4.89 r_work: 0.3282 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26985 Z= 0.150 Angle : 0.521 7.018 37188 Z= 0.272 Chirality : 0.046 0.153 4548 Planarity : 0.004 0.038 4830 Dihedral : 4.078 56.598 5203 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.71 % Allowed : 7.46 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.14), residues: 3708 helix: 2.00 (0.21), residues: 663 sheet: 1.14 (0.16), residues: 1044 loop : 0.24 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 64 HIS 0.004 0.001 HIS B1088 PHE 0.020 0.002 PHE B 898 TYR 0.024 0.001 TYR C1067 ARG 0.003 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 45) link_NAG-ASN : angle 1.89774 ( 135) link_BETA1-4 : bond 0.00377 ( 15) link_BETA1-4 : angle 1.23621 ( 45) hydrogen bonds : bond 0.04806 ( 1291) hydrogen bonds : angle 5.44968 ( 3594) SS BOND : bond 0.00263 ( 45) SS BOND : angle 1.10281 ( 90) covalent geometry : bond 0.00353 (26880) covalent geometry : angle 0.50533 (36918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 2.570 Fit side-chains revert: symmetry clash REVERT: A 613 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: A 773 GLU cc_start: 0.8656 (tt0) cc_final: 0.8217 (tt0) REVERT: A 1002 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: B 633 TRP cc_start: 0.7702 (OUTLIER) cc_final: 0.6790 (m100) REVERT: B 773 GLU cc_start: 0.8644 (tt0) cc_final: 0.8190 (tt0) REVERT: B 1010 GLN cc_start: 0.8648 (pt0) cc_final: 0.8226 (mt0) REVERT: C 750 SER cc_start: 0.8306 (t) cc_final: 0.7849 (m) REVERT: C 790 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8346 (mmmt) REVERT: F 34 MET cc_start: 0.7816 (mmm) cc_final: 0.7463 (mmt) REVERT: F 95 TYR cc_start: 0.7295 (m-80) cc_final: 0.6947 (m-80) outliers start: 35 outliers final: 17 residues processed: 233 average time/residue: 1.1319 time to fit residues: 317.3041 Evaluate side-chains 224 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 148 optimal weight: 4.9990 chunk 265 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 294 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 364 optimal weight: 50.0000 chunk 354 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 327 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 658 ASN A1010 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 658 ASN B 751 ASN B 907 ASN B1005 GLN E 77 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C1002 GLN C1005 GLN C1010 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.220518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.171859 restraints weight = 26074.235| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 4.96 r_work: 0.3255 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26985 Z= 0.193 Angle : 0.556 7.140 37188 Z= 0.291 Chirality : 0.047 0.157 4548 Planarity : 0.004 0.039 4830 Dihedral : 4.094 56.651 5201 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.46 % Allowed : 7.89 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3708 helix: 1.88 (0.21), residues: 663 sheet: 1.13 (0.16), residues: 1029 loop : 0.16 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 104 HIS 0.005 0.001 HIS B1088 PHE 0.024 0.002 PHE A 898 TYR 0.025 0.002 TYR C1067 ARG 0.005 0.000 ARG A1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 45) link_NAG-ASN : angle 1.97285 ( 135) link_BETA1-4 : bond 0.00395 ( 15) link_BETA1-4 : angle 1.25893 ( 45) hydrogen bonds : bond 0.05236 ( 1291) hydrogen bonds : angle 5.51238 ( 3594) SS BOND : bond 0.00343 ( 45) SS BOND : angle 1.25518 ( 90) covalent geometry : bond 0.00466 (26880) covalent geometry : angle 0.53981 (36918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.8658 (tt0) cc_final: 0.8389 (tt0) REVERT: B 298 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: B 633 TRP cc_start: 0.7712 (OUTLIER) cc_final: 0.6691 (m100) REVERT: B 773 GLU cc_start: 0.8713 (tt0) cc_final: 0.8253 (tt0) REVERT: C 750 SER cc_start: 0.8346 (t) cc_final: 0.7877 (m) REVERT: C 790 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8369 (mmmt) REVERT: F 95 TYR cc_start: 0.7356 (m-80) cc_final: 0.7018 (m-80) outliers start: 30 outliers final: 17 residues processed: 232 average time/residue: 1.1464 time to fit residues: 316.7677 Evaluate side-chains 224 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 0 optimal weight: 30.0000 chunk 101 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 279 optimal weight: 40.0000 chunk 235 optimal weight: 9.9990 chunk 158 optimal weight: 50.0000 chunk 352 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 202 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 658 ASN A1002 GLN A1010 GLN B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 658 ASN B 751 ASN B1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 658 ASN C 751 ASN C1002 GLN C1005 GLN C1010 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.221709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.175856 restraints weight = 26067.606| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 4.57 r_work: 0.3315 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26985 Z= 0.124 Angle : 0.503 7.233 37188 Z= 0.263 Chirality : 0.045 0.150 4548 Planarity : 0.004 0.038 4830 Dihedral : 3.921 56.280 5201 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.36 % Allowed : 8.04 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.14), residues: 3708 helix: 2.07 (0.21), residues: 663 sheet: 1.09 (0.16), residues: 1020 loop : 0.20 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.004 0.001 HIS B1088 PHE 0.017 0.001 PHE B 898 TYR 0.021 0.001 TYR C1067 ARG 0.002 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 45) link_NAG-ASN : angle 1.83468 ( 135) link_BETA1-4 : bond 0.00368 ( 15) link_BETA1-4 : angle 1.21324 ( 45) hydrogen bonds : bond 0.04508 ( 1291) hydrogen bonds : angle 5.36025 ( 3594) SS BOND : bond 0.00220 ( 45) SS BOND : angle 1.01814 ( 90) covalent geometry : bond 0.00284 (26880) covalent geometry : angle 0.48852 (36918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8814 (m-80) cc_final: 0.8605 (m-80) REVERT: A 633 TRP cc_start: 0.7698 (OUTLIER) cc_final: 0.6950 (m100) REVERT: A 773 GLU cc_start: 0.8538 (tt0) cc_final: 0.8091 (tt0) REVERT: B 576 VAL cc_start: 0.8172 (t) cc_final: 0.7950 (p) REVERT: B 773 GLU cc_start: 0.8606 (tt0) cc_final: 0.8188 (tt0) REVERT: B 1010 GLN cc_start: 0.8637 (pt0) cc_final: 0.8180 (mt0) REVERT: C 576 VAL cc_start: 0.8188 (t) cc_final: 0.7889 (p) REVERT: C 750 SER cc_start: 0.8322 (t) cc_final: 0.7889 (m) REVERT: C 790 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8332 (mmmt) REVERT: F 34 MET cc_start: 0.7779 (mmm) cc_final: 0.7514 (mmt) outliers start: 28 outliers final: 16 residues processed: 227 average time/residue: 1.1894 time to fit residues: 329.9345 Evaluate side-chains 222 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 63 optimal weight: 1.9990 chunk 282 optimal weight: 40.0000 chunk 245 optimal weight: 30.0000 chunk 147 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 163 optimal weight: 50.0000 chunk 23 optimal weight: 3.9990 chunk 340 optimal weight: 0.5980 chunk 295 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 658 ASN A 675 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN H 77 ASN B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 613 GLN B 658 ASN B1005 GLN E 77 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 751 ASN C1005 GLN C1010 GLN F 77 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.228547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.188887 restraints weight = 27081.675| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.94 r_work: 0.3920 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 26985 Z= 0.283 Angle : 0.644 9.189 37188 Z= 0.336 Chirality : 0.051 0.168 4548 Planarity : 0.005 0.040 4830 Dihedral : 4.373 30.305 5199 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.17 % Allowed : 8.43 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.13), residues: 3708 helix: 1.56 (0.21), residues: 663 sheet: 0.99 (0.15), residues: 1047 loop : 0.03 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 104 HIS 0.007 0.002 HIS B1088 PHE 0.032 0.003 PHE A 898 TYR 0.028 0.002 TYR C1067 ARG 0.006 0.001 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 45) link_NAG-ASN : angle 2.19440 ( 135) link_BETA1-4 : bond 0.00393 ( 15) link_BETA1-4 : angle 1.36859 ( 45) hydrogen bonds : bond 0.06126 ( 1291) hydrogen bonds : angle 5.68426 ( 3594) SS BOND : bond 0.00474 ( 45) SS BOND : angle 1.60900 ( 90) covalent geometry : bond 0.00695 (26880) covalent geometry : angle 0.62597 (36918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 633 TRP cc_start: 0.7840 (OUTLIER) cc_final: 0.7000 (m100) REVERT: B 773 GLU cc_start: 0.8399 (tt0) cc_final: 0.7974 (tt0) REVERT: C 750 SER cc_start: 0.8517 (t) cc_final: 0.8141 (m) REVERT: C 790 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8172 (mmmt) outliers start: 24 outliers final: 17 residues processed: 232 average time/residue: 1.1667 time to fit residues: 320.9376 Evaluate side-chains 230 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 196 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 301 optimal weight: 0.7980 chunk 293 optimal weight: 8.9990 chunk 341 optimal weight: 0.5980 chunk 291 optimal weight: 10.0000 chunk 357 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 229 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 275 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 658 ASN A 675 GLN A1002 GLN B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 658 ASN E 77 ASN C 658 ASN C1005 GLN C1010 GLN F 77 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.228589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.187482 restraints weight = 27091.111| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 1.87 r_work: 0.3958 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26985 Z= 0.132 Angle : 0.526 12.084 37188 Z= 0.273 Chirality : 0.045 0.182 4548 Planarity : 0.004 0.038 4830 Dihedral : 3.996 25.947 5199 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.07 % Allowed : 9.36 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3708 helix: 2.07 (0.21), residues: 645 sheet: 1.07 (0.16), residues: 1020 loop : 0.16 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 64 HIS 0.004 0.001 HIS B1088 PHE 0.019 0.001 PHE C 65 TYR 0.020 0.001 TYR C1067 ARG 0.009 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 45) link_NAG-ASN : angle 2.26434 ( 135) link_BETA1-4 : bond 0.00372 ( 15) link_BETA1-4 : angle 1.22502 ( 45) hydrogen bonds : bond 0.04664 ( 1291) hydrogen bonds : angle 5.41212 ( 3594) SS BOND : bond 0.00241 ( 45) SS BOND : angle 1.09037 ( 90) covalent geometry : bond 0.00304 (26880) covalent geometry : angle 0.50564 (36918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 633 TRP cc_start: 0.7786 (OUTLIER) cc_final: 0.7033 (m100) REVERT: B 773 GLU cc_start: 0.8326 (tt0) cc_final: 0.7898 (tt0) REVERT: C 576 VAL cc_start: 0.8135 (t) cc_final: 0.7930 (p) REVERT: C 750 SER cc_start: 0.8367 (t) cc_final: 0.8018 (m) REVERT: C 790 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8122 (mmmt) outliers start: 22 outliers final: 17 residues processed: 221 average time/residue: 1.0714 time to fit residues: 284.3333 Evaluate side-chains 219 residues out of total 3279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 88 optimal weight: 2.9990 chunk 327 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 chunk 282 optimal weight: 40.0000 chunk 215 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 321 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 658 ASN A 675 GLN A1002 GLN B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 613 GLN B 658 ASN B1005 GLN E 77 ASN C 658 ASN C1005 GLN C1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.227821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.187311 restraints weight = 27175.395| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.84 r_work: 0.3948 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 26985 Z= 0.195 Angle : 0.568 8.497 37188 Z= 0.296 Chirality : 0.047 0.156 4548 Planarity : 0.004 0.041 4830 Dihedral : 4.116 27.233 5199 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.36 % Allowed : 9.11 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.14), residues: 3708 helix: 1.98 (0.21), residues: 645 sheet: 1.07 (0.16), residues: 1017 loop : 0.14 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 64 HIS 0.005 0.001 HIS B1088 PHE 0.024 0.002 PHE B 898 TYR 0.026 0.002 TYR C1067 ARG 0.009 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 45) link_NAG-ASN : angle 2.19920 ( 135) link_BETA1-4 : bond 0.00370 ( 15) link_BETA1-4 : angle 1.25806 ( 45) hydrogen bonds : bond 0.05284 ( 1291) hydrogen bonds : angle 5.48617 ( 3594) SS BOND : bond 0.00349 ( 45) SS BOND : angle 1.30371 ( 90) covalent geometry : bond 0.00471 (26880) covalent geometry : angle 0.54842 (36918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19794.84 seconds wall clock time: 341 minutes 29.82 seconds (20489.82 seconds total)