Starting phenix.real_space_refine on Thu Mar 5 20:41:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jv4_22492/03_2026/7jv4_22492.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jv4_22492/03_2026/7jv4_22492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jv4_22492/03_2026/7jv4_22492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jv4_22492/03_2026/7jv4_22492.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jv4_22492/03_2026/7jv4_22492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jv4_22492/03_2026/7jv4_22492.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.055 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 114 5.16 5 C 15865 2.51 5 N 4319 2.21 5 O 4864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25162 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7244 Classifications: {'peptide': 975} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 48, 'TRANS': 926} Chain breaks: 14 Unresolved non-hydrogen bonds: 391 Unresolved non-hydrogen angles: 495 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 20, 'GLU:plan': 17, 'ASN:plan1': 11, 'PHE:plan': 4, 'TYR:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 239 Chain: "B" Number of atoms: 6719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6719 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 45, 'TRANS': 903} Chain breaks: 14 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 966 Unresolved non-hydrogen dihedrals: 615 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ASP:plan': 22, 'ASN:plan1': 22, 'GLU:plan': 17, 'PHE:plan': 16, 'GLN:plan1': 7, 'TYR:plan': 15, 'ARG:plan': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 487 Chain: "C" Number of atoms: 6991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 6991 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 47, 'TRANS': 915} Chain breaks: 11 Unresolved non-hydrogen bonds: 555 Unresolved non-hydrogen angles: 707 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASN:plan1': 15, 'ASP:plan': 21, 'GLN:plan1': 9, 'GLU:plan': 18, 'PHE:plan': 6, 'ARG:plan': 9, 'TYR:plan': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 365 Chain: "H" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 582 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 5, 'PHE:plan': 3, 'TYR:plan': 9, 'TRP:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 215 Chain: "L" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 552 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'HIS:plan': 2, 'TYR:plan': 6, 'TRP:plan': 2, 'PHE:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 144 Chain: "F" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 582 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 5, 'PHE:plan': 3, 'TYR:plan': 9, 'TRP:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 215 Chain: "G" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 546 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'HIS:plan': 2, 'TYR:plan': 6, 'TRP:plan': 2, 'PHE:plan': 3, 'ARG:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 149 Chain: "D" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 582 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 5, 'PHE:plan': 3, 'TYR:plan': 9, 'TRP:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 215 Chain: "E" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 552 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'HIS:plan': 2, 'TYR:plan': 6, 'TRP:plan': 2, 'PHE:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 144 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.97, per 1000 atoms: 0.24 Number of scatterers: 25162 At special positions: 0 Unit cell: (136.5, 149.1, 214.2, 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 114 16.00 O 4864 8.00 N 4319 7.00 C 15865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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=1.55 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.24 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.01 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.01 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C 165 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6604 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 62 sheets defined 22.4% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.608A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.752A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 501 through 501 No H-bonds generated for 'chain 'A' and resid 501 through 501' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' 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 759 removed outlier: 6.961A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.850A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.296A 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 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: 3.644A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.218A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.927A 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.987A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.505A 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 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 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 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.946A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'L' and resid 30 through 34 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'G' and resid 30 through 34 Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.919A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.487A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.936A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.324A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.210A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.793A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.948A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.599A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.428A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.428A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.766A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.641A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.533A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.314A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.828A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.161A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.161A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.385A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.056A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.414A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.414A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.541A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.990A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.518A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.645A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.384A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.719A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.223A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.223A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.448A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.681A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.877A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.074A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.396A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.775A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.061A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.627A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AF6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.087A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AF9, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AG1, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.596A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AG3, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AG4, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.079A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AG6, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AG7, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.624A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 9 through 12 1285 hydrogen bonds defined for protein. 3405 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 7898 1.34 - 1.48: 7018 1.48 - 1.62: 10560 1.62 - 1.76: 3 1.76 - 1.90: 136 Bond restraints: 25615 Sorted by residual: bond pdb=" CD GLN C 607 " pdb=" NE2 GLN C 607 " ideal model delta sigma weight residual 1.328 1.204 0.124 2.10e-02 2.27e+03 3.51e+01 bond pdb=" CD GLN B 607 " pdb=" NE2 GLN B 607 " ideal model delta sigma weight residual 1.328 1.204 0.124 2.10e-02 2.27e+03 3.51e+01 bond pdb=" CD GLN A 607 " pdb=" NE2 GLN A 607 " ideal model delta sigma weight residual 1.328 1.204 0.124 2.10e-02 2.27e+03 3.50e+01 bond pdb=" NE ARG B 466 " pdb=" CZ ARG B 466 " ideal model delta sigma weight residual 1.326 1.380 -0.054 1.10e-02 8.26e+03 2.37e+01 bond pdb=" CB ILE B 210 " pdb=" CG1 ILE B 210 " ideal model delta sigma weight residual 1.530 1.626 -0.096 2.00e-02 2.50e+03 2.30e+01 ... (remaining 25610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 31750 2.24 - 4.49: 2817 4.49 - 6.73: 437 6.73 - 8.98: 35 8.98 - 11.22: 1 Bond angle restraints: 35040 Sorted by residual: angle pdb=" N ALA A 890 " pdb=" CA ALA A 890 " pdb=" C ALA A 890 " ideal model delta sigma weight residual 111.71 120.47 -8.76 1.15e+00 7.56e-01 5.80e+01 angle pdb=" C ASP B1139 " pdb=" N PRO B1140 " pdb=" CA PRO B1140 " ideal model delta sigma weight residual 119.56 127.24 -7.68 1.02e+00 9.61e-01 5.67e+01 angle pdb=" C ASP A1139 " pdb=" N PRO A1140 " pdb=" CA PRO A1140 " ideal model delta sigma weight residual 119.56 127.22 -7.66 1.02e+00 9.61e-01 5.64e+01 angle pdb=" C THR C 599 " pdb=" N PRO C 600 " pdb=" CA PRO C 600 " ideal model delta sigma weight residual 119.56 127.19 -7.63 1.02e+00 9.61e-01 5.59e+01 angle pdb=" C ASP C1139 " pdb=" N PRO C1140 " pdb=" CA PRO C1140 " ideal model delta sigma weight residual 119.56 127.09 -7.53 1.02e+00 9.61e-01 5.44e+01 ... (remaining 35035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15364 17.97 - 35.93: 386 35.93 - 53.90: 80 53.90 - 71.87: 37 71.87 - 89.83: 18 Dihedral angle restraints: 15885 sinusoidal: 5661 harmonic: 10224 Sorted by residual: dihedral pdb=" C ALA A 890 " pdb=" N ALA A 890 " pdb=" CA ALA A 890 " pdb=" CB ALA A 890 " ideal model delta harmonic sigma weight residual -122.60 -149.69 27.09 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" N ALA A 890 " pdb=" C ALA A 890 " pdb=" CA ALA A 890 " pdb=" CB ALA A 890 " ideal model delta harmonic sigma weight residual 122.90 146.02 -23.12 0 2.50e+00 1.60e-01 8.55e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 169.43 -76.43 1 1.00e+01 1.00e-02 7.35e+01 ... (remaining 15882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 4245 0.217 - 0.435: 99 0.435 - 0.652: 0 0.652 - 0.870: 0 0.870 - 1.087: 1 Chirality restraints: 4345 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.66e+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 -2.56 0.16 2.00e-02 2.50e+03 6.13e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.11e+01 ... (remaining 4342 not shown) Planarity restraints: 4600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " -0.042 2.00e-02 2.50e+03 4.13e-02 2.13e+01 pdb=" CG ASN B 61 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " 0.061 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " -0.031 2.00e-02 2.50e+03 3.11e-02 1.21e+01 pdb=" CG ASN C 61 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " 0.046 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 266 " -0.044 2.00e-02 2.50e+03 2.42e-02 1.17e+01 pdb=" CG TYR A 266 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 266 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 266 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 266 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 266 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 266 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 266 " -0.038 2.00e-02 2.50e+03 ... (remaining 4597 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 10210 2.91 - 3.41: 22046 3.41 - 3.90: 40668 3.90 - 4.40: 44839 4.40 - 4.90: 75417 Nonbonded interactions: 193180 Sorted by model distance: nonbonded pdb=" NZ LYS C1028 " pdb=" O PHE C1042 " model vdw 2.412 3.120 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.422 3.120 nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.449 3.120 nonbonded pdb=" N ALA C 520 " pdb=" O ALA C 520 " model vdw 2.455 2.496 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.465 3.120 ... (remaining 193175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 52 or (resid 53 and ( \ name N or name CA or name C or name O or name CB )) or resid 54 through 66 or re \ sid 82 through 93 or (resid 94 and (name N or name CA or name C or name O or nam \ e CB )) or resid 95 through 99 or (resid 100 and (name N or name CA or name C or \ name O or name CB )) or resid 101 through 108 or (resid 109 through 121 and (na \ me N or name CA or name C or name O or name CB )) or resid 122 through 124 or (r \ esid 125 through 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 through 134 or (resid 140 and (name N or name CA or name C or name O \ or name CB )) or resid 166 through 172 or (resid 186 through 187 and (name N or \ name CA or name C or name O or name CB )) or resid 188 through 196 or resid 200 \ through 210 or (resid 215 and (name N or name CA or name C or name O or name CB \ )) or resid 216 through 217 or (resid 218 and (name N or name CA or name C or na \ me O or name CB )) or resid 219 through 223 or (resid 224 and (name N or name CA \ or name C or name O or name CB )) or resid 225 through 227 or (resid 228 throug \ h 229 and (name N or name CA or name C or name O or name CB )) or resid 230 thro \ ugh 241 or (resid 242 through 263 and (name N or name CA or name C or name O or \ name CB )) or resid 265 through 297 or (resid 298 and (name N or name CA or name \ C or name O or name CB )) or resid 299 through 323 or (resid 324 and (name N or \ name CA or name C or name O or name CB )) or resid 325 through 331 or (resid 33 \ 2 through 334 and (name N or name CA or name C or name O or name CB )) or resid \ 335 through 339 or (resid 340 through 341 and (name N or name CA or name C or na \ me O or name CB )) or resid 342 through 344 or (resid 345 through 360 and (name \ N or name CA or name C or name O or name CB )) or resid 361 or (resid 362 throug \ h 378 and (name N or name CA or name C or name O or name CB )) or resid 379 or ( \ resid 380 and (name N or name CA or name C or name O or name CB )) or resid 381 \ or (resid 382 through 383 and (name N or name CA or name C or name O or name CB \ )) or resid 384 or (resid 385 through 390 and (name N or name CA or name C or na \ me O or name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA \ or name C or name O or name CB )) or resid 404 or (resid 405 through 411 and (n \ ame N or name CA or name C or name O or name CB )) or resid 412 through 413 or ( \ resid 414 through 415 and (name N or name CA or name C or name O or name CB )) o \ r (resid 416 through 425 and (name N or name CA or name C or name O or name CB ) \ ) or resid 426 through 428 or (resid 429 through 430 and (name N or name CA or n \ ame C or name O or name CB )) or resid 431 through 432 or (resid 433 through 442 \ and (name N or name CA or name C or name O or name CB )) or (resid 448 through \ 454 and (name N or name CA or name C or name O or name CB )) or resid 463 throug \ h 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) or \ resid 480 through 486 or (resid 487 and (name N or name CA or name C or name O o \ r name CB )) or resid 488 or (resid 489 through 490 and (name N or name CA or na \ me C or name O or name CB )) or resid 491 or (resid 492 through 495 and (name N \ or name CA or name C or name O or name CB )) or resid 496 or (resid 497 through \ 498 and (name N or name CA or name C or name O or name CB )) or resid 499 throug \ h 500 or (resid 501 through 503 and (name N or name CA or name C or name O or na \ me CB )) or resid 504 through 507 or (resid 508 through 515 and (name N or name \ CA or name C or name O or name CB )) or (resid 522 through 524 and (name N or na \ me CA or name C or name O or name CB )) or resid 525 through 530 or (resid 531 t \ hrough 537 and (name N or name CA or name C or name O or name CB )) or resid 538 \ through 546 or (resid 547 and (name N or name CA or name C or name O or name CB \ )) or resid 548 through 554 or (resid 555 through 556 and (name N or name CA or \ name C or name O or name CB )) or resid 557 or (resid 558 and (name N or name C \ A or name C or name O or name CB )) or resid 559 through 563 or (resid 564 and ( \ name N or name CA or name C or name O or name CB )) or resid 565 through 573 or \ (resid 574 through 575 and (name N or name CA or name C or name O or name CB )) \ or resid 576 through 580 or (resid 581 through 583 and (name N or name CA or nam \ e C or name O or name CB )) or resid 584 through 585 or (resid 586 and (name N o \ r name CA or name C or name O or name CB )) or resid 587 through 590 or (resid 5 \ 91 through 592 and (name N or name CA or name C or name O or name CB )) or resid \ 593 through 617 or (resid 618 through 620 and (name N or name CA or name C or n \ ame O or name CB )) or resid 641 through 645 or (resid 646 through 647 and (name \ N or name CA or name C or name O or name CB )) or resid 648 through 653 or (res \ id 654 and (name N or name CA or name C or name O or name CB )) or resid 655 thr \ ough 657 or (resid 658 and (name N or name CA or name C or name O or name CB )) \ or resid 659 through 662 or (resid 663 and (name N or name CA or name C or name \ O or name CB )) or resid 664 through 747 or (resid 748 and (name N or name CA or \ name C or name O or name CB )) or resid 749 through 785 or (resid 786 and (name \ N or name CA or name C or name O or name CB )) or resid 787 through 793 or (res \ id 794 and (name N or name CA or name C or name O or name CB )) or resid 795 thr \ ough 813 or (resid 814 and (name N or name CA or name C or name O or name CB )) \ or resid 815 through 826 or (resid 827 and (name N or name CA or name C or name \ O or name CB )) or resid 856 through 935 or (resid 936 and (name N or name CA or \ name C or name O or name CB )) or resid 937 through 984 or (resid 985 and (name \ N or name CA or name C or name O or name CB )) or resid 986 through 987 or (res \ id 988 through 990 and (name N or name CA or name C or name O or name CB )) or r \ esid 991 through 1044 or (resid 1045 and (name N or name CA or name C or name O \ or name CB )) or resid 1046 through 1072 or (resid 1073 and (name N or name CA o \ r name C or name O or name CB )) or resid 1074 through 1083 or (resid 1084 and ( \ name N or name CA or name C or name O or name CB )) or resid 1085 through 1141 o \ r (resid 1142 and (name N or name CA or name C or name O or name CB )) or resid \ 1143 through 1311)) selection = (chain 'B' and (resid 27 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 51 or (resid 52 through 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 66 or resi \ d 82 through 87 or (resid 88 and (name N or name CA or name C or name O or name \ CB )) or resid 89 through 96 or (resid 97 through 100 and (name N or name CA or \ name C or name O or name CB )) or resid 101 through 109 or (resid 110 through 11 \ 3 and (name N or name CA or name C or name O or name CB )) or (resid 116 through \ 121 and (name N or name CA or name C or name O or name CB )) or resid 122 throu \ gh 135 or resid 166 or (resid 167 through 187 and (name N or name CA or name C o \ r name O or name CB )) or resid 188 through 189 or (resid 190 through 191 and (n \ ame N or name CA or name C or name O or name CB )) or resid 192 through 195 or ( \ resid 196 and (name N or name CA or name C or name O or name CB )) or resid 200 \ through 205 or (resid 206 and (name N or name CA or name C or name O or name CB \ )) or resid 207 through 217 or (resid 218 and (name N or name CA or name C or na \ me O or name CB )) or resid 219 through 223 or (resid 224 and (name N or name CA \ or name C or name O or name CB )) or resid 225 through 228 or (resid 229 and (n \ ame N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 an \ d (name N or name CA or name C or name O or name CB )) or resid 232 through 238 \ or (resid 239 and (name N or name CA or name C or name O or name CB )) or resid \ 240 through 241 or (resid 242 through 263 and (name N or name CA or name C or na \ me O or name CB )) or resid 265 through 297 or (resid 298 and (name N or name CA \ or name C or name O or name CB )) or resid 299 through 323 or (resid 324 and (n \ ame N or name CA or name C or name O or name CB )) or resid 325 through 442 or r \ esid 448 through 454 or resid 463 through 464 or (resid 465 through 466 and (nam \ e N or name CA or name C or name O or name CB )) or resid 480 through 501 or res \ id 503 through 555 or (resid 556 and (name N or name CA or name C or name O or n \ ame CB )) or resid 557 or (resid 558 and (name N or name CA or name C or name O \ or name CB )) or resid 559 through 563 or (resid 564 and (name N or name CA or n \ ame C or name O or name CB )) or resid 565 through 567 or (resid 568 through 571 \ and (name N or name CA or name C or name O or name CB )) or resid 572 through 5 \ 81 or (resid 582 through 583 and (name N or name CA or name C or name O or name \ CB )) or resid 584 through 613 or (resid 614 and (name N or name CA or name C or \ name O or name CB )) or resid 615 through 617 or (resid 618 through 620 and (na \ me N or name CA or name C or name O or name CB )) or resid 641 through 645 or (r \ esid 646 through 647 and (name N or name CA or name C or name O or name CB )) or \ resid 648 through 653 or (resid 654 and (name N or name CA or name C or name O \ or name CB )) or resid 655 through 674 or (resid 675 through 676 and (name N or \ name CA or name C or name O or name CB )) or resid 690 through 793 or (resid 794 \ and (name N or name CA or name C or name O or name CB )) or resid 795 or (resid \ 796 and (name N or name CA or name C or name O or name CB )) or resid 797 throu \ gh 807 or (resid 808 and (name N or name CA or name C or name O or name CB )) or \ resid 809 or (resid 810 through 811 and (name N or name CA or name C or name O \ or name CB )) or resid 813 through 824 or (resid 825 and (name N or name CA or n \ ame C or name O or name CB )) or resid 826 through 827 or (resid 856 and (name N \ or name CA or name C or name O or name CB )) or resid 857 through 920 or (resid \ 921 and (name N or name CA or name C or name O or name CB )) or resid 922 throu \ gh 939 or (resid 940 through 944 and (name N or name CA or name C or name O or n \ ame CB )) or resid 945 through 956 or (resid 957 through 958 and (name N or name \ CA or name C or name O or name CB )) or resid 959 through 984 or (resid 985 and \ (name N or name CA or name C or name O or name CB )) or resid 986 through 987 o \ r (resid 988 through 990 and (name N or name CA or name C or name O or name CB ) \ ) or resid 991 through 1072 or (resid 1073 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1074 through 1083 or (resid 1084 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1085 through 1091 or (resid 1092 \ and (name N or name CA or name C or name O or name CB )) or resid 1093 through \ 1117 or (resid 1118 and (name N or name CA or name C or name O or name CB )) or \ resid 1119 through 1126 or (resid 1127 and (name N or name CA or name C or name \ O or name CB )) or resid 1128 through 1138 or (resid 1139 and (name N or name CA \ or name C or name O or name CB )) or resid 1140 through 1311)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or re \ sid 95 or (resid 96 through 100 and (name N or name CA or name C or name O or na \ me CB )) or resid 101 through 109 or (resid 110 through 113 and (name N or name \ CA or name C or name O or name CB )) or (resid 116 through 121 and (name N or na \ me CA or name C or name O or name CB )) or resid 122 through 134 or (resid 140 a \ nd (name N or name CA or name C or name O or name CB )) or resid 166 or (resid 1 \ 67 through 187 and (name N or name CA or name C or name O or name CB )) or resid \ 188 through 189 or (resid 190 through 191 and (name N or name CA or name C or n \ ame O or name CB )) or resid 192 through 195 or (resid 196 and (name N or name C \ A or name C or name O or name CB )) or resid 200 through 205 or (resid 206 and ( \ name N or name CA or name C or name O or name CB )) or resid 207 through 210 or \ resid 215 through 227 or (resid 228 through 229 and (name N or name CA or name C \ or name O or name CB )) or resid 230 or (resid 231 and (name N or name CA or na \ me C or name O or name CB )) or resid 232 or (resid 233 and (name N or name CA o \ r name C or name O or name CB )) or resid 234 through 238 or (resid 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 through 308 or (re \ sid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 th \ rough 331 or (resid 332 through 334 and (name N or name CA or name C or name O o \ r name CB )) or resid 335 through 340 or (resid 341 and (name N or name CA or na \ me C or name O or name CB )) or resid 342 through 346 or (resid 347 through 360 \ and (name N or name CA or name C or name O or name CB )) or resid 361 or (resid \ 362 through 378 and (name N or name CA or name C or name O or name CB )) or resi \ d 379 or (resid 380 and (name N or name CA or name C or name O or name CB )) or \ resid 381 or (resid 382 through 383 and (name N or name CA or name C or name O o \ r name CB )) or resid 384 or (resid 385 through 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391 or (resid 392 through 403 and (name N \ or name CA or name C or name O or name CB )) or resid 404 through 428 or (resid \ 429 through 430 and (name N or name CA or name C or name O or name CB )) or resi \ d 431 through 432 or (resid 433 through 454 and (name N or name CA or name C or \ name O or name CB )) or resid 463 through 501 or resid 503 through 507 or (resid \ 508 through 515 and (name N or name CA or name C or name O or name CB )) or (re \ sid 522 through 524 and (name N or name CA or name C or name O or name CB )) or \ resid 525 through 527 or (resid 528 through 537 and (name N or name CA or name C \ or name O or name CB )) or resid 538 through 546 or (resid 547 and (name N or n \ ame CA or name C or name O or name CB )) or resid 548 through 568 or (resid 569 \ through 571 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 2 through 580 or (resid 581 through 583 and (name N or name CA or name C or name \ O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA o \ r name C or name O or name CB )) or resid 587 through 590 or (resid 591 through \ 592 and (name N or name CA or name C or name O or name CB )) or resid 593 throug \ h 657 or (resid 658 and (name N or name CA or name C or name O or name CB )) or \ resid 659 through 660 or (resid 661 and (name N or name CA or name C or name O o \ r name CB )) or resid 662 through 674 or (resid 675 through 676 and (name N or n \ ame CA or name C or name O or name CB )) or resid 690 through 747 or (resid 748 \ and (name N or name CA or name C or name O or name CB )) or resid 749 through 78 \ 5 or (resid 786 and (name N or name CA or name C or name O or name CB )) or resi \ d 787 through 795 or (resid 796 and (name N or name CA or name C or name O or na \ me CB )) or resid 797 through 807 or (resid 808 and (name N or name CA or name C \ or name O or name CB )) or resid 809 or (resid 810 through 811 and (name N or n \ ame CA or name C or name O or name CB )) or resid 813 through 824 or (resid 825 \ and (name N or name CA or name C or name O or name CB )) or resid 826 or (resid \ 827 through 856 and (name N or name CA or name C or name O or name CB )) or resi \ d 857 through 866 or (resid 867 through 868 and (name N or name CA or name C or \ name O or name CB )) or resid 869 through 920 or (resid 921 and (name N or name \ CA or name C or name O or name CB )) or resid 922 through 935 or (resid 936 and \ (name N or name CA or name C or name O or name CB )) or resid 937 through 939 or \ (resid 940 through 944 and (name N or name CA or name C or name O or name CB )) \ or resid 945 through 949 or (resid 950 and (name N or name CA or name C or name \ O or name CB )) or resid 951 through 956 or (resid 957 through 958 and (name N \ or name CA or name C or name O or name CB )) or resid 959 through 978 or (resid \ 979 and (name N or name CA or name C or name O or name CB )) or resid 980 throug \ h 1016 or (resid 1017 and (name N or name CA or name C or name O or name CB )) o \ r resid 1018 through 1138 or (resid 1139 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1140 through 1141 or (resid 1142 and (name N or name \ CA or name C or name O or name CB )) or resid 1143 or (resid 1144 and (name N or \ name CA or name C or name O or name CB )) or resid 1302 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'E' and (resid 2 through 62 or (resid 63 through 65 and (name N or name C \ A or name C or name O or name CB )) or resid 66 through 110)) selection = chain 'G' selection = (chain 'L' and (resid 2 through 46 or (resid 47 through 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 110)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.460 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 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 : 0.013 0.483 25718 Z= 0.683 Angle : 1.410 11.225 35304 Z= 0.944 Chirality : 0.090 1.087 4345 Planarity : 0.005 0.028 4553 Dihedral : 9.409 89.831 9146 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.13), residues: 3472 helix: 0.16 (0.18), residues: 692 sheet: 1.00 (0.16), residues: 860 loop : 0.53 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.044 0.005 TYR A 266 PHE 0.023 0.004 PHE A 898 TRP 0.019 0.005 TRP A 64 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.01191 (25615) covalent geometry : angle 1.39662 (35040) SS BOND : bond 0.07895 ( 45) SS BOND : angle 3.13451 ( 90) hydrogen bonds : bond 0.17140 ( 1227) hydrogen bonds : angle 8.55055 ( 3405) link_BETA1-4 : bond 0.05519 ( 11) link_BETA1-4 : angle 3.01858 ( 33) link_NAG-ASN : bond 0.05641 ( 47) link_NAG-ASN : angle 2.19679 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 372 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8138 (mm) cc_final: 0.7871 (mt) REVERT: B 878 LEU cc_start: 0.8895 (tp) cc_final: 0.8679 (mt) REVERT: C 365 TYR cc_start: 0.8531 (m-80) cc_final: 0.8304 (m-80) REVERT: C 463 PRO cc_start: 0.8005 (Cg_exo) cc_final: 0.7755 (Cg_endo) REVERT: C 1105 THR cc_start: 0.9116 (t) cc_final: 0.8853 (p) outliers start: 2 outliers final: 0 residues processed: 374 average time/residue: 0.1690 time to fit residues: 98.9228 Evaluate side-chains 143 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 10.0000 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 655 HIS A 914 ASN A 919 ASN A 955 ASN A1048 HIS A1119 ASN A1135 ASN B 321 GLN B 607 GLN B 703 ASN B 764 ASN B1048 HIS C 66 HIS C 607 GLN C 913 GLN C1048 HIS C1101 HIS C1119 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.147207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.117614 restraints weight = 48702.267| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 4.60 r_work: 0.3249 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25718 Z= 0.142 Angle : 0.626 11.271 35304 Z= 0.329 Chirality : 0.046 0.277 4345 Planarity : 0.004 0.048 4553 Dihedral : 5.068 58.198 4916 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.50 % Favored : 98.44 % Rotamer: Outliers : 1.62 % Allowed : 5.97 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.14), residues: 3472 helix: 1.75 (0.20), residues: 663 sheet: 0.82 (0.16), residues: 930 loop : 0.39 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 577 TYR 0.022 0.001 TYR A1067 PHE 0.022 0.002 PHE C 106 TRP 0.015 0.001 TRP C 353 HIS 0.009 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00307 (25615) covalent geometry : angle 0.60126 (35040) SS BOND : bond 0.00407 ( 45) SS BOND : angle 1.87585 ( 90) hydrogen bonds : bond 0.04736 ( 1227) hydrogen bonds : angle 6.28104 ( 3405) link_BETA1-4 : bond 0.00746 ( 11) link_BETA1-4 : angle 1.93791 ( 33) link_NAG-ASN : bond 0.00614 ( 47) link_NAG-ASN : angle 2.28888 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.8083 (mm) cc_final: 0.7731 (mt) REVERT: A 747 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7864 (t) REVERT: B 306 PHE cc_start: 0.8551 (m-10) cc_final: 0.8223 (m-10) REVERT: B 342 PHE cc_start: 0.6067 (m-10) cc_final: 0.5414 (m-80) REVERT: B 1123 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.7909 (m) REVERT: C 365 TYR cc_start: 0.8743 (m-80) cc_final: 0.8489 (m-80) REVERT: C 463 PRO cc_start: 0.8306 (Cg_exo) cc_final: 0.8080 (Cg_endo) REVERT: C 725 GLU cc_start: 0.8516 (tt0) cc_final: 0.8304 (tt0) REVERT: C 1105 THR cc_start: 0.9310 (t) cc_final: 0.9095 (p) outliers start: 34 outliers final: 18 residues processed: 199 average time/residue: 0.1381 time to fit residues: 46.5025 Evaluate side-chains 146 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 551 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 308 optimal weight: 50.0000 chunk 170 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN A 955 ASN A1002 GLN A1119 ASN B1005 GLN C 207 HIS C 804 GLN C 935 GLN C1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.142583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.108995 restraints weight = 47996.033| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.37 r_work: 0.3181 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 25718 Z= 0.223 Angle : 0.617 12.967 35304 Z= 0.320 Chirality : 0.046 0.391 4345 Planarity : 0.004 0.051 4553 Dihedral : 4.788 55.811 4916 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 2.05 % Allowed : 7.35 % Favored : 90.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3472 helix: 1.77 (0.20), residues: 661 sheet: 0.46 (0.16), residues: 974 loop : 0.29 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1014 TYR 0.019 0.002 TYR C1067 PHE 0.020 0.002 PHE C 275 TRP 0.012 0.001 TRP C 353 HIS 0.008 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00525 (25615) covalent geometry : angle 0.59248 (35040) SS BOND : bond 0.00441 ( 45) SS BOND : angle 2.07238 ( 90) hydrogen bonds : bond 0.04404 ( 1227) hydrogen bonds : angle 5.82195 ( 3405) link_BETA1-4 : bond 0.00546 ( 11) link_BETA1-4 : angle 1.44627 ( 33) link_NAG-ASN : bond 0.00431 ( 47) link_NAG-ASN : angle 2.17857 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.8139 (mm) cc_final: 0.7762 (mt) REVERT: A 565 PHE cc_start: 0.8397 (p90) cc_final: 0.8071 (p90) REVERT: A 1135 ASN cc_start: 0.7464 (t0) cc_final: 0.7261 (t0) REVERT: B 306 PHE cc_start: 0.8607 (m-10) cc_final: 0.8256 (m-10) REVERT: B 1123 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8090 (m) REVERT: C 463 PRO cc_start: 0.8226 (Cg_exo) cc_final: 0.7968 (Cg_endo) REVERT: C 725 GLU cc_start: 0.8569 (tt0) cc_final: 0.8336 (tt0) REVERT: C 960 ASN cc_start: 0.8673 (m-40) cc_final: 0.8390 (t0) REVERT: C 1105 THR cc_start: 0.9209 (t) cc_final: 0.8961 (p) REVERT: C 1130 ILE cc_start: 0.7856 (mt) cc_final: 0.7611 (mp) outliers start: 43 outliers final: 24 residues processed: 172 average time/residue: 0.1271 time to fit residues: 37.9942 Evaluate side-chains 140 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 608 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 135 optimal weight: 7.9990 chunk 329 optimal weight: 20.0000 chunk 85 optimal weight: 0.5980 chunk 130 optimal weight: 50.0000 chunk 23 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.143318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.104273 restraints weight = 48102.997| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.21 r_work: 0.3221 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 25718 Z= 0.159 Angle : 0.542 11.812 35304 Z= 0.280 Chirality : 0.045 0.349 4345 Planarity : 0.004 0.054 4553 Dihedral : 4.589 54.236 4916 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.84 % Rotamer: Outliers : 2.00 % Allowed : 8.31 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3472 helix: 1.97 (0.21), residues: 652 sheet: 0.36 (0.15), residues: 1013 loop : 0.23 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.019 0.001 TYR B1067 PHE 0.013 0.001 PHE B1121 TRP 0.011 0.001 TRP C 353 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00364 (25615) covalent geometry : angle 0.51797 (35040) SS BOND : bond 0.00343 ( 45) SS BOND : angle 1.89621 ( 90) hydrogen bonds : bond 0.03824 ( 1227) hydrogen bonds : angle 5.52112 ( 3405) link_BETA1-4 : bond 0.00413 ( 11) link_BETA1-4 : angle 1.29088 ( 33) link_NAG-ASN : bond 0.00371 ( 47) link_NAG-ASN : angle 2.04116 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 305 SER cc_start: 0.9109 (t) cc_final: 0.8725 (p) REVERT: A 450 ASN cc_start: 0.8597 (m-40) cc_final: 0.7674 (t0) REVERT: A 565 PHE cc_start: 0.8491 (p90) cc_final: 0.8063 (p90) REVERT: A 1135 ASN cc_start: 0.7601 (t0) cc_final: 0.7314 (t0) REVERT: B 306 PHE cc_start: 0.8639 (m-10) cc_final: 0.8234 (m-10) REVERT: B 342 PHE cc_start: 0.5991 (m-80) cc_final: 0.5407 (m-80) REVERT: B 740 MET cc_start: 0.8296 (mtp) cc_final: 0.8094 (mtt) REVERT: C 463 PRO cc_start: 0.8366 (Cg_exo) cc_final: 0.8131 (Cg_endo) REVERT: C 960 ASN cc_start: 0.8816 (m-40) cc_final: 0.8487 (t0) REVERT: C 1105 THR cc_start: 0.9165 (t) cc_final: 0.8870 (p) REVERT: C 1130 ILE cc_start: 0.8105 (mt) cc_final: 0.7832 (mp) outliers start: 42 outliers final: 31 residues processed: 165 average time/residue: 0.1354 time to fit residues: 38.3331 Evaluate side-chains 149 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 334 optimal weight: 50.0000 chunk 330 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 804 GLN B 901 GLN C1119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.140374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109339 restraints weight = 48256.948| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.09 r_work: 0.3183 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 25718 Z= 0.235 Angle : 0.605 12.463 35304 Z= 0.308 Chirality : 0.046 0.356 4345 Planarity : 0.004 0.042 4553 Dihedral : 4.853 49.576 4916 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Rotamer: Outliers : 2.48 % Allowed : 8.83 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 3472 helix: 1.84 (0.21), residues: 644 sheet: 0.25 (0.15), residues: 992 loop : 0.02 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1014 TYR 0.019 0.002 TYR C1067 PHE 0.019 0.002 PHE C 275 TRP 0.012 0.001 TRP A 886 HIS 0.007 0.002 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00556 (25615) covalent geometry : angle 0.58263 (35040) SS BOND : bond 0.00404 ( 45) SS BOND : angle 1.91390 ( 90) hydrogen bonds : bond 0.04128 ( 1227) hydrogen bonds : angle 5.55210 ( 3405) link_BETA1-4 : bond 0.00408 ( 11) link_BETA1-4 : angle 1.21310 ( 33) link_NAG-ASN : bond 0.00351 ( 47) link_NAG-ASN : angle 2.16011 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 126 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 305 SER cc_start: 0.9129 (t) cc_final: 0.8747 (p) REVERT: A 450 ASN cc_start: 0.8682 (m-40) cc_final: 0.7790 (t0) REVERT: A 574 ASP cc_start: 0.8189 (t0) cc_final: 0.7884 (t0) REVERT: B 306 PHE cc_start: 0.8685 (m-10) cc_final: 0.8377 (m-10) REVERT: B 878 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8839 (mt) REVERT: C 983 ARG cc_start: 0.8992 (mtp-110) cc_final: 0.8643 (mtp85) REVERT: C 1105 THR cc_start: 0.9206 (t) cc_final: 0.8857 (p) REVERT: C 1130 ILE cc_start: 0.8167 (mt) cc_final: 0.7965 (mp) outliers start: 52 outliers final: 35 residues processed: 164 average time/residue: 0.1317 time to fit residues: 37.4514 Evaluate side-chains 153 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 50.0000 chunk 330 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 311 optimal weight: 50.0000 chunk 260 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 290 optimal weight: 40.0000 chunk 207 optimal weight: 3.9990 chunk 279 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.141106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109212 restraints weight = 48095.552| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.19 r_work: 0.3182 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25718 Z= 0.177 Angle : 0.544 9.531 35304 Z= 0.278 Chirality : 0.045 0.332 4345 Planarity : 0.004 0.054 4553 Dihedral : 4.680 58.032 4916 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 2.20 % Allowed : 9.31 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3472 helix: 2.01 (0.21), residues: 630 sheet: 0.21 (0.16), residues: 976 loop : -0.03 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.018 0.001 TYR B1067 PHE 0.015 0.002 PHE B1121 TRP 0.020 0.001 TRP A 104 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00413 (25615) covalent geometry : angle 0.52263 (35040) SS BOND : bond 0.00386 ( 45) SS BOND : angle 1.67888 ( 90) hydrogen bonds : bond 0.03777 ( 1227) hydrogen bonds : angle 5.39926 ( 3405) link_BETA1-4 : bond 0.00409 ( 11) link_BETA1-4 : angle 1.17087 ( 33) link_NAG-ASN : bond 0.00327 ( 47) link_NAG-ASN : angle 2.04307 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 305 SER cc_start: 0.9074 (t) cc_final: 0.8770 (p) REVERT: A 450 ASN cc_start: 0.8615 (m-40) cc_final: 0.7786 (t0) REVERT: A 574 ASP cc_start: 0.8351 (t0) cc_final: 0.8081 (t0) REVERT: A 740 MET cc_start: 0.8908 (tpp) cc_final: 0.8687 (mtp) REVERT: A 759 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7890 (t80) REVERT: B 878 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8834 (mt) REVERT: C 983 ARG cc_start: 0.8975 (mtp-110) cc_final: 0.8632 (mtp85) REVERT: C 1105 THR cc_start: 0.9052 (t) cc_final: 0.8733 (p) outliers start: 46 outliers final: 37 residues processed: 154 average time/residue: 0.1388 time to fit residues: 37.2057 Evaluate side-chains 156 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 262 optimal weight: 0.6980 chunk 326 optimal weight: 50.0000 chunk 127 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 275 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.140239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.106915 restraints weight = 47721.498| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.17 r_work: 0.3168 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25718 Z= 0.186 Angle : 0.549 9.033 35304 Z= 0.280 Chirality : 0.045 0.332 4345 Planarity : 0.004 0.044 4553 Dihedral : 4.596 42.657 4916 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.06 % Rotamer: Outliers : 2.63 % Allowed : 9.12 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3472 helix: 1.92 (0.21), residues: 642 sheet: 0.18 (0.16), residues: 970 loop : -0.06 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.018 0.001 TYR B1067 PHE 0.019 0.002 PHE A 456 TRP 0.022 0.001 TRP A 104 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00438 (25615) covalent geometry : angle 0.52823 (35040) SS BOND : bond 0.00380 ( 45) SS BOND : angle 1.60017 ( 90) hydrogen bonds : bond 0.03795 ( 1227) hydrogen bonds : angle 5.35128 ( 3405) link_BETA1-4 : bond 0.00359 ( 11) link_BETA1-4 : angle 1.13694 ( 33) link_NAG-ASN : bond 0.00321 ( 47) link_NAG-ASN : angle 2.01995 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 121 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 305 SER cc_start: 0.9053 (t) cc_final: 0.8717 (p) REVERT: A 408 ARG cc_start: 0.8494 (ptm-80) cc_final: 0.8194 (ttp-110) REVERT: A 450 ASN cc_start: 0.8595 (m-40) cc_final: 0.7757 (t0) REVERT: A 574 ASP cc_start: 0.8361 (t0) cc_final: 0.8069 (t0) REVERT: B 306 PHE cc_start: 0.8672 (m-10) cc_final: 0.8267 (m-10) REVERT: B 878 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8825 (mt) REVERT: C 983 ARG cc_start: 0.9014 (mtp-110) cc_final: 0.8668 (mtp85) REVERT: C 1105 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8730 (p) outliers start: 55 outliers final: 44 residues processed: 160 average time/residue: 0.1372 time to fit residues: 38.1121 Evaluate side-chains 159 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 325 optimal weight: 50.0000 chunk 228 optimal weight: 0.1980 chunk 338 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 22 optimal weight: 0.0470 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 30.0000 chunk 152 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 258 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.140695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109289 restraints weight = 48329.952| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.02 r_work: 0.3201 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25718 Z= 0.122 Angle : 0.506 8.995 35304 Z= 0.258 Chirality : 0.044 0.322 4345 Planarity : 0.003 0.041 4553 Dihedral : 4.331 38.672 4916 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.19 % Favored : 97.78 % Rotamer: Outliers : 2.20 % Allowed : 9.64 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 3472 helix: 2.06 (0.21), residues: 647 sheet: 0.24 (0.16), residues: 962 loop : 0.02 (0.15), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.017 0.001 TYR B1067 PHE 0.014 0.001 PHE A 456 TRP 0.029 0.001 TRP A 104 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00279 (25615) covalent geometry : angle 0.48662 (35040) SS BOND : bond 0.00284 ( 45) SS BOND : angle 1.46392 ( 90) hydrogen bonds : bond 0.03482 ( 1227) hydrogen bonds : angle 5.21138 ( 3405) link_BETA1-4 : bond 0.00389 ( 11) link_BETA1-4 : angle 1.11881 ( 33) link_NAG-ASN : bond 0.00314 ( 47) link_NAG-ASN : angle 1.89967 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 305 SER cc_start: 0.8982 (t) cc_final: 0.8696 (p) REVERT: A 408 ARG cc_start: 0.8489 (ptm-80) cc_final: 0.8192 (ttp-110) REVERT: A 450 ASN cc_start: 0.8570 (m-40) cc_final: 0.7746 (t0) REVERT: A 574 ASP cc_start: 0.8309 (t0) cc_final: 0.8042 (t0) REVERT: A 759 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7934 (t80) REVERT: B 306 PHE cc_start: 0.8664 (m-10) cc_final: 0.8338 (m-10) REVERT: B 878 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8793 (mt) REVERT: B 1104 VAL cc_start: 0.9558 (OUTLIER) cc_final: 0.9353 (p) REVERT: C 697 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7727 (ttt) REVERT: C 983 ARG cc_start: 0.8952 (mtp-110) cc_final: 0.8600 (mtp85) REVERT: C 1105 THR cc_start: 0.8980 (t) cc_final: 0.8719 (p) outliers start: 46 outliers final: 36 residues processed: 154 average time/residue: 0.1375 time to fit residues: 37.0966 Evaluate side-chains 153 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 97 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 246 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.140215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108905 restraints weight = 48178.071| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.16 r_work: 0.3170 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 25718 Z= 0.194 Angle : 0.554 9.421 35304 Z= 0.282 Chirality : 0.045 0.323 4345 Planarity : 0.004 0.039 4553 Dihedral : 4.514 38.960 4916 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 2.34 % Allowed : 10.07 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3472 helix: 1.93 (0.21), residues: 644 sheet: 0.22 (0.16), residues: 940 loop : -0.09 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1014 TYR 0.018 0.001 TYR B1067 PHE 0.021 0.002 PHE B1121 TRP 0.029 0.002 TRP A 104 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00457 (25615) covalent geometry : angle 0.53532 (35040) SS BOND : bond 0.00302 ( 45) SS BOND : angle 1.49415 ( 90) hydrogen bonds : bond 0.03764 ( 1227) hydrogen bonds : angle 5.30120 ( 3405) link_BETA1-4 : bond 0.00354 ( 11) link_BETA1-4 : angle 1.10935 ( 33) link_NAG-ASN : bond 0.00317 ( 47) link_NAG-ASN : angle 1.97444 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8490 (ptm-80) cc_final: 0.8208 (ttp-110) REVERT: A 450 ASN cc_start: 0.8626 (m-40) cc_final: 0.7803 (t0) REVERT: A 489 TYR cc_start: 0.6942 (m-10) cc_final: 0.6515 (m-80) REVERT: A 574 ASP cc_start: 0.8328 (t0) cc_final: 0.8036 (t0) REVERT: A 759 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7856 (t80) REVERT: B 306 PHE cc_start: 0.8702 (m-10) cc_final: 0.8398 (m-10) REVERT: B 878 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8816 (mt) REVERT: C 1105 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8744 (p) outliers start: 49 outliers final: 40 residues processed: 151 average time/residue: 0.1400 time to fit residues: 36.5432 Evaluate side-chains 158 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 305 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 328 optimal weight: 20.0000 chunk 316 optimal weight: 0.7980 chunk 331 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.140687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.108088 restraints weight = 47829.280| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.06 r_work: 0.3189 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25718 Z= 0.133 Angle : 0.509 9.050 35304 Z= 0.260 Chirality : 0.044 0.317 4345 Planarity : 0.004 0.041 4553 Dihedral : 4.303 37.888 4916 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 2.00 % Allowed : 10.60 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3472 helix: 2.07 (0.21), residues: 642 sheet: 0.27 (0.16), residues: 945 loop : -0.02 (0.15), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 983 TYR 0.017 0.001 TYR B1067 PHE 0.020 0.001 PHE A 456 TRP 0.037 0.001 TRP A 104 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00308 (25615) covalent geometry : angle 0.49217 (35040) SS BOND : bond 0.00268 ( 45) SS BOND : angle 1.28709 ( 90) hydrogen bonds : bond 0.03453 ( 1227) hydrogen bonds : angle 5.16806 ( 3405) link_BETA1-4 : bond 0.00447 ( 11) link_BETA1-4 : angle 1.10576 ( 33) link_NAG-ASN : bond 0.00312 ( 47) link_NAG-ASN : angle 1.85475 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8482 (ptm-80) cc_final: 0.8209 (ttp-110) REVERT: A 450 ASN cc_start: 0.8540 (m-40) cc_final: 0.7807 (t0) REVERT: A 489 TYR cc_start: 0.6930 (m-10) cc_final: 0.6600 (m-80) REVERT: A 574 ASP cc_start: 0.8286 (t0) cc_final: 0.7977 (t0) REVERT: A 759 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7935 (t80) REVERT: B 878 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8798 (mt) REVERT: C 697 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7725 (ttt) REVERT: C 983 ARG cc_start: 0.8937 (mtp-110) cc_final: 0.8671 (ptm160) REVERT: C 1105 THR cc_start: 0.8984 (t) cc_final: 0.8756 (p) outliers start: 42 outliers final: 33 residues processed: 148 average time/residue: 0.1323 time to fit residues: 33.7401 Evaluate side-chains 150 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 300 optimal weight: 40.0000 chunk 43 optimal weight: 0.3980 chunk 246 optimal weight: 0.6980 chunk 223 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 177 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 234 optimal weight: 0.0170 chunk 258 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 641 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.140193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.108033 restraints weight = 48334.916| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.05 r_work: 0.3212 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25718 Z= 0.108 Angle : 0.485 8.267 35304 Z= 0.248 Chirality : 0.043 0.318 4345 Planarity : 0.004 0.041 4553 Dihedral : 4.055 37.304 4916 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.96 % Allowed : 10.60 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 3472 helix: 2.20 (0.21), residues: 642 sheet: 0.34 (0.16), residues: 948 loop : 0.01 (0.15), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.017 0.001 TYR B1067 PHE 0.026 0.001 PHE A 456 TRP 0.041 0.001 TRP A 104 HIS 0.003 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00244 (25615) covalent geometry : angle 0.46870 (35040) SS BOND : bond 0.00233 ( 45) SS BOND : angle 1.13188 ( 90) hydrogen bonds : bond 0.03289 ( 1227) hydrogen bonds : angle 5.03369 ( 3405) link_BETA1-4 : bond 0.00446 ( 11) link_BETA1-4 : angle 1.09677 ( 33) link_NAG-ASN : bond 0.00316 ( 47) link_NAG-ASN : angle 1.76110 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5644.83 seconds wall clock time: 97 minutes 7.21 seconds (5827.21 seconds total)