Starting phenix.real_space_refine on Fri Mar 6 01:49:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qo7_14086/03_2026/7qo7_14086.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qo7_14086/03_2026/7qo7_14086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qo7_14086/03_2026/7qo7_14086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qo7_14086/03_2026/7qo7_14086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qo7_14086/03_2026/7qo7_14086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qo7_14086/03_2026/7qo7_14086.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 17092 2.51 5 N 4372 2.21 5 O 5284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 26865 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 8610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8610 Classifications: {'peptide': 1101} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 56, 'TRANS': 1044} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8589 Classifications: {'peptide': 1096} Link IDs: {'PTRANS': 56, 'TRANS': 1039} Chain breaks: 4 Chain: "C" Number of atoms: 8596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8596 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1041} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.56, per 1000 atoms: 0.24 Number of scatterers: 26865 At special positions: 0 Unit cell: (146.193, 155.797, 194.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 5284 8.00 N 4372 7.00 C 17092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.04 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.04 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " BETA1-6 " NAG Y 1 " - " FUC Y 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 231 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 328 " " NAG A1304 " - " ASN A 613 " " NAG A1305 " - " ASN A 654 " " NAG B1301 " - " ASN B 613 " " NAG B1302 " - " ASN B 328 " " NAG B1303 " - " ASN B 654 " " NAG B1304 " - " ASN B1071 " " NAG B1305 " - " ASN B 61 " " NAG C1301 " - " ASN C 600 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 613 " " NAG C1304 " - " ASN C 654 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 159 " " NAG F 1 " - " ASN A 135 " " NAG G 1 " - " ASN A 279 " " NAG H 1 " - " ASN A 706 " " NAG I 1 " - " ASN A1131 " " NAG J 1 " - " ASN A1095 " " NAG K 1 " - " ASN A 714 " " NAG L 1 " - " ASN A 798 " " NAG M 1 " - " ASN A1071 " " NAG N 1 " - " ASN B 798 " " NAG O 1 " - " ASN B 714 " " NAG P 1 " - " ASN B 706 " " NAG Q 1 " - " ASN B1131 " " NAG R 1 " - " ASN B1095 " " NAG S 1 " - " ASN B 279 " " NAG T 1 " - " ASN C1095 " " NAG U 1 " - " ASN C1131 " " NAG V 1 " - " ASN C 706 " " NAG W 1 " - " ASN C 714 " " NAG X 1 " - " ASN C 798 " " NAG Y 1 " - " ASN C1071 " " NAG Z 1 " - " ASN C 279 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6174 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 47 sheets defined 23.4% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.955A pdb=" N ASN A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.200A pdb=" N PHE A 152 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.076A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.606A pdb=" N ALA A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.968A pdb=" N TYR A 498 " --> pdb=" O ARG A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 757 through 780 Processing helix chain 'A' and resid 813 through 824 Processing helix chain 'A' and resid 825 through 827 No H-bonds generated for 'chain 'A' and resid 825 through 827' Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.691A pdb=" N ILE A 867 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.616A pdb=" N GLY A 886 " --> pdb=" O TRP A 883 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY A 888 " --> pdb=" O PHE A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 937 removed outlier: 4.363A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.548A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.894A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 368 Processing helix chain 'B' and resid 380 through 384 removed outlier: 4.168A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 618 through 622 removed outlier: 4.033A pdb=" N ILE B 621 " --> pdb=" O PRO B 618 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS B 622 " --> pdb=" O VAL B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 622' Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.526A pdb=" N ILE B 739 " --> pdb=" O CYS B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 752 removed outlier: 4.251A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 780 removed outlier: 3.538A pdb=" N ILE B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 778 " --> pdb=" O ASN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 824 Processing helix chain 'B' and resid 863 through 882 removed outlier: 3.676A pdb=" N ILE B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.507A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 910 through 937 removed outlier: 6.744A pdb=" N LYS B 918 " --> pdb=" O TYR B 914 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.644A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 980 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.972A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 removed outlier: 4.023A pdb=" N PHE C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.180A pdb=" N ALA C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 440 removed outlier: 3.528A pdb=" N SER C 440 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 449 removed outlier: 4.322A pdb=" N TYR C 448 " --> pdb=" O ASN C 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 449 " --> pdb=" O TYR C 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 445 through 449' Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 620 through 624 removed outlier: 4.120A pdb=" N ALA C 623 " --> pdb=" O ALA C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 removed outlier: 3.553A pdb=" N CYS C 740 " --> pdb=" O THR C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.514A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 757 through 780 removed outlier: 3.547A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 824 Processing helix chain 'C' and resid 846 through 852 removed outlier: 3.575A pdb=" N GLN C 850 " --> pdb=" O LEU C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 909 through 937 removed outlier: 4.292A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.649A pdb=" N GLN C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 980 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.616A pdb=" N GLU C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.316A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 221 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A 198 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP A 225 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE A 196 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 190 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 199 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 201 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.828A pdb=" N GLN A 268 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.718A pdb=" N GLY A 105 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 104 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER A 114 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS A 129 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 127 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.785A pdb=" N ARG A 100 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 7.235A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 322 through 325 removed outlier: 3.975A pdb=" N ARG A 325 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 550 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.570A pdb=" N ALA A 432 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N CYS A 429 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 510 " --> pdb=" O CYS A 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.097A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.592A pdb=" N ALA A 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 725 removed outlier: 6.904A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 725 removed outlier: 6.904A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.735A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB7, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.096A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU B 221 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE B 198 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP B 225 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE B 196 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 190 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR B 199 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 201 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 51 removed outlier: 4.081A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.809A pdb=" N PHE B 55 " --> pdb=" O GLN B 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 268 " --> pdb=" O PHE B 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AC4, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.564A pdb=" N ARG B 234 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 105 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 114 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 127 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLU B 130 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N CYS B 161 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLN B 132 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N ASN B 159 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 308 through 316 removed outlier: 7.274A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 322 through 323 removed outlier: 3.931A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 352 through 355 removed outlier: 3.528A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 375 through 376 removed outlier: 3.555A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 572 through 574 Processing sheet with id=AD1, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.105A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 692 " --> pdb=" O CYS B 668 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.511A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.511A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD5, first strand: chain 'B' and resid 784 through 785 Processing sheet with id=AD6, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.752A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.927A pdb=" N GLN C 268 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AE1, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.800A pdb=" N CYS C 129 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLU C 130 " --> pdb=" O CYS C 161 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N CYS C 161 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N GLN C 132 " --> pdb=" O ASN C 159 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N ASN C 159 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 186 through 192 removed outlier: 3.543A pdb=" N LYS C 201 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 199 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE C 196 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP C 225 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.660A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.301A pdb=" N LYS C 353 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 513 " --> pdb=" O THR C 390 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL C 392 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER C 511 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA C 394 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL C 509 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 507 " --> pdb=" O PHE C 397 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE C 397 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.301A pdb=" N LYS C 353 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 513 " --> pdb=" O THR C 390 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL C 392 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER C 511 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA C 394 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL C 509 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 510 " --> pdb=" O CYS C 429 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS C 429 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 535 through 537 removed outlier: 3.546A pdb=" N GLY C 547 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 585 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.084A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.537A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.537A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.673A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1117 through 1119 801 hydrogen bonds defined for protein. 2217 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: 6.59 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8423 1.34 - 1.46: 6425 1.46 - 1.58: 12479 1.58 - 1.70: 1 1.70 - 1.82: 147 Bond restraints: 27475 Sorted by residual: bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.603 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" C1 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.410 1.470 -0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" C5 BMA V 3 " pdb=" O5 BMA V 3 " ideal model delta sigma weight residual 1.417 1.473 -0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.51e+00 ... (remaining 27470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 36303 1.68 - 3.35: 850 3.35 - 5.03: 144 5.03 - 6.70: 69 6.70 - 8.38: 4 Bond angle restraints: 37370 Sorted by residual: angle pdb=" C PHE B 372 " pdb=" N THR B 373 " pdb=" CA THR B 373 " ideal model delta sigma weight residual 121.54 129.61 -8.07 1.91e+00 2.74e-01 1.78e+01 angle pdb=" N ILE B 205 " pdb=" CA ILE B 205 " pdb=" C ILE B 205 " ideal model delta sigma weight residual 113.71 109.90 3.81 9.50e-01 1.11e+00 1.61e+01 angle pdb=" N ILE A 831 " pdb=" CA ILE A 831 " pdb=" C ILE A 831 " ideal model delta sigma weight residual 111.91 108.54 3.37 8.90e-01 1.26e+00 1.44e+01 angle pdb=" N PRO B 983 " pdb=" CA PRO B 983 " pdb=" C PRO B 983 " ideal model delta sigma weight residual 110.70 114.39 -3.69 1.22e+00 6.72e-01 9.15e+00 angle pdb=" C ILE B 192 " pdb=" N ASP B 193 " pdb=" CA ASP B 193 " ideal model delta sigma weight residual 122.46 126.68 -4.22 1.41e+00 5.03e-01 8.96e+00 ... (remaining 37365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.63: 16069 24.63 - 49.25: 886 49.25 - 73.88: 145 73.88 - 98.50: 165 98.50 - 123.13: 161 Dihedral angle restraints: 17426 sinusoidal: 7827 harmonic: 9599 Sorted by residual: dihedral pdb=" CB CYS C 837 " pdb=" SG CYS C 837 " pdb=" SG CYS C 848 " pdb=" CB CYS C 848 " ideal model delta sinusoidal sigma weight residual 93.00 -178.45 -88.55 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS A 333 " pdb=" SG CYS A 333 " pdb=" SG CYS A 358 " pdb=" CB CYS A 358 " ideal model delta sinusoidal sigma weight residual -86.00 -22.41 -63.59 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS A 477 " pdb=" SG CYS A 477 " pdb=" SG CYS A 485 " pdb=" CB CYS A 485 " ideal model delta sinusoidal sigma weight residual 93.00 152.34 -59.34 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 17423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4374 0.123 - 0.247: 57 0.247 - 0.370: 21 0.370 - 0.494: 0 0.494 - 0.617: 1 Chirality restraints: 4453 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN C 706 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 135 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 654 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 4450 not shown) Planarity restraints: 4755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 369 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO B 370 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 370 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 370 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " 0.013 2.00e-02 2.50e+03 1.41e-02 4.97e+00 pdb=" CG TRP B 64 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 630 " 0.015 2.00e-02 2.50e+03 1.34e-02 4.49e+00 pdb=" CG TRP A 630 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 630 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 630 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 630 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 630 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 630 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 630 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 630 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 630 " 0.005 2.00e-02 2.50e+03 ... (remaining 4752 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 853 2.71 - 3.26: 26221 3.26 - 3.81: 40534 3.81 - 4.35: 49159 4.35 - 4.90: 84367 Nonbonded interactions: 201134 Sorted by model distance: nonbonded pdb=" OG1 THR B1113 " pdb=" OD1 ASP B1115 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR A 753 " pdb=" OD1 ASP A 991 " model vdw 2.173 3.040 nonbonded pdb=" OH TYR B 377 " pdb=" O PRO B 409 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR A 89 " pdb=" OE1 GLU A 186 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR A 106 " pdb=" O ASN A 231 " model vdw 2.222 3.040 ... (remaining 201129 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 19 through 837 or resid 848 through 1304)) selection = (chain 'B' and (resid 19 through 441 or resid 444 through 1304)) selection = (chain 'C' and (resid 19 through 837 or resid 848 through 1304)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'M' } ncs_group { reference = (chain 'F' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) } 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.200 Find NCS groups from input model: 0.890 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: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.004 0.084 27598 Z= 0.180 Angle : 0.664 17.607 37697 Z= 0.303 Chirality : 0.050 0.617 4453 Planarity : 0.004 0.056 4718 Dihedral : 21.438 123.130 11126 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.98 % Favored : 93.81 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % 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: -0.66 (0.15), residues: 3261 helix: 1.72 (0.22), residues: 682 sheet: -0.01 (0.24), residues: 508 loop : -1.38 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 243 TYR 0.026 0.001 TYR A 901 PHE 0.029 0.001 PHE C 65 TRP 0.039 0.001 TRP B 64 HIS 0.003 0.000 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00364 (27475) covalent geometry : angle 0.63644 (37370) SS BOND : bond 0.00222 ( 42) SS BOND : angle 0.72611 ( 84) hydrogen bonds : bond 0.19614 ( 762) hydrogen bonds : angle 7.55348 ( 2217) link_ALPHA1-3 : bond 0.00795 ( 1) link_ALPHA1-3 : angle 1.29496 ( 3) link_BETA1-4 : bond 0.00995 ( 42) link_BETA1-4 : angle 2.55970 ( 126) link_BETA1-6 : bond 0.01106 ( 1) link_BETA1-6 : angle 1.07638 ( 3) link_NAG-ASN : bond 0.00418 ( 37) link_NAG-ASN : angle 2.30343 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 899 MET cc_start: 0.7989 (tpp) cc_final: 0.7762 (tpt) REVERT: B 749 LEU cc_start: 0.8980 (mp) cc_final: 0.8505 (tt) REVERT: C 262 TYR cc_start: 0.7118 (p90) cc_final: 0.6734 (p90) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.1619 time to fit residues: 49.6032 Evaluate side-chains 130 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0670 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 178 GLN A 202 HIS A 989 GLN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 GLN ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.152338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089314 restraints weight = 55633.036| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.65 r_work: 0.3148 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27598 Z= 0.208 Angle : 0.731 18.375 37697 Z= 0.342 Chirality : 0.051 0.613 4453 Planarity : 0.005 0.066 4718 Dihedral : 17.572 111.554 5199 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.99 % Favored : 92.76 % Rotamer: Outliers : 0.59 % Allowed : 6.01 % Favored : 93.40 % 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: -0.97 (0.14), residues: 3261 helix: 1.57 (0.21), residues: 680 sheet: -0.16 (0.23), residues: 499 loop : -1.64 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 574 TYR 0.021 0.002 TYR B1064 PHE 0.028 0.002 PHE B 903 TRP 0.031 0.002 TRP A 630 HIS 0.006 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00498 (27475) covalent geometry : angle 0.69360 (37370) SS BOND : bond 0.00395 ( 42) SS BOND : angle 1.23693 ( 84) hydrogen bonds : bond 0.05581 ( 762) hydrogen bonds : angle 5.75885 ( 2217) link_ALPHA1-3 : bond 0.00438 ( 1) link_ALPHA1-3 : angle 1.43535 ( 3) link_BETA1-4 : bond 0.01048 ( 42) link_BETA1-4 : angle 3.20702 ( 126) link_BETA1-6 : bond 0.01435 ( 1) link_BETA1-6 : angle 2.06938 ( 3) link_NAG-ASN : bond 0.00402 ( 37) link_NAG-ASN : angle 2.51938 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 737 MET cc_start: 0.8955 (ttm) cc_final: 0.8754 (ttm) REVERT: B 749 LEU cc_start: 0.9174 (mp) cc_final: 0.8753 (tt) REVERT: C 262 TYR cc_start: 0.7019 (p90) cc_final: 0.6715 (p90) REVERT: C 266 TYR cc_start: 0.7721 (m-80) cc_final: 0.7479 (m-80) REVERT: C 961 LYS cc_start: 0.9234 (tmmt) cc_final: 0.9015 (tmmt) REVERT: C 1007 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8554 (mp10) outliers start: 17 outliers final: 9 residues processed: 155 average time/residue: 0.1500 time to fit residues: 39.9266 Evaluate side-chains 138 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1007 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 67 optimal weight: 1.9990 chunk 321 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 323 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** 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 = 0.4292 r_free = 0.4292 target = 0.152059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.090346 restraints weight = 56196.137| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.50 r_work: 0.3143 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27598 Z= 0.157 Angle : 0.654 18.241 37697 Z= 0.306 Chirality : 0.048 0.603 4453 Planarity : 0.004 0.072 4718 Dihedral : 14.165 110.959 5199 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.10 % Favored : 93.65 % Rotamer: Outliers : 0.87 % Allowed : 8.66 % Favored : 90.47 % 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: -0.96 (0.14), residues: 3261 helix: 1.68 (0.21), residues: 674 sheet: -0.29 (0.23), residues: 510 loop : -1.62 (0.12), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 185 TYR 0.017 0.001 TYR B1064 PHE 0.017 0.001 PHE B 903 TRP 0.020 0.001 TRP A 630 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00370 (27475) covalent geometry : angle 0.61324 (37370) SS BOND : bond 0.00309 ( 42) SS BOND : angle 1.14234 ( 84) hydrogen bonds : bond 0.05188 ( 762) hydrogen bonds : angle 5.40644 ( 2217) link_ALPHA1-3 : bond 0.00704 ( 1) link_ALPHA1-3 : angle 1.41222 ( 3) link_BETA1-4 : bond 0.01025 ( 42) link_BETA1-4 : angle 3.06401 ( 126) link_BETA1-6 : bond 0.01648 ( 1) link_BETA1-6 : angle 1.10505 ( 3) link_NAG-ASN : bond 0.00406 ( 37) link_NAG-ASN : angle 2.61901 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 737 MET cc_start: 0.8911 (ttm) cc_final: 0.8666 (ttm) REVERT: B 667 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8935 (mm) REVERT: B 749 LEU cc_start: 0.9217 (mp) cc_final: 0.8787 (tt) REVERT: C 104 PHE cc_start: 0.8233 (m-80) cc_final: 0.7728 (m-80) REVERT: C 756 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8209 (t80) REVERT: C 961 LYS cc_start: 0.9206 (tmmt) cc_final: 0.8954 (tptt) outliers start: 25 outliers final: 17 residues processed: 164 average time/residue: 0.1622 time to fit residues: 45.3371 Evaluate side-chains 149 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1078 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 86 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 447 ASN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.153723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086347 restraints weight = 56021.376| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.77 r_work: 0.3103 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27598 Z= 0.171 Angle : 0.648 18.409 37697 Z= 0.307 Chirality : 0.048 0.641 4453 Planarity : 0.004 0.074 4718 Dihedral : 12.431 114.704 5199 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.24 % Favored : 92.52 % Rotamer: Outliers : 1.40 % Allowed : 11.10 % Favored : 87.50 % 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: -1.05 (0.14), residues: 3261 helix: 1.60 (0.21), residues: 676 sheet: -0.33 (0.23), residues: 483 loop : -1.68 (0.12), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1104 TYR 0.017 0.001 TYR A1064 PHE 0.016 0.001 PHE B 903 TRP 0.054 0.002 TRP A 630 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00409 (27475) covalent geometry : angle 0.60593 (37370) SS BOND : bond 0.00328 ( 42) SS BOND : angle 1.21218 ( 84) hydrogen bonds : bond 0.05253 ( 762) hydrogen bonds : angle 5.24925 ( 2217) link_ALPHA1-3 : bond 0.00631 ( 1) link_ALPHA1-3 : angle 1.46548 ( 3) link_BETA1-4 : bond 0.01016 ( 42) link_BETA1-4 : angle 3.05988 ( 126) link_BETA1-6 : bond 0.01826 ( 1) link_BETA1-6 : angle 1.83572 ( 3) link_NAG-ASN : bond 0.00396 ( 37) link_NAG-ASN : angle 2.64599 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 1.000 Fit side-chains REVERT: A 242 HIS cc_start: 0.5486 (t70) cc_final: 0.5236 (t70) REVERT: A 737 MET cc_start: 0.8883 (ttm) cc_final: 0.8659 (ttt) REVERT: B 426 PHE cc_start: 0.7028 (p90) cc_final: 0.6798 (p90) REVERT: B 749 LEU cc_start: 0.9255 (mp) cc_final: 0.8702 (tt) REVERT: B 756 PHE cc_start: 0.8779 (m-80) cc_final: 0.8551 (m-80) REVERT: C 212 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6788 (m-30) REVERT: C 494 PHE cc_start: 0.1874 (OUTLIER) cc_final: 0.0550 (t80) REVERT: C 756 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8307 (t80) outliers start: 40 outliers final: 22 residues processed: 171 average time/residue: 0.1583 time to fit residues: 46.4332 Evaluate side-chains 155 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1078 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 43 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 250 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 240 optimal weight: 7.9990 chunk 159 optimal weight: 0.0980 chunk 121 optimal weight: 0.0870 chunk 255 optimal weight: 40.0000 chunk 70 optimal weight: 0.5980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 989 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** 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 = 0.4299 r_free = 0.4299 target = 0.152489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.091026 restraints weight = 55866.862| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.52 r_work: 0.3156 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27598 Z= 0.115 Angle : 0.615 18.123 37697 Z= 0.289 Chirality : 0.046 0.600 4453 Planarity : 0.004 0.076 4718 Dihedral : 11.736 114.654 5199 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.73 % Favored : 94.02 % Rotamer: Outliers : 1.19 % Allowed : 12.64 % Favored : 86.17 % 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: -0.92 (0.14), residues: 3261 helix: 1.76 (0.21), residues: 673 sheet: -0.20 (0.24), residues: 469 loop : -1.62 (0.12), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 980 TYR 0.017 0.001 TYR B1064 PHE 0.012 0.001 PHE C1118 TRP 0.040 0.001 TRP A 630 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00256 (27475) covalent geometry : angle 0.57332 (37370) SS BOND : bond 0.00242 ( 42) SS BOND : angle 1.10441 ( 84) hydrogen bonds : bond 0.04444 ( 762) hydrogen bonds : angle 5.02797 ( 2217) link_ALPHA1-3 : bond 0.00615 ( 1) link_ALPHA1-3 : angle 1.64194 ( 3) link_BETA1-4 : bond 0.00984 ( 42) link_BETA1-4 : angle 2.97425 ( 126) link_BETA1-6 : bond 0.01747 ( 1) link_BETA1-6 : angle 1.66583 ( 3) link_NAG-ASN : bond 0.00402 ( 37) link_NAG-ASN : angle 2.55603 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 1.015 Fit side-chains REVERT: A 242 HIS cc_start: 0.5451 (t70) cc_final: 0.5224 (t70) REVERT: B 362 TYR cc_start: 0.7890 (m-80) cc_final: 0.7420 (m-80) REVERT: B 749 LEU cc_start: 0.9207 (mp) cc_final: 0.8723 (tt) REVERT: B 756 PHE cc_start: 0.8730 (m-80) cc_final: 0.8478 (m-80) REVERT: B 982 ASP cc_start: 0.7679 (p0) cc_final: 0.6811 (p0) REVERT: C 212 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6677 (m-30) REVERT: C 494 PHE cc_start: 0.1916 (OUTLIER) cc_final: 0.0538 (t80) REVERT: C 749 LEU cc_start: 0.8798 (mp) cc_final: 0.8348 (tp) REVERT: C 980 ARG cc_start: 0.7236 (mtm110) cc_final: 0.6356 (mpt180) REVERT: C 1007 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8411 (mp10) outliers start: 34 outliers final: 17 residues processed: 170 average time/residue: 0.1527 time to fit residues: 44.6451 Evaluate side-chains 153 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1007 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 88 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 233 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 199 optimal weight: 0.4980 chunk 115 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 168 GLN A 183 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 ASN B 923 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.151697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.085405 restraints weight = 55478.786| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.66 r_work: 0.3073 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 27598 Z= 0.234 Angle : 0.704 18.102 37697 Z= 0.337 Chirality : 0.049 0.704 4453 Planarity : 0.005 0.076 4718 Dihedral : 11.292 116.100 5199 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.00 % Favored : 91.72 % Rotamer: Outliers : 1.43 % Allowed : 14.21 % Favored : 84.36 % 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: -1.23 (0.14), residues: 3261 helix: 1.44 (0.21), residues: 675 sheet: -0.43 (0.24), residues: 465 loop : -1.78 (0.12), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1104 TYR 0.028 0.002 TYR B 366 PHE 0.025 0.002 PHE A 217 TRP 0.036 0.002 TRP A 630 HIS 0.005 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00568 (27475) covalent geometry : angle 0.66325 (37370) SS BOND : bond 0.00422 ( 42) SS BOND : angle 1.45693 ( 84) hydrogen bonds : bond 0.06188 ( 762) hydrogen bonds : angle 5.32168 ( 2217) link_ALPHA1-3 : bond 0.00590 ( 1) link_ALPHA1-3 : angle 1.62970 ( 3) link_BETA1-4 : bond 0.00979 ( 42) link_BETA1-4 : angle 2.99950 ( 126) link_BETA1-6 : bond 0.01847 ( 1) link_BETA1-6 : angle 1.69333 ( 3) link_NAG-ASN : bond 0.00408 ( 37) link_NAG-ASN : angle 2.83779 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.924 Fit side-chains REVERT: A 239 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7897 (mm) REVERT: A 242 HIS cc_start: 0.5526 (t70) cc_final: 0.5243 (t70) REVERT: B 749 LEU cc_start: 0.9238 (mp) cc_final: 0.8611 (tt) REVERT: B 756 PHE cc_start: 0.8765 (m-80) cc_final: 0.8524 (m-80) REVERT: C 494 PHE cc_start: 0.1651 (OUTLIER) cc_final: 0.0300 (t80) REVERT: C 749 LEU cc_start: 0.8836 (mp) cc_final: 0.8467 (tp) outliers start: 41 outliers final: 25 residues processed: 167 average time/residue: 0.1527 time to fit residues: 43.6716 Evaluate side-chains 154 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1078 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 271 optimal weight: 8.9990 chunk 304 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 309 optimal weight: 5.9990 chunk 326 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 308 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 250 optimal weight: 30.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 GLN B 66 HIS ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.151663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.090174 restraints weight = 55699.384| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.53 r_work: 0.3141 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27598 Z= 0.118 Angle : 0.626 18.001 37697 Z= 0.295 Chirality : 0.046 0.623 4453 Planarity : 0.004 0.077 4718 Dihedral : 10.547 117.668 5199 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.38 % Favored : 93.31 % Rotamer: Outliers : 1.19 % Allowed : 14.98 % Favored : 83.83 % 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: -1.05 (0.14), residues: 3261 helix: 1.66 (0.21), residues: 673 sheet: -0.33 (0.23), residues: 473 loop : -1.68 (0.12), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 980 TYR 0.017 0.001 TYR B1064 PHE 0.015 0.001 PHE A 217 TRP 0.035 0.001 TRP A 630 HIS 0.002 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00261 (27475) covalent geometry : angle 0.58416 (37370) SS BOND : bond 0.00275 ( 42) SS BOND : angle 0.96804 ( 84) hydrogen bonds : bond 0.04631 ( 762) hydrogen bonds : angle 5.00942 ( 2217) link_ALPHA1-3 : bond 0.00533 ( 1) link_ALPHA1-3 : angle 1.82954 ( 3) link_BETA1-4 : bond 0.00990 ( 42) link_BETA1-4 : angle 3.01392 ( 126) link_BETA1-6 : bond 0.01900 ( 1) link_BETA1-6 : angle 1.82392 ( 3) link_NAG-ASN : bond 0.00396 ( 37) link_NAG-ASN : angle 2.65137 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: B 749 LEU cc_start: 0.9040 (mp) cc_final: 0.8747 (tt) REVERT: B 756 PHE cc_start: 0.8711 (m-80) cc_final: 0.8459 (m-80) REVERT: C 163 PHE cc_start: 0.8072 (t80) cc_final: 0.7745 (t80) REVERT: C 494 PHE cc_start: 0.1673 (OUTLIER) cc_final: 0.0303 (t80) REVERT: C 749 LEU cc_start: 0.8841 (mp) cc_final: 0.8544 (tp) REVERT: C 980 ARG cc_start: 0.7508 (mtm110) cc_final: 0.6570 (mpt180) REVERT: C 1007 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8599 (mp10) outliers start: 34 outliers final: 18 residues processed: 167 average time/residue: 0.1495 time to fit residues: 43.0104 Evaluate side-chains 151 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1078 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 272 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 199 optimal weight: 0.0070 chunk 164 optimal weight: 8.9990 chunk 234 optimal weight: 8.9990 chunk 273 optimal weight: 0.9980 chunk 279 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 281 optimal weight: 0.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 HIS ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** 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 = 0.4286 r_free = 0.4286 target = 0.153235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.086681 restraints weight = 56109.023| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.71 r_work: 0.3105 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27598 Z= 0.150 Angle : 0.635 17.904 37697 Z= 0.301 Chirality : 0.047 0.640 4453 Planarity : 0.004 0.077 4718 Dihedral : 10.125 119.872 5199 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.08 % Favored : 92.61 % Rotamer: Outliers : 1.05 % Allowed : 15.54 % Favored : 83.41 % 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: 3261 helix: 1.63 (0.21), residues: 676 sheet: -0.35 (0.23), residues: 480 loop : -1.70 (0.12), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1104 TYR 0.017 0.001 TYR B1064 PHE 0.017 0.001 PHE A 217 TRP 0.041 0.002 TRP A 630 HIS 0.003 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00353 (27475) covalent geometry : angle 0.59377 (37370) SS BOND : bond 0.00305 ( 42) SS BOND : angle 1.06185 ( 84) hydrogen bonds : bond 0.04909 ( 762) hydrogen bonds : angle 4.99281 ( 2217) link_ALPHA1-3 : bond 0.00321 ( 1) link_ALPHA1-3 : angle 1.97855 ( 3) link_BETA1-4 : bond 0.00980 ( 42) link_BETA1-4 : angle 2.90581 ( 126) link_BETA1-6 : bond 0.01819 ( 1) link_BETA1-6 : angle 1.80116 ( 3) link_NAG-ASN : bond 0.00373 ( 37) link_NAG-ASN : angle 2.74184 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.965 Fit side-chains REVERT: A 242 HIS cc_start: 0.5499 (t70) cc_final: 0.5185 (t70) REVERT: B 749 LEU cc_start: 0.9224 (mp) cc_final: 0.8660 (tt) REVERT: B 756 PHE cc_start: 0.8790 (m-80) cc_final: 0.8517 (m-80) REVERT: C 163 PHE cc_start: 0.8078 (t80) cc_final: 0.7791 (t80) REVERT: C 494 PHE cc_start: 0.1702 (OUTLIER) cc_final: 0.0323 (t80) REVERT: C 749 LEU cc_start: 0.8830 (mp) cc_final: 0.8551 (tp) REVERT: C 1007 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8643 (mp10) outliers start: 30 outliers final: 20 residues processed: 163 average time/residue: 0.1500 time to fit residues: 42.0733 Evaluate side-chains 157 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain C residue 1078 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 240 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 177 optimal weight: 0.7980 chunk 317 optimal weight: 1.9990 chunk 141 optimal weight: 30.0000 chunk 286 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 320 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1068 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.152522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.091619 restraints weight = 54637.498| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.40 r_work: 0.3214 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27598 Z= 0.139 Angle : 0.627 17.916 37697 Z= 0.297 Chirality : 0.047 0.626 4453 Planarity : 0.004 0.078 4718 Dihedral : 9.880 118.290 5199 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.35 % Favored : 93.31 % Rotamer: Outliers : 0.87 % Allowed : 15.99 % Favored : 83.14 % 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: -1.02 (0.14), residues: 3261 helix: 1.66 (0.21), residues: 674 sheet: -0.29 (0.23), residues: 499 loop : -1.68 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 454 TYR 0.017 0.001 TYR B1064 PHE 0.019 0.001 PHE A 217 TRP 0.039 0.002 TRP A 630 HIS 0.003 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00327 (27475) covalent geometry : angle 0.58671 (37370) SS BOND : bond 0.00280 ( 42) SS BOND : angle 0.98108 ( 84) hydrogen bonds : bond 0.04680 ( 762) hydrogen bonds : angle 4.92982 ( 2217) link_ALPHA1-3 : bond 0.00269 ( 1) link_ALPHA1-3 : angle 2.15126 ( 3) link_BETA1-4 : bond 0.00996 ( 42) link_BETA1-4 : angle 2.85289 ( 126) link_BETA1-6 : bond 0.01795 ( 1) link_BETA1-6 : angle 1.85500 ( 3) link_NAG-ASN : bond 0.00382 ( 37) link_NAG-ASN : angle 2.69850 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 242 HIS cc_start: 0.5506 (t70) cc_final: 0.5179 (t70) REVERT: B 749 LEU cc_start: 0.9050 (mp) cc_final: 0.8810 (tt) REVERT: B 756 PHE cc_start: 0.8789 (m-80) cc_final: 0.8513 (m-80) REVERT: C 163 PHE cc_start: 0.8028 (t80) cc_final: 0.7768 (t80) REVERT: C 323 ILE cc_start: 0.6450 (OUTLIER) cc_final: 0.6242 (mm) REVERT: C 494 PHE cc_start: 0.1686 (OUTLIER) cc_final: 0.0364 (t80) REVERT: C 749 LEU cc_start: 0.8823 (mp) cc_final: 0.8554 (tp) REVERT: C 1007 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8541 (mp10) outliers start: 25 outliers final: 20 residues processed: 158 average time/residue: 0.1515 time to fit residues: 41.0773 Evaluate side-chains 156 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1078 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 142 optimal weight: 0.0020 chunk 267 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 302 optimal weight: 0.0770 chunk 291 optimal weight: 4.9990 chunk 258 optimal weight: 40.0000 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.8152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN B 457 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.153015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088511 restraints weight = 55913.653| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.60 r_work: 0.3185 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27598 Z= 0.162 Angle : 0.645 17.749 37697 Z= 0.308 Chirality : 0.047 0.648 4453 Planarity : 0.004 0.078 4718 Dihedral : 9.693 117.419 5199 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.27 % Favored : 92.43 % Rotamer: Outliers : 0.98 % Allowed : 15.96 % Favored : 83.07 % 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: -1.10 (0.14), residues: 3261 helix: 1.59 (0.21), residues: 676 sheet: -0.36 (0.23), residues: 504 loop : -1.73 (0.12), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1104 TYR 0.017 0.001 TYR B1064 PHE 0.017 0.001 PHE C 326 TRP 0.041 0.002 TRP A 630 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00385 (27475) covalent geometry : angle 0.60539 (37370) SS BOND : bond 0.00317 ( 42) SS BOND : angle 1.08275 ( 84) hydrogen bonds : bond 0.05047 ( 762) hydrogen bonds : angle 4.98532 ( 2217) link_ALPHA1-3 : bond 0.00309 ( 1) link_ALPHA1-3 : angle 2.12264 ( 3) link_BETA1-4 : bond 0.00963 ( 42) link_BETA1-4 : angle 2.83354 ( 126) link_BETA1-6 : bond 0.01809 ( 1) link_BETA1-6 : angle 1.87259 ( 3) link_NAG-ASN : bond 0.00376 ( 37) link_NAG-ASN : angle 2.78638 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 242 HIS cc_start: 0.5471 (t70) cc_final: 0.5175 (t70) REVERT: B 630 TRP cc_start: 0.7393 (t60) cc_final: 0.7136 (t60) REVERT: B 749 LEU cc_start: 0.9230 (mp) cc_final: 0.8698 (tt) REVERT: B 756 PHE cc_start: 0.8798 (m-80) cc_final: 0.8529 (m-80) REVERT: C 163 PHE cc_start: 0.8118 (t80) cc_final: 0.7852 (t80) REVERT: C 323 ILE cc_start: 0.6572 (OUTLIER) cc_final: 0.6366 (mm) REVERT: C 494 PHE cc_start: 0.1686 (OUTLIER) cc_final: 0.0346 (t80) REVERT: C 749 LEU cc_start: 0.8815 (mp) cc_final: 0.8557 (tp) REVERT: C 1007 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8560 (mp10) outliers start: 28 outliers final: 25 residues processed: 158 average time/residue: 0.1542 time to fit residues: 41.7914 Evaluate side-chains 159 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 275 optimal weight: 4.9990 chunk 282 optimal weight: 0.2980 chunk 233 optimal weight: 8.9990 chunk 205 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 260 optimal weight: 40.0000 chunk 69 optimal weight: 2.9990 chunk 287 optimal weight: 0.5980 chunk 296 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** 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 = 0.4307 r_free = 0.4307 target = 0.153085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.088640 restraints weight = 55661.003| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.60 r_work: 0.3187 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 27598 Z= 0.174 Angle : 0.755 59.191 37697 Z= 0.396 Chirality : 0.047 0.649 4453 Planarity : 0.004 0.078 4718 Dihedral : 9.695 117.429 5199 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.27 % Favored : 92.43 % Rotamer: Outliers : 1.01 % Allowed : 16.06 % Favored : 82.93 % 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: -1.11 (0.14), residues: 3261 helix: 1.58 (0.21), residues: 676 sheet: -0.38 (0.23), residues: 504 loop : -1.73 (0.12), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1104 TYR 0.017 0.001 TYR B1064 PHE 0.015 0.001 PHE A 217 TRP 0.096 0.003 TRP A 630 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00402 (27475) covalent geometry : angle 0.72218 (37370) SS BOND : bond 0.00314 ( 42) SS BOND : angle 1.07024 ( 84) hydrogen bonds : bond 0.05049 ( 762) hydrogen bonds : angle 4.98791 ( 2217) link_ALPHA1-3 : bond 0.00306 ( 1) link_ALPHA1-3 : angle 2.12481 ( 3) link_BETA1-4 : bond 0.01028 ( 42) link_BETA1-4 : angle 2.86034 ( 126) link_BETA1-6 : bond 0.01758 ( 1) link_BETA1-6 : angle 1.84265 ( 3) link_NAG-ASN : bond 0.00375 ( 37) link_NAG-ASN : angle 2.78421 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8846.38 seconds wall clock time: 151 minutes 25.20 seconds (9085.20 seconds total)