Starting phenix.real_space_refine on Sat Jul 4 11:12:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gas_29905/07_2026/8gas_29905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gas_29905/07_2026/8gas_29905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gas_29905/07_2026/8gas_29905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gas_29905/07_2026/8gas_29905.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gas_29905/07_2026/8gas_29905.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gas_29905/07_2026/8gas_29905.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gas_29905/07_2026/8gas_29905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gas_29905/07_2026/8gas_29905.map" } resolution = 4.04 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= 0.013 sd= 0.074 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 129 5.16 5 C 12696 2.51 5 N 3369 2.21 5 O 4059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20253 Number of models: 1 Model: "" Number of chains: 39 Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 939 Classifications: {'peptide': 121} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 114} Chain: "G" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3472 Classifications: {'peptide': 442} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "A" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 939 Classifications: {'peptide': 121} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3472 Classifications: {'peptide': 442} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 939 Classifications: {'peptide': 121} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 114} Chain: "J" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3472 Classifications: {'peptide': 442} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "M" 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 chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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 chiralities: 3 Chain: "S" 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 chiralities: 4 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 chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 3 Chain: "Y" 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 chiralities: 3 Chain: "Z" 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 chiralities: 4 Chain: "a" 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 chiralities: 3 Chain: "b" 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 chiralities: 2 Chain: "c" 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 chiralities: 2 Chain: "d" 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 chiralities: 2 Chain: "e" 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 chiralities: 3 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 chiralities: 3 Chain: "g" 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 chiralities: 4 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" 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 chiralities: 2 Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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 chiralities: 2 Chain: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.56, per 1000 atoms: 0.23 Number of scatterers: 20253 At special positions: 0 Unit cell: (142.749, 150.262, 122.356, 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 129 16.00 O 4059 8.00 N 3369 7.00 C 12696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 433 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 433 " distance=2.04 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.03 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " 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 S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " " BMA g 3 " - " MAN g 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " 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-ASN " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG D 601 " - " ASN D 133 " " NAG D 602 " - " ASN D 156 " " NAG D 603 " - " ASN D 160 " " NAG D 604 " - " ASN D 197 " " NAG D 605 " - " ASN D 276 " " NAG D 606 " - " ASN D 301 " " NAG D 607 " - " ASN D 355 " " NAG D 608 " - " ASN D 339 " " NAG D 609 " - " ASN D 392 " " NAG D 610 " - " ASN D 234 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 156 " " NAG G 603 " - " ASN G 160 " " NAG G 604 " - " ASN G 197 " " NAG G 605 " - " ASN G 276 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 355 " " NAG G 608 " - " ASN G 339 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 234 " " NAG J 601 " - " ASN J 133 " " NAG J 602 " - " ASN J 156 " " NAG J 603 " - " ASN J 160 " " NAG J 604 " - " ASN J 197 " " NAG J 605 " - " ASN J 276 " " NAG J 606 " - " ASN J 301 " " NAG J 607 " - " ASN J 355 " " NAG J 608 " - " ASN J 339 " " NAG J 609 " - " ASN J 392 " " NAG J 610 " - " ASN J 234 " " NAG K 701 " - " ASN K 611 " " NAG K 702 " - " ASN K 637 " " NAG M 1 " - " ASN G 88 " " NAG N 1 " - " ASN G 295 " " NAG O 1 " - " ASN G 332 " " NAG P 1 " - " ASN G 363 " " NAG Q 1 " - " ASN G 386 " " NAG R 1 " - " ASN G 448 " " NAG S 1 " - " ASN G 262 " " NAG T 1 " - " ASN D 88 " " NAG U 1 " - " ASN D 295 " " NAG V 1 " - " ASN D 332 " " NAG W 1 " - " ASN D 363 " " NAG X 1 " - " ASN D 386 " " NAG Y 1 " - " ASN D 448 " " NAG Z 1 " - " ASN D 262 " " NAG a 1 " - " ASN J 88 " " NAG b 1 " - " ASN J 295 " " NAG c 1 " - " ASN J 332 " " NAG d 1 " - " ASN J 363 " " NAG e 1 " - " ASN J 386 " " NAG f 1 " - " ASN J 448 " " NAG g 1 " - " ASN J 262 " Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 817.6 milliseconds 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4470 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 39 sheets defined 22.3% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.760A pdb=" N LYS H 64 " --> pdb=" O GLY H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.038A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.572A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.529A pdb=" N ARG G 151 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 350 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.654A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 381 removed outlier: 3.580A pdb=" N GLY G 380 " --> pdb=" O ASN G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 391 removed outlier: 3.788A pdb=" N PHE G 391 " --> pdb=" O SER G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 484 removed outlier: 4.064A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 Processing helix chain 'B' and resid 523 through 528 removed outlier: 3.586A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.846A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 537 through 542' Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.543A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.828A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.828A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.510A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.832A pdb=" N LYS C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.999A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.538A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 126' Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.529A pdb=" N ARG D 151 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 350 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.635A pdb=" N THR D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 381 removed outlier: 3.569A pdb=" N GLY D 380 " --> pdb=" O ASN D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.815A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 484 removed outlier: 4.040A pdb=" N ASN D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 521 Processing helix chain 'E' and resid 523 through 528 removed outlier: 3.654A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 542 removed outlier: 3.906A pdb=" N ALA E 541 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 537 through 542' Processing helix chain 'E' and resid 543 through 545 No H-bonds generated for 'chain 'E' and resid 543 through 545' Processing helix chain 'E' and resid 572 through 596 removed outlier: 3.527A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 619 through 624 removed outlier: 3.820A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.761A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 662 removed outlier: 3.540A pdb=" N LEU E 646 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.615A pdb=" N LYS I 64 " --> pdb=" O GLY I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 98 through 117 removed outlier: 4.012A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE J 109 " --> pdb=" O HIS J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 126 removed outlier: 3.569A pdb=" N LEU J 125 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS J 126 " --> pdb=" O THR J 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 122 through 126' Processing helix chain 'J' and resid 139 through 151 Processing helix chain 'J' and resid 334 through 350 Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.819A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 381 removed outlier: 3.601A pdb=" N GLY J 380 " --> pdb=" O ASN J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 391 removed outlier: 3.825A pdb=" N PHE J 391 " --> pdb=" O SER J 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 484 removed outlier: 4.047A pdb=" N ASN J 478 " --> pdb=" O ASP J 474 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP J 479 " --> pdb=" O MET J 475 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 517 through 521 Processing helix chain 'K' and resid 523 through 528 removed outlier: 3.579A pdb=" N GLY K 527 " --> pdb=" O GLY K 524 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 534 removed outlier: 3.515A pdb=" N SER K 534 " --> pdb=" O MET K 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 537 through 542 removed outlier: 3.809A pdb=" N ALA K 541 " --> pdb=" O LEU K 537 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG K 542 " --> pdb=" O THR K 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 537 through 542' Processing helix chain 'K' and resid 543 through 545 No H-bonds generated for 'chain 'K' and resid 543 through 545' Processing helix chain 'K' and resid 572 through 596 removed outlier: 3.537A pdb=" N ASP K 589 " --> pdb=" O ARG K 585 " (cutoff:3.500A) Processing helix chain 'K' and resid 611 through 615 Processing helix chain 'K' and resid 618 through 624 removed outlier: 3.816A pdb=" N ASP K 624 " --> pdb=" O SER K 620 " (cutoff:3.500A) Processing helix chain 'K' and resid 627 through 636 removed outlier: 3.686A pdb=" N TRP K 631 " --> pdb=" O THR K 627 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS K 633 " --> pdb=" O LEU K 629 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU K 634 " --> pdb=" O GLN K 630 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE K 635 " --> pdb=" O TRP K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 638 through 662 removed outlier: 3.572A pdb=" N LEU K 646 " --> pdb=" O ILE K 642 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU K 647 " --> pdb=" O TYR K 643 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU K 648 " --> pdb=" O GLY K 644 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.522A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.875A pdb=" N ILE L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU L 37 " --> pdb=" O ARG L 46 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.573A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 9 through 10 removed outlier: 3.936A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 495 through 499 Processing sheet with id=AA6, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.907A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA9, first strand: chain 'G' and resid 181 through 182 Processing sheet with id=AB1, first strand: chain 'G' and resid 202 through 203 removed outlier: 7.326A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 259 through 261 removed outlier: 4.380A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 298 current: chain 'G' and resid 360 through 361 Processing sheet with id=AB3, first strand: chain 'G' and resid 271 through 273 removed outlier: 7.140A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 443 through 456 current: chain 'G' and resid 416 through 420 Processing sheet with id=AB4, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.922A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.511A pdb=" N THR A 5 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 21 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.878A pdb=" N ILE A 85 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 37 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ARG A 46 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.512A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 20 " --> pdb=" O MET C 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.875A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 495 through 499 removed outlier: 3.509A pdb=" N CYS E 604 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.928A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AC4, first strand: chain 'D' and resid 181 through 182 Processing sheet with id=AC5, first strand: chain 'D' and resid 202 through 203 removed outlier: 7.341A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 259 through 261 removed outlier: 4.367A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 271 through 273 removed outlier: 7.138A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 359 " --> pdb=" O TRP D 395 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.956A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.609A pdb=" N THR F 5 " --> pdb=" O LYS F 24 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE F 21 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.868A pdb=" N ILE F 85 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU F 37 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ARG F 46 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.532A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 9 through 10 removed outlier: 3.989A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TRP I 47 " --> pdb=" O LYS I 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP I 50 " --> pdb=" O ASN I 58 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 495 through 499 removed outlier: 5.137A pdb=" N VAL J 36 " --> pdb=" O THR K 606 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR K 606 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS K 604 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 45 through 46 removed outlier: 3.511A pdb=" N ILE J 84 " --> pdb=" O THR J 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'J' and resid 130 through 133 Processing sheet with id=AD8, first strand: chain 'J' and resid 181 through 182 Processing sheet with id=AD9, first strand: chain 'J' and resid 202 through 203 removed outlier: 6.971A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 259 through 261 removed outlier: 4.385A pdb=" N GLY J 451 " --> pdb=" O LEU J 260 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N VAL J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N VAL J 292 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ASN J 448 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N THR J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR J 450 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS J 330 " --> pdb=" O THR J 297 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 271 through 273 removed outlier: 7.133A pdb=" N THR J 450 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N THR J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ASN J 448 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N VAL J 292 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N VAL J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER J 393 " --> pdb=" O PHE J 361 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 304 through 312 removed outlier: 6.884A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) 593 hydrogen bonds defined for protein. 1470 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: 3.67 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4681 1.33 - 1.46: 5583 1.46 - 1.58: 10220 1.58 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 20658 Sorted by residual: bond pdb=" C GLU C 100B" pdb=" N PRO C 100C" ideal model delta sigma weight residual 1.334 1.359 -0.025 8.40e-03 1.42e+04 8.82e+00 bond pdb=" C GLY I 53 " pdb=" N SER I 54 " ideal model delta sigma weight residual 1.335 1.304 0.031 1.35e-02 5.49e+03 5.24e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.36e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.18e+00 ... (remaining 20653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 27204 1.88 - 3.77: 710 3.77 - 5.65: 107 5.65 - 7.54: 31 7.54 - 9.42: 4 Bond angle restraints: 28056 Sorted by residual: angle pdb=" C LEU C 82 " pdb=" N SER C 82A" pdb=" CA SER C 82A" ideal model delta sigma weight residual 121.70 131.12 -9.42 1.80e+00 3.09e-01 2.74e+01 angle pdb=" C LEU H 82 " pdb=" N SER H 82A" pdb=" CA SER H 82A" ideal model delta sigma weight residual 121.70 131.12 -9.42 1.80e+00 3.09e-01 2.74e+01 angle pdb=" C LEU I 82 " pdb=" N SER I 82A" pdb=" CA SER I 82A" ideal model delta sigma weight residual 121.70 131.10 -9.40 1.80e+00 3.09e-01 2.73e+01 angle pdb=" N ILE J 309 " pdb=" CA ILE J 309 " pdb=" C ILE J 309 " ideal model delta sigma weight residual 112.96 109.51 3.45 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CA GLN K 652 " pdb=" CB GLN K 652 " pdb=" CG GLN K 652 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.08e+00 ... (remaining 28051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9987 17.98 - 35.96: 1243 35.96 - 53.94: 258 53.94 - 71.93: 95 71.93 - 89.91: 30 Dihedral angle restraints: 11613 sinusoidal: 4656 harmonic: 6957 Sorted by residual: dihedral pdb=" CB CYS J 201 " pdb=" SG CYS J 201 " pdb=" SG CYS J 433 " pdb=" CB CYS J 433 " ideal model delta sinusoidal sigma weight residual 93.00 29.92 63.08 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS D 201 " pdb=" SG CYS D 201 " pdb=" SG CYS D 433 " pdb=" CB CYS D 433 " ideal model delta sinusoidal sigma weight residual 93.00 31.57 61.43 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual 93.00 31.71 61.29 1 1.00e+01 1.00e-02 4.99e+01 ... (remaining 11610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3388 0.134 - 0.268: 26 0.268 - 0.402: 6 0.402 - 0.536: 0 0.536 - 0.670: 3 Chirality restraints: 3423 Sorted by residual: chirality pdb=" C1 NAG E 701 " pdb=" ND2 ASN E 611 " pdb=" C2 NAG E 701 " pdb=" O5 NAG E 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C1 NAG K 701 " pdb=" ND2 ASN K 611 " pdb=" C2 NAG K 701 " pdb=" O5 NAG K 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 611 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 ... (remaining 3420 not shown) Planarity restraints: 3501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 213 " 0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO D 214 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO D 214 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 214 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 213 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO G 214 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO G 214 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 214 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 213 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO J 214 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO J 214 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 214 " -0.032 5.00e-02 4.00e+02 ... (remaining 3498 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 330 2.64 - 3.20: 18788 3.20 - 3.77: 29634 3.77 - 4.33: 40102 4.33 - 4.90: 65069 Nonbonded interactions: 153923 Sorted by model distance: nonbonded pdb=" OE2 GLU J 275 " pdb=" NZ LYS J 282 " model vdw 2.069 3.120 nonbonded pdb=" O3 NAG a 1 " pdb=" O5 NAG a 2 " model vdw 2.131 3.040 nonbonded pdb=" O3 NAG T 1 " pdb=" O5 NAG T 2 " model vdw 2.131 3.040 nonbonded pdb=" O3 NAG M 1 " pdb=" O5 NAG M 2 " model vdw 2.132 3.040 nonbonded pdb=" O ASN G 377 " pdb=" ND2 ASN G 377 " model vdw 2.167 3.120 ... (remaining 153918 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' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'S' selection = chain 'Z' selection = chain 'g' } 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 group one per residue 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: 2.250 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.970 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 0.057 20793 Z= 0.201 Angle : 0.722 13.202 28419 Z= 0.320 Chirality : 0.052 0.670 3423 Planarity : 0.004 0.089 3444 Dihedral : 17.037 89.906 7017 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.79 % Favored : 95.09 % Rotamer: Outliers : 0.09 % Allowed : 22.73 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % 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: -0.68 (0.18), residues: 2382 helix: 1.64 (0.31), residues: 324 sheet: -0.58 (0.20), residues: 690 loop : -0.88 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 360 TYR 0.030 0.001 TYR J 435 PHE 0.016 0.001 PHE D 391 TRP 0.022 0.001 TRP I 100D HIS 0.006 0.000 HIS D 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (20658) covalent geometry : angle 0.68339 / 0.31 (28056) SS BOND : bond 0.00336 / 0.21 ( 42) SS BOND : angle 1.22248 / 0.72 ( 84) hydrogen bonds : bond 0.25150 / 16.62 ( 578) hydrogen bonds : angle 8.60803 / 5.97 ( 1470) link_ALPHA1-3 : bond 0.00432 / 0.22 ( 3) link_ALPHA1-3 : angle 1.52130 / 0.98 ( 9) link_BETA1-4 : bond 0.00349 / 0.22 ( 33) link_BETA1-4 : angle 1.98172 / 1.40 ( 99) link_NAG-ASN : bond 0.00598 / 0.46 ( 57) link_NAG-ASN : angle 2.63966 / 2.20 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 275 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 ILE cc_start: 0.7425 (pt) cc_final: 0.7076 (mm) REVERT: L 77 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.8011 (ttp-170) REVERT: L 81 GLU cc_start: 0.8497 (mp0) cc_final: 0.8214 (mp0) REVERT: H 32 TYR cc_start: 0.8456 (m-80) cc_final: 0.8151 (m-80) REVERT: G 259 LEU cc_start: 0.7891 (mp) cc_final: 0.7618 (mp) REVERT: C 34 ILE cc_start: 0.8704 (mm) cc_final: 0.8222 (mm) REVERT: C 91 TYR cc_start: 0.6373 (m-10) cc_final: 0.6132 (m-10) REVERT: E 639 THR cc_start: 0.7488 (m) cc_final: 0.6777 (t) REVERT: F 21 ILE cc_start: 0.8650 (pt) cc_final: 0.8350 (mm) REVERT: I 45 LEU cc_start: 0.7222 (mm) cc_final: 0.6764 (mm) REVERT: I 51 ILE cc_start: 0.8040 (tp) cc_final: 0.7565 (tp) outliers start: 2 outliers final: 0 residues processed: 277 average time/residue: 0.1515 time to fit residues: 63.1172 Evaluate side-chains 146 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.3980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.0370 overall best weight: 1.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN G 99 ASN G 330 HIS A 17 GLN A 96 GLN C 81 GLN D 99 ASN D 330 HIS I 81 GLN J 99 ASN J 103 GLN J 330 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.071006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.052446 restraints weight = 100140.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.054210 restraints weight = 56222.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.055427 restraints weight = 38780.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.056265 restraints weight = 30272.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.056888 restraints weight = 25532.576| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20793 Z= 0.155 Angle : 0.756 15.589 28419 Z= 0.363 Chirality : 0.049 0.494 3423 Planarity : 0.005 0.087 3444 Dihedral : 4.734 30.815 2592 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.42 % Favored : 93.45 % Rotamer: Outliers : 0.05 % Allowed : 3.79 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.18), residues: 2382 helix: 1.41 (0.29), residues: 351 sheet: -0.73 (0.18), residues: 750 loop : -0.97 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 103 TYR 0.027 0.002 TYR I 91 PHE 0.021 0.002 PHE D 159 TRP 0.033 0.002 TRP K 571 HIS 0.006 0.001 HIS D 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (20658) covalent geometry : angle 0.70079 / 0.35 (28056) SS BOND : bond 0.00395 / 0.30 ( 42) SS BOND : angle 1.38396 / 0.97 ( 84) hydrogen bonds : bond 0.05051 / 3.37 ( 578) hydrogen bonds : angle 6.22590 / 4.26 ( 1470) link_ALPHA1-3 : bond 0.00549 / 0.27 ( 3) link_ALPHA1-3 : angle 1.67631 / 0.94 ( 9) link_BETA1-4 : bond 0.00497 / 0.32 ( 33) link_BETA1-4 : angle 1.93668 / 1.32 ( 99) link_NAG-ASN : bond 0.00615 / 0.45 ( 57) link_NAG-ASN : angle 3.35366 / 2.61 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 ASP cc_start: 0.8044 (t0) cc_final: 0.7716 (t70) REVERT: H 32 TYR cc_start: 0.9008 (m-80) cc_final: 0.7963 (m-80) REVERT: H 34 ILE cc_start: 0.8952 (mm) cc_final: 0.8671 (mm) REVERT: G 104 MET cc_start: 0.9339 (ttm) cc_final: 0.8963 (ttm) REVERT: G 210 PHE cc_start: 0.8424 (m-10) cc_final: 0.8216 (m-10) REVERT: G 271 MET cc_start: 0.8049 (mmp) cc_final: 0.7746 (mmm) REVERT: B 518 VAL cc_start: 0.9553 (m) cc_final: 0.9328 (p) REVERT: B 543 ASN cc_start: 0.8760 (t0) cc_final: 0.8554 (t0) REVERT: B 643 TYR cc_start: 0.8421 (m-10) cc_final: 0.8123 (m-10) REVERT: C 23 LYS cc_start: 0.8704 (mptt) cc_final: 0.8447 (tptp) REVERT: C 34 ILE cc_start: 0.8931 (mm) cc_final: 0.8581 (mm) REVERT: D 475 MET cc_start: 0.7096 (mmm) cc_final: 0.6677 (mmm) REVERT: E 543 ASN cc_start: 0.8762 (t0) cc_final: 0.8514 (t0) REVERT: E 639 THR cc_start: 0.7835 (m) cc_final: 0.7294 (t) REVERT: E 643 TYR cc_start: 0.8082 (m-10) cc_final: 0.7808 (m-10) REVERT: F 4 MET cc_start: 0.5573 (mmt) cc_final: 0.5360 (mmm) REVERT: I 5 GLN cc_start: 0.8356 (mm110) cc_final: 0.8096 (mm-40) REVERT: I 32 TYR cc_start: 0.8582 (m-80) cc_final: 0.7660 (m-80) REVERT: I 34 ILE cc_start: 0.8477 (tp) cc_final: 0.8227 (tp) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.1366 time to fit residues: 43.4598 Evaluate side-chains 139 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 188 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 162 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS G 348 GLN B 652 GLN A 17 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN D 249 HIS D 348 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN E 618 ASN J 249 HIS J 348 GLN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 591 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.063586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.045894 restraints weight = 103737.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.047394 restraints weight = 57260.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.048171 restraints weight = 39596.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048603 restraints weight = 31161.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.048916 restraints weight = 28513.483| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 20793 Z= 0.312 Angle : 0.892 15.691 28419 Z= 0.431 Chirality : 0.052 0.490 3423 Planarity : 0.005 0.052 3444 Dihedral : 5.534 33.796 2592 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.72 % Favored : 92.15 % Rotamer: Outliers : 0.28 % Allowed : 5.49 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.24 (0.17), residues: 2382 helix: 0.58 (0.27), residues: 351 sheet: -1.09 (0.17), residues: 801 loop : -0.97 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 429 TYR 0.017 0.002 TYR E 638 PHE 0.033 0.003 PHE D 361 TRP 0.023 0.002 TRP B 628 HIS 0.007 0.002 HIS J 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.31 (20658) covalent geometry : angle 0.84439 / 0.42 (28056) SS BOND : bond 0.00451 / 0.30 ( 42) SS BOND : angle 1.68309 / 1.08 ( 84) hydrogen bonds : bond 0.05078 / 3.37 ( 578) hydrogen bonds : angle 5.94165 / 4.02 ( 1470) link_ALPHA1-3 : bond 0.00579 / 0.29 ( 3) link_ALPHA1-3 : angle 1.72382 / 1.10 ( 9) link_BETA1-4 : bond 0.00618 / 0.43 ( 33) link_BETA1-4 : angle 2.08704 / 1.40 ( 99) link_NAG-ASN : bond 0.00814 / 0.56 ( 57) link_NAG-ASN : angle 3.35836 / 2.53 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 ASP cc_start: 0.8160 (t0) cc_final: 0.7717 (t70) REVERT: L 74 LYS cc_start: 0.9045 (mmpt) cc_final: 0.8763 (mmmt) REVERT: L 81 GLU cc_start: 0.8548 (mp0) cc_final: 0.8261 (mp0) REVERT: H 5 GLN cc_start: 0.8196 (mm110) cc_final: 0.7941 (mm-40) REVERT: H 23 LYS cc_start: 0.8839 (mttt) cc_final: 0.8604 (tptp) REVERT: H 32 TYR cc_start: 0.9180 (m-80) cc_final: 0.8324 (m-80) REVERT: H 102 TYR cc_start: 0.7728 (m-80) cc_final: 0.7493 (m-80) REVERT: G 104 MET cc_start: 0.9442 (ttm) cc_final: 0.9116 (ttm) REVERT: G 210 PHE cc_start: 0.8776 (m-10) cc_final: 0.8479 (m-10) REVERT: G 271 MET cc_start: 0.8044 (mmp) cc_final: 0.7483 (mmm) REVERT: B 626 MET cc_start: 0.8820 (ppp) cc_final: 0.8445 (ppp) REVERT: A 77 ARG cc_start: 0.8682 (mtp-110) cc_final: 0.8427 (tmm160) REVERT: C 32 TYR cc_start: 0.8660 (m-10) cc_final: 0.8167 (m-10) REVERT: C 34 ILE cc_start: 0.8964 (mm) cc_final: 0.8609 (mm) REVERT: D 271 MET cc_start: 0.7731 (mmp) cc_final: 0.7371 (mmm) REVERT: D 426 MET cc_start: 0.9051 (tpp) cc_final: 0.8839 (tpp) REVERT: E 626 MET cc_start: 0.7800 (ppp) cc_final: 0.7584 (ppp) REVERT: E 647 GLU cc_start: 0.9115 (pm20) cc_final: 0.8751 (pm20) REVERT: F 21 ILE cc_start: 0.8689 (mm) cc_final: 0.8013 (pt) REVERT: I 5 GLN cc_start: 0.8434 (mm110) cc_final: 0.7669 (mp10) REVERT: I 23 LYS cc_start: 0.8752 (mttt) cc_final: 0.8266 (tptp) REVERT: J 210 PHE cc_start: 0.8788 (m-80) cc_final: 0.8525 (m-10) REVERT: K 535 MET cc_start: 0.9363 (mpp) cc_final: 0.8908 (mpp) REVERT: K 543 ASN cc_start: 0.9086 (t0) cc_final: 0.8873 (t0) outliers start: 6 outliers final: 1 residues processed: 153 average time/residue: 0.1404 time to fit residues: 33.3888 Evaluate side-chains 112 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 GLN A 17 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 99 ASN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.064841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.046623 restraints weight = 102508.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.048897 restraints weight = 59398.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.049639 restraints weight = 35603.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.050041 restraints weight = 28623.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.050124 restraints weight = 26020.719| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20793 Z= 0.180 Angle : 0.731 14.722 28419 Z= 0.352 Chirality : 0.048 0.469 3423 Planarity : 0.004 0.044 3444 Dihedral : 5.290 35.840 2592 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.55 % Favored : 93.32 % Rotamer: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.01 (0.17), residues: 2382 helix: 1.22 (0.29), residues: 351 sheet: -1.14 (0.18), residues: 759 loop : -0.84 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 542 TYR 0.015 0.002 TYR A 86 PHE 0.019 0.002 PHE G 383 TRP 0.021 0.001 TRP B 628 HIS 0.007 0.001 HIS D 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (20658) covalent geometry : angle 0.68410 / 0.34 (28056) SS BOND : bond 0.00357 / 0.25 ( 42) SS BOND : angle 1.57911 / 0.99 ( 84) hydrogen bonds : bond 0.04070 / 2.73 ( 578) hydrogen bonds : angle 5.43170 / 3.71 ( 1470) link_ALPHA1-3 : bond 0.00688 / 0.34 ( 3) link_ALPHA1-3 : angle 1.49307 / 0.93 ( 9) link_BETA1-4 : bond 0.00455 / 0.31 ( 33) link_BETA1-4 : angle 1.85067 / 1.27 ( 99) link_NAG-ASN : bond 0.00572 / 0.43 ( 57) link_NAG-ASN : angle 2.93927 / 2.28 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 ASP cc_start: 0.8261 (t0) cc_final: 0.7836 (t70) REVERT: L 74 LYS cc_start: 0.9055 (mmpt) cc_final: 0.8789 (mmmt) REVERT: L 81 GLU cc_start: 0.8319 (mp0) cc_final: 0.8011 (mp0) REVERT: H 32 TYR cc_start: 0.9169 (m-80) cc_final: 0.8239 (m-80) REVERT: H 34 ILE cc_start: 0.9214 (mm) cc_final: 0.8941 (mm) REVERT: G 53 PHE cc_start: 0.6484 (t80) cc_final: 0.6137 (t80) REVERT: G 271 MET cc_start: 0.8145 (mmp) cc_final: 0.7704 (mmm) REVERT: B 535 MET cc_start: 0.9288 (mtm) cc_final: 0.8921 (mtm) REVERT: B 543 ASN cc_start: 0.9050 (t0) cc_final: 0.8492 (t0) REVERT: B 584 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8441 (tm-30) REVERT: B 626 MET cc_start: 0.8710 (ppp) cc_final: 0.8510 (ppp) REVERT: B 643 TYR cc_start: 0.8499 (m-10) cc_final: 0.8195 (m-10) REVERT: A 77 ARG cc_start: 0.8801 (mtp-110) cc_final: 0.8495 (tmm160) REVERT: A 81 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6630 (tp30) REVERT: C 32 TYR cc_start: 0.8606 (m-10) cc_final: 0.8291 (m-10) REVERT: D 271 MET cc_start: 0.7695 (mmp) cc_final: 0.7399 (mmm) REVERT: E 543 ASN cc_start: 0.9241 (t0) cc_final: 0.8701 (t0) REVERT: E 626 MET cc_start: 0.8006 (ppp) cc_final: 0.7739 (ppp) REVERT: E 647 GLU cc_start: 0.9050 (pm20) cc_final: 0.8744 (pm20) REVERT: F 4 MET cc_start: 0.6399 (mmt) cc_final: 0.5792 (mmp) REVERT: F 21 ILE cc_start: 0.8684 (mm) cc_final: 0.8050 (pt) REVERT: F 27 ASP cc_start: 0.7254 (m-30) cc_final: 0.6916 (m-30) REVERT: J 107 ASP cc_start: 0.8831 (t70) cc_final: 0.8446 (t70) REVERT: J 426 MET cc_start: 0.8842 (tpp) cc_final: 0.7808 (ttm) REVERT: K 535 MET cc_start: 0.9251 (mpp) cc_final: 0.8842 (mpp) REVERT: K 543 ASN cc_start: 0.9084 (t0) cc_final: 0.8801 (t0) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1391 time to fit residues: 35.1679 Evaluate side-chains 116 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 229 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN G 422 GLN A 17 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN ** J 374 HIS ** 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 = 0.3500 r_free = 0.3500 target = 0.063633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.045630 restraints weight = 104245.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.047698 restraints weight = 61329.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048442 restraints weight = 37890.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.049003 restraints weight = 30025.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049137 restraints weight = 26972.179| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 20793 Z= 0.251 Angle : 0.808 14.775 28419 Z= 0.387 Chirality : 0.050 0.476 3423 Planarity : 0.005 0.047 3444 Dihedral : 5.486 35.390 2592 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.52 % Favored : 91.35 % Rotamer: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.25 (0.17), residues: 2382 helix: 0.76 (0.28), residues: 351 sheet: -1.33 (0.17), residues: 822 loop : -0.83 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 542 TYR 0.016 0.002 TYR H 102 PHE 0.028 0.002 PHE D 361 TRP 0.026 0.002 TRP K 628 HIS 0.006 0.001 HIS D 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.25 (20658) covalent geometry : angle 0.75833 / 0.38 (28056) SS BOND : bond 0.00510 / 0.38 ( 42) SS BOND : angle 1.56830 / 1.00 ( 84) hydrogen bonds : bond 0.04295 / 2.86 ( 578) hydrogen bonds : angle 5.49374 / 3.74 ( 1470) link_ALPHA1-3 : bond 0.00568 / 0.28 ( 3) link_ALPHA1-3 : angle 1.61026 / 1.01 ( 9) link_BETA1-4 : bond 0.00510 / 0.34 ( 33) link_BETA1-4 : angle 2.00063 / 1.36 ( 99) link_NAG-ASN : bond 0.00676 / 0.48 ( 57) link_NAG-ASN : angle 3.24366 / 2.43 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 ASP cc_start: 0.8193 (t0) cc_final: 0.7846 (t70) REVERT: L 74 LYS cc_start: 0.9081 (mmpt) cc_final: 0.8837 (mmmt) REVERT: L 81 GLU cc_start: 0.8548 (mp0) cc_final: 0.8343 (mp0) REVERT: H 34 ILE cc_start: 0.9251 (mm) cc_final: 0.8937 (mm) REVERT: G 271 MET cc_start: 0.8217 (mmp) cc_final: 0.7793 (mmm) REVERT: G 426 MET cc_start: 0.9134 (tpp) cc_final: 0.8896 (tpp) REVERT: B 535 MET cc_start: 0.9279 (mtm) cc_final: 0.8639 (mpp) REVERT: B 584 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8364 (tm-30) REVERT: B 643 TYR cc_start: 0.8495 (m-10) cc_final: 0.8104 (m-10) REVERT: B 647 GLU cc_start: 0.9188 (pm20) cc_final: 0.8916 (pm20) REVERT: A 77 ARG cc_start: 0.8810 (mtp-110) cc_final: 0.8488 (tmm160) REVERT: C 34 ILE cc_start: 0.9099 (mm) cc_final: 0.8773 (mm) REVERT: D 271 MET cc_start: 0.7789 (mmp) cc_final: 0.7468 (mmm) REVERT: D 426 MET cc_start: 0.9000 (tpp) cc_final: 0.8718 (tpp) REVERT: E 604 CYS cc_start: 0.4285 (t) cc_final: 0.4069 (t) REVERT: E 626 MET cc_start: 0.8237 (ppp) cc_final: 0.7955 (ppp) REVERT: E 647 GLU cc_start: 0.9095 (pm20) cc_final: 0.8824 (pm20) REVERT: F 4 MET cc_start: 0.6438 (mmt) cc_final: 0.5824 (mmm) REVERT: F 21 ILE cc_start: 0.8727 (mm) cc_final: 0.8066 (pt) REVERT: I 5 GLN cc_start: 0.8245 (mm110) cc_final: 0.7952 (mm-40) REVERT: J 107 ASP cc_start: 0.8859 (t70) cc_final: 0.8425 (t70) REVERT: J 426 MET cc_start: 0.8890 (tpp) cc_final: 0.8063 (ttm) REVERT: K 535 MET cc_start: 0.9288 (mpp) cc_final: 0.8837 (mpp) REVERT: K 543 ASN cc_start: 0.9181 (t0) cc_final: 0.8868 (t0) REVERT: K 647 GLU cc_start: 0.8878 (pm20) cc_final: 0.8312 (pm20) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.1398 time to fit residues: 32.6854 Evaluate side-chains 110 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 208 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 96 GLN G 99 ASN A 96 GLN D 85 HIS ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.063835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.045941 restraints weight = 103131.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.048170 restraints weight = 58470.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.048899 restraints weight = 35376.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.049438 restraints weight = 28577.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.049567 restraints weight = 25712.109| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20793 Z= 0.215 Angle : 0.764 14.586 28419 Z= 0.367 Chirality : 0.049 0.466 3423 Planarity : 0.004 0.043 3444 Dihedral : 5.409 36.628 2592 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.10 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.17 (0.18), residues: 2382 helix: 0.95 (0.29), residues: 351 sheet: -1.34 (0.17), residues: 792 loop : -0.79 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 419 TYR 0.029 0.002 TYR A 86 PHE 0.021 0.002 PHE D 361 TRP 0.027 0.002 TRP K 628 HIS 0.006 0.001 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (20658) covalent geometry : angle 0.71769 / 0.36 (28056) SS BOND : bond 0.00603 / 0.33 ( 42) SS BOND : angle 1.44143 / 0.88 ( 84) hydrogen bonds : bond 0.04009 / 2.65 ( 578) hydrogen bonds : angle 5.37253 / 3.68 ( 1470) link_ALPHA1-3 : bond 0.00655 / 0.33 ( 3) link_ALPHA1-3 : angle 1.51656 / 0.95 ( 9) link_BETA1-4 : bond 0.00398 / 0.27 ( 33) link_BETA1-4 : angle 1.94788 / 1.33 ( 99) link_NAG-ASN : bond 0.00591 / 0.44 ( 57) link_NAG-ASN : angle 3.02406 / 2.30 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 ASP cc_start: 0.8113 (t0) cc_final: 0.7791 (t70) REVERT: L 74 LYS cc_start: 0.9096 (mmpt) cc_final: 0.8893 (mmmt) REVERT: H 34 ILE cc_start: 0.9289 (mm) cc_final: 0.8989 (mm) REVERT: G 271 MET cc_start: 0.8235 (mmp) cc_final: 0.7839 (mmm) REVERT: B 535 MET cc_start: 0.9274 (mtm) cc_final: 0.8916 (mtm) REVERT: B 548 ILE cc_start: 0.7091 (mm) cc_final: 0.6870 (mm) REVERT: B 584 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8377 (tm-30) REVERT: B 647 GLU cc_start: 0.9166 (pm20) cc_final: 0.8873 (pm20) REVERT: A 77 ARG cc_start: 0.8806 (mtp-110) cc_final: 0.8516 (tmm160) REVERT: C 34 ILE cc_start: 0.9149 (mm) cc_final: 0.8828 (mm) REVERT: D 271 MET cc_start: 0.7799 (mmp) cc_final: 0.7481 (mmm) REVERT: D 426 MET cc_start: 0.8606 (tpp) cc_final: 0.8188 (ttm) REVERT: E 535 MET cc_start: 0.9285 (mtm) cc_final: 0.9018 (mtm) REVERT: E 543 ASN cc_start: 0.9328 (t0) cc_final: 0.8811 (t0) REVERT: E 647 GLU cc_start: 0.9181 (pm20) cc_final: 0.8884 (pm20) REVERT: F 4 MET cc_start: 0.6577 (mmt) cc_final: 0.5947 (mmm) REVERT: F 21 ILE cc_start: 0.8727 (mm) cc_final: 0.8069 (pt) REVERT: F 27 ASP cc_start: 0.7145 (m-30) cc_final: 0.6926 (m-30) REVERT: J 107 ASP cc_start: 0.8878 (t70) cc_final: 0.8315 (t70) REVERT: J 271 MET cc_start: 0.7824 (mmm) cc_final: 0.7459 (mmm) REVERT: K 535 MET cc_start: 0.9240 (mpp) cc_final: 0.8722 (mpp) REVERT: K 543 ASN cc_start: 0.9168 (t0) cc_final: 0.8835 (t0) REVERT: K 626 MET cc_start: 0.8083 (ppp) cc_final: 0.7814 (ppp) REVERT: K 647 GLU cc_start: 0.8944 (pm20) cc_final: 0.8379 (pm20) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1377 time to fit residues: 32.0657 Evaluate side-chains 111 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 199 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 96 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 GLN J 203 GLN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.062882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.045118 restraints weight = 104550.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.047269 restraints weight = 59134.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.047902 restraints weight = 36629.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048308 restraints weight = 30175.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.048518 restraints weight = 27444.922| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20793 Z= 0.250 Angle : 0.804 14.510 28419 Z= 0.387 Chirality : 0.049 0.467 3423 Planarity : 0.004 0.043 3444 Dihedral : 5.553 36.702 2592 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.73 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.18 (0.17), residues: 2382 helix: 1.02 (0.28), residues: 351 sheet: -1.28 (0.18), residues: 771 loop : -0.90 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 503 TYR 0.020 0.002 TYR C 102 PHE 0.024 0.002 PHE J 361 TRP 0.046 0.002 TRP G 479 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.25 (20658) covalent geometry : angle 0.75820 / 0.38 (28056) SS BOND : bond 0.00412 / 0.30 ( 42) SS BOND : angle 1.59980 / 1.02 ( 84) hydrogen bonds : bond 0.04256 / 2.82 ( 578) hydrogen bonds : angle 5.43379 / 3.71 ( 1470) link_ALPHA1-3 : bond 0.00589 / 0.29 ( 3) link_ALPHA1-3 : angle 1.54361 / 0.96 ( 9) link_BETA1-4 : bond 0.00451 / 0.31 ( 33) link_BETA1-4 : angle 2.02514 / 1.38 ( 99) link_NAG-ASN : bond 0.00642 / 0.47 ( 57) link_NAG-ASN : angle 3.04484 / 2.31 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 ASP cc_start: 0.8109 (t0) cc_final: 0.7747 (t70) REVERT: L 81 GLU cc_start: 0.8513 (mp0) cc_final: 0.8286 (tt0) REVERT: G 104 MET cc_start: 0.9500 (ttm) cc_final: 0.9282 (ttm) REVERT: G 271 MET cc_start: 0.8286 (mmp) cc_final: 0.7864 (mmm) REVERT: B 535 MET cc_start: 0.9279 (mtm) cc_final: 0.8914 (mtm) REVERT: B 584 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8385 (tm-30) REVERT: B 626 MET cc_start: 0.8900 (ppp) cc_final: 0.8513 (ppp) REVERT: B 647 GLU cc_start: 0.9162 (pm20) cc_final: 0.8867 (pm20) REVERT: B 654 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8356 (mt-10) REVERT: A 27 ASP cc_start: 0.8727 (t70) cc_final: 0.8524 (t70) REVERT: A 77 ARG cc_start: 0.8843 (mtp-110) cc_final: 0.8524 (tmm160) REVERT: C 23 LYS cc_start: 0.9045 (tptt) cc_final: 0.8734 (tptp) REVERT: C 32 TYR cc_start: 0.8806 (m-10) cc_final: 0.8520 (m-10) REVERT: C 34 ILE cc_start: 0.9176 (mm) cc_final: 0.8851 (mm) REVERT: D 95 MET cc_start: 0.7370 (ttm) cc_final: 0.7068 (ttm) REVERT: D 271 MET cc_start: 0.7871 (mmp) cc_final: 0.7590 (mmm) REVERT: D 426 MET cc_start: 0.8719 (tpp) cc_final: 0.8274 (ttm) REVERT: E 535 MET cc_start: 0.9269 (mtm) cc_final: 0.8989 (mtm) REVERT: E 647 GLU cc_start: 0.9192 (pm20) cc_final: 0.8828 (pm20) REVERT: F 21 ILE cc_start: 0.8733 (mm) cc_final: 0.8117 (pt) REVERT: J 107 ASP cc_start: 0.8670 (t70) cc_final: 0.8418 (t70) REVERT: J 271 MET cc_start: 0.7804 (mmm) cc_final: 0.7376 (mmm) REVERT: K 535 MET cc_start: 0.9258 (mpp) cc_final: 0.8741 (mpp) REVERT: K 574 LYS cc_start: 0.8466 (mptt) cc_final: 0.7985 (mtpp) REVERT: K 647 GLU cc_start: 0.9033 (pm20) cc_final: 0.8520 (pm20) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1282 time to fit residues: 29.1778 Evaluate side-chains 113 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 214 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** 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 = 0.3469 r_free = 0.3469 target = 0.062402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.044693 restraints weight = 104468.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.046870 restraints weight = 58760.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.047695 restraints weight = 35376.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.048032 restraints weight = 28156.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048242 restraints weight = 26341.314| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20793 Z= 0.255 Angle : 0.812 14.220 28419 Z= 0.391 Chirality : 0.049 0.472 3423 Planarity : 0.004 0.041 3444 Dihedral : 5.685 36.853 2592 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.23 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.28 (0.17), residues: 2382 helix: 1.26 (0.29), residues: 333 sheet: -1.38 (0.17), residues: 819 loop : -0.97 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.014 0.002 TYR K 638 PHE 0.024 0.002 PHE L 62 TRP 0.046 0.002 TRP G 479 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.26 (20658) covalent geometry : angle 0.76717 / 0.38 (28056) SS BOND : bond 0.00424 / 0.31 ( 42) SS BOND : angle 1.48039 / 1.00 ( 84) hydrogen bonds : bond 0.04248 / 2.82 ( 578) hydrogen bonds : angle 5.51023 / 3.78 ( 1470) link_ALPHA1-3 : bond 0.00665 / 0.33 ( 3) link_ALPHA1-3 : angle 1.54211 / 0.96 ( 9) link_BETA1-4 : bond 0.00465 / 0.32 ( 33) link_BETA1-4 : angle 2.05009 / 1.40 ( 99) link_NAG-ASN : bond 0.00644 / 0.47 ( 57) link_NAG-ASN : angle 3.04252 / 2.28 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 ASP cc_start: 0.8238 (t0) cc_final: 0.7894 (t70) REVERT: L 74 LYS cc_start: 0.9133 (mmpt) cc_final: 0.8911 (mmmt) REVERT: H 5 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7564 (mm-40) REVERT: H 34 ILE cc_start: 0.9243 (mm) cc_final: 0.8992 (mm) REVERT: G 271 MET cc_start: 0.8288 (mmp) cc_final: 0.7866 (mmm) REVERT: B 530 MET cc_start: 0.8676 (mpp) cc_final: 0.8253 (mpp) REVERT: B 535 MET cc_start: 0.9249 (mtm) cc_final: 0.8911 (mtm) REVERT: B 548 ILE cc_start: 0.7080 (mm) cc_final: 0.6873 (mm) REVERT: B 584 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 654 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8356 (mt-10) REVERT: A 77 ARG cc_start: 0.8825 (mtp-110) cc_final: 0.8534 (tmm160) REVERT: C 23 LYS cc_start: 0.9083 (tptt) cc_final: 0.8776 (tptp) REVERT: C 32 TYR cc_start: 0.8868 (m-10) cc_final: 0.8572 (m-10) REVERT: C 34 ILE cc_start: 0.9211 (mm) cc_final: 0.8912 (mm) REVERT: D 107 ASP cc_start: 0.8806 (t70) cc_final: 0.8328 (t70) REVERT: D 271 MET cc_start: 0.7921 (mmp) cc_final: 0.7616 (mmm) REVERT: E 535 MET cc_start: 0.9330 (mtm) cc_final: 0.9030 (mtm) REVERT: E 626 MET cc_start: 0.8708 (ppp) cc_final: 0.8466 (ppp) REVERT: E 647 GLU cc_start: 0.9188 (pm20) cc_final: 0.8837 (pm20) REVERT: F 4 MET cc_start: 0.6412 (mmt) cc_final: 0.5952 (mmp) REVERT: F 21 ILE cc_start: 0.8765 (mm) cc_final: 0.8202 (pt) REVERT: J 107 ASP cc_start: 0.8714 (t70) cc_final: 0.8474 (t70) REVERT: J 271 MET cc_start: 0.7682 (mmm) cc_final: 0.7257 (mmm) REVERT: K 535 MET cc_start: 0.9266 (mpp) cc_final: 0.8643 (mpp) REVERT: K 574 LYS cc_start: 0.8393 (mptt) cc_final: 0.7888 (mtpp) REVERT: K 647 GLU cc_start: 0.9145 (pm20) cc_final: 0.8767 (pm20) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1404 time to fit residues: 30.9487 Evaluate side-chains 111 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 238 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 96 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 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 = 0.3505 r_free = 0.3505 target = 0.063766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.045904 restraints weight = 102468.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.048210 restraints weight = 57941.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.048939 restraints weight = 34655.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.049286 restraints weight = 27936.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.049357 restraints weight = 25844.443| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20793 Z= 0.146 Angle : 0.733 13.882 28419 Z= 0.352 Chirality : 0.048 0.453 3423 Planarity : 0.004 0.041 3444 Dihedral : 5.402 36.812 2592 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.60 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.18), residues: 2382 helix: 1.21 (0.30), residues: 351 sheet: -1.28 (0.18), residues: 789 loop : -0.74 (0.19), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.016 0.001 TYR B 638 PHE 0.018 0.002 PHE D 210 TRP 0.041 0.002 TRP G 479 HIS 0.006 0.001 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (20658) covalent geometry : angle 0.68930 / 0.34 (28056) SS BOND : bond 0.00347 / 0.25 ( 42) SS BOND : angle 1.44504 / 1.04 ( 84) hydrogen bonds : bond 0.03672 / 2.45 ( 578) hydrogen bonds : angle 5.21872 / 3.59 ( 1470) link_ALPHA1-3 : bond 0.00534 / 0.27 ( 3) link_ALPHA1-3 : angle 1.43905 / 0.91 ( 9) link_BETA1-4 : bond 0.00392 / 0.26 ( 33) link_BETA1-4 : angle 1.96857 / 1.36 ( 99) link_NAG-ASN : bond 0.00525 / 0.41 ( 57) link_NAG-ASN : angle 2.80617 / 2.15 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 ASP cc_start: 0.8251 (t0) cc_final: 0.7914 (t70) REVERT: L 74 LYS cc_start: 0.9122 (mmpt) cc_final: 0.8919 (mmmt) REVERT: L 81 GLU cc_start: 0.8486 (mp0) cc_final: 0.8276 (tt0) REVERT: H 34 ILE cc_start: 0.9269 (mm) cc_final: 0.9029 (mm) REVERT: G 271 MET cc_start: 0.8232 (mmp) cc_final: 0.7818 (mmm) REVERT: G 426 MET cc_start: 0.8907 (tpp) cc_final: 0.8660 (tpp) REVERT: B 535 MET cc_start: 0.9211 (mtm) cc_final: 0.8652 (mpp) REVERT: B 548 ILE cc_start: 0.7123 (mm) cc_final: 0.6896 (mm) REVERT: B 584 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8351 (tm-30) REVERT: B 626 MET cc_start: 0.8801 (ppp) cc_final: 0.8392 (ppp) REVERT: B 647 GLU cc_start: 0.9134 (pm20) cc_final: 0.8823 (pm20) REVERT: B 654 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8376 (mt-10) REVERT: A 77 ARG cc_start: 0.8869 (mtp-110) cc_final: 0.8571 (tmm160) REVERT: C 23 LYS cc_start: 0.9044 (tptt) cc_final: 0.8674 (tptp) REVERT: C 32 TYR cc_start: 0.8718 (m-10) cc_final: 0.8442 (m-10) REVERT: C 34 ILE cc_start: 0.9217 (mm) cc_final: 0.8891 (mm) REVERT: D 107 ASP cc_start: 0.8733 (t70) cc_final: 0.8243 (t70) REVERT: D 271 MET cc_start: 0.7846 (mmp) cc_final: 0.7609 (mmm) REVERT: E 535 MET cc_start: 0.9329 (mtm) cc_final: 0.8981 (mtm) REVERT: E 543 ASN cc_start: 0.9276 (t0) cc_final: 0.8879 (t0) REVERT: E 626 MET cc_start: 0.8618 (ppp) cc_final: 0.8303 (ppp) REVERT: E 647 GLU cc_start: 0.9156 (pm20) cc_final: 0.8807 (pm20) REVERT: F 4 MET cc_start: 0.6420 (mmt) cc_final: 0.5962 (mmp) REVERT: F 21 ILE cc_start: 0.8788 (mm) cc_final: 0.8154 (pt) REVERT: J 107 ASP cc_start: 0.8652 (t70) cc_final: 0.8411 (t70) REVERT: J 271 MET cc_start: 0.7618 (mmm) cc_final: 0.7242 (mmm) REVERT: K 535 MET cc_start: 0.9290 (mpp) cc_final: 0.8687 (mpp) REVERT: K 543 ASN cc_start: 0.9109 (t0) cc_final: 0.8760 (t0) REVERT: K 574 LYS cc_start: 0.8406 (mptt) cc_final: 0.7892 (mtpp) REVERT: K 647 GLU cc_start: 0.9055 (pm20) cc_final: 0.8810 (pm20) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1316 time to fit residues: 32.5333 Evaluate side-chains 115 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 9 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 96 GLN G 302 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN D 203 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** J 374 HIS ** 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 = 0.3502 r_free = 0.3502 target = 0.063638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045842 restraints weight = 103910.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048033 restraints weight = 57733.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.048772 restraints weight = 35621.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.049173 restraints weight = 28880.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.049392 restraints weight = 26406.124| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20793 Z= 0.164 Angle : 0.737 13.709 28419 Z= 0.355 Chirality : 0.048 0.444 3423 Planarity : 0.004 0.043 3444 Dihedral : 5.361 36.357 2592 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.81 % Favored : 92.02 % Rotamer: Outliers : 0.05 % Allowed : 0.19 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.98 (0.18), residues: 2382 helix: 1.37 (0.29), residues: 351 sheet: -1.19 (0.18), residues: 783 loop : -0.78 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 61 TYR 0.015 0.001 TYR K 638 PHE 0.015 0.002 PHE J 383 TRP 0.046 0.002 TRP G 479 HIS 0.004 0.001 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (20658) covalent geometry : angle 0.69381 / 0.34 (28056) SS BOND : bond 0.00333 / 0.26 ( 42) SS BOND : angle 1.51648 / 1.05 ( 84) hydrogen bonds : bond 0.03681 / 2.44 ( 578) hydrogen bonds : angle 5.24066 / 3.61 ( 1470) link_ALPHA1-3 : bond 0.00531 / 0.26 ( 3) link_ALPHA1-3 : angle 1.46957 / 0.92 ( 9) link_BETA1-4 : bond 0.00391 / 0.26 ( 33) link_BETA1-4 : angle 1.96649 / 1.36 ( 99) link_NAG-ASN : bond 0.00510 / 0.39 ( 57) link_NAG-ASN : angle 2.78415 / 2.12 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 ASP cc_start: 0.8273 (t0) cc_final: 0.7952 (t70) REVERT: L 74 LYS cc_start: 0.9152 (mmpt) cc_final: 0.8944 (mmmt) REVERT: H 5 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7599 (mm-40) REVERT: H 34 ILE cc_start: 0.9261 (mm) cc_final: 0.9013 (mm) REVERT: G 271 MET cc_start: 0.8238 (mmp) cc_final: 0.7841 (mmm) REVERT: B 535 MET cc_start: 0.9238 (mtm) cc_final: 0.8615 (mpp) REVERT: B 548 ILE cc_start: 0.7303 (mm) cc_final: 0.7098 (mm) REVERT: B 584 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 647 GLU cc_start: 0.9132 (pm20) cc_final: 0.8808 (pm20) REVERT: B 654 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8386 (mt-10) REVERT: A 77 ARG cc_start: 0.8843 (mtp-110) cc_final: 0.8471 (tmm160) REVERT: C 23 LYS cc_start: 0.9054 (tptt) cc_final: 0.8679 (tptp) REVERT: C 32 TYR cc_start: 0.8734 (m-10) cc_final: 0.8490 (m-10) REVERT: C 34 ILE cc_start: 0.9215 (mm) cc_final: 0.8886 (mm) REVERT: D 107 ASP cc_start: 0.8710 (t70) cc_final: 0.8208 (t70) REVERT: D 150 MET cc_start: 0.8452 (ppp) cc_final: 0.8063 (ppp) REVERT: D 271 MET cc_start: 0.7855 (mmp) cc_final: 0.7638 (mmm) REVERT: E 535 MET cc_start: 0.9351 (mtm) cc_final: 0.9008 (mtm) REVERT: E 543 ASN cc_start: 0.9289 (t0) cc_final: 0.8880 (t0) REVERT: E 626 MET cc_start: 0.8578 (ppp) cc_final: 0.8339 (ppp) REVERT: F 4 MET cc_start: 0.6931 (mmt) cc_final: 0.6478 (mmp) REVERT: F 21 ILE cc_start: 0.8813 (mm) cc_final: 0.8478 (tp) REVERT: F 24 LYS cc_start: 0.8477 (tmtt) cc_final: 0.8274 (tptp) REVERT: I 71 VAL cc_start: 0.8361 (m) cc_final: 0.8104 (t) REVERT: J 271 MET cc_start: 0.7657 (mmm) cc_final: 0.7274 (mmm) REVERT: K 535 MET cc_start: 0.9313 (mpp) cc_final: 0.8620 (mpp) REVERT: K 574 LYS cc_start: 0.8400 (mptt) cc_final: 0.7902 (mtpp) REVERT: K 647 GLU cc_start: 0.9116 (pm20) cc_final: 0.8884 (pm20) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.1341 time to fit residues: 31.6307 Evaluate side-chains 113 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 52 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 211 optimal weight: 7.9990 chunk 84 optimal weight: 0.0270 chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 96 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.064706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.046856 restraints weight = 102268.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.049172 restraints weight = 57364.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.050017 restraints weight = 34216.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.050315 restraints weight = 27006.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.050385 restraints weight = 25273.486| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20793 Z= 0.124 Angle : 0.706 13.455 28419 Z= 0.340 Chirality : 0.047 0.435 3423 Planarity : 0.004 0.039 3444 Dihedral : 5.134 36.370 2592 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.88 % Favored : 92.99 % Rotamer: Outliers : 0.05 % Allowed : 0.28 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.18), residues: 2382 helix: 1.47 (0.30), residues: 351 sheet: -1.10 (0.18), residues: 795 loop : -0.70 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 77 TYR 0.020 0.001 TYR C 91 PHE 0.014 0.001 PHE G 376 TRP 0.042 0.002 TRP G 479 HIS 0.005 0.001 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (20658) covalent geometry : angle 0.66664 / 0.33 (28056) SS BOND : bond 0.00298 / 0.22 ( 42) SS BOND : angle 1.32599 / 0.91 ( 84) hydrogen bonds : bond 0.03373 / 2.26 ( 578) hydrogen bonds : angle 5.07794 / 3.51 ( 1470) link_ALPHA1-3 : bond 0.00515 / 0.26 ( 3) link_ALPHA1-3 : angle 1.41492 / 0.90 ( 9) link_BETA1-4 : bond 0.00422 / 0.27 ( 33) link_BETA1-4 : angle 1.91078 / 1.34 ( 99) link_NAG-ASN : bond 0.00464 / 0.37 ( 57) link_NAG-ASN : angle 2.62141 / 2.02 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2631.75 seconds wall clock time: 46 minutes 51.63 seconds (2811.63 seconds total)