Starting phenix.real_space_refine on Sun Aug 24 14:00:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gas_29905/08_2025/8gas_29905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gas_29905/08_2025/8gas_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_29905/08_2025/8gas_29905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gas_29905/08_2025/8gas_29905.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gas_29905/08_2025/8gas_29905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gas_29905/08_2025/8gas_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-2.0-5787/lib/python3.9/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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 30 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 dihedrals: 6 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 dihedrals: 30 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 dihedrals: 6 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 dihedrals: 30 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.69, 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: 2.00 Conformation dependent library (CDL) restraints added in 687.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.79 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: 3.08 Time building geometry restraints manager: 2.43 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 - 22.16: 12019 22.16 - 44.33: 1139 44.33 - 66.49: 217 66.49 - 88.65: 103 88.65 - 110.82: 58 Dihedral angle restraints: 13536 sinusoidal: 6579 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 13533 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: 0.010 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.340 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 19.301 110.817 8940 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 aren 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 covalent geometry : bond 0.00416 (20658) covalent geometry : angle 0.68339 (28056) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.22248 ( 84) hydrogen bonds : bond 0.25150 ( 578) hydrogen bonds : angle 8.60803 ( 1470) link_ALPHA1-3 : bond 0.00432 ( 3) link_ALPHA1-3 : angle 1.52130 ( 9) link_BETA1-4 : bond 0.00349 ( 33) link_BETA1-4 : angle 1.98172 ( 99) link_NAG-ASN : bond 0.00598 ( 57) link_NAG-ASN : angle 2.63966 ( 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 : 0.833 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: 0.7489 (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: 0.1616 time to fit residues: 66.9420 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 : 0.563 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3667 r_free = 0.3667 target = 0.071054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.052479 restraints weight = 100125.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.054254 restraints weight = 56207.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.055474 restraints weight = 38785.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.056290 restraints weight = 30285.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.056911 restraints weight = 25594.597| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20793 Z= 0.153 Angle : 0.772 15.616 28419 Z= 0.368 Chirality : 0.050 0.513 3423 Planarity : 0.005 0.082 3444 Dihedral : 12.848 76.784 4515 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.30 % Favored : 93.58 % Rotamer: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.31 % 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 aren not related in a simple way. whole: -0.83 (0.18), residues: 2382 helix: 1.41 (0.29), residues: 351 sheet: -0.72 (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 J 360 TYR 0.026 0.002 TYR I 91 PHE 0.022 0.002 PHE D 159 TRP 0.027 0.002 TRP K 571 HIS 0.005 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00343 (20658) covalent geometry : angle 0.71333 (28056) SS BOND : bond 0.00353 ( 42) SS BOND : angle 1.40717 ( 84) hydrogen bonds : bond 0.05196 ( 578) hydrogen bonds : angle 6.26247 ( 1470) link_ALPHA1-3 : bond 0.01032 ( 3) link_ALPHA1-3 : angle 2.71620 ( 9) link_BETA1-4 : bond 0.00626 ( 33) link_BETA1-4 : angle 2.30228 ( 99) link_NAG-ASN : bond 0.00568 ( 57) link_NAG-ASN : angle 3.35449 ( 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 : 0.897 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: 0.8041 (t0) cc_final: 0.7713 (t70) REVERT: L 77 ARG cc_start: 0.8881 (mtp-110) cc_final: 0.8194 (ttp-170) REVERT: H 32 TYR cc_start: 0.9005 (m-80) cc_final: 0.7963 (m-80) REVERT: H 34 ILE cc_start: 0.8964 (mm) cc_final: 0.8681 (mm) REVERT: G 104 MET cc_start: 0.9338 (ttm) cc_final: 0.8962 (ttm) REVERT: G 210 PHE cc_start: 0.8418 (m-10) cc_final: 0.8210 (m-10) REVERT: G 271 MET cc_start: 0.8053 (mmp) cc_final: 0.7779 (mmm) REVERT: B 518 VAL cc_start: 0.9557 (m) cc_final: 0.9332 (p) REVERT: B 543 ASN cc_start: 0.8756 (t0) cc_final: 0.8551 (t0) REVERT: B 643 TYR cc_start: 0.8415 (m-10) cc_final: 0.8123 (m-10) REVERT: C 23 LYS cc_start: 0.8706 (mptt) cc_final: 0.8452 (tptp) REVERT: C 34 ILE cc_start: 0.8911 (mm) cc_final: 0.8571 (mm) REVERT: D 475 MET cc_start: 0.7128 (mmm) cc_final: 0.6697 (mmm) REVERT: E 543 ASN cc_start: 0.8750 (t0) cc_final: 0.8504 (t0) REVERT: E 639 THR cc_start: 0.7854 (m) cc_final: 0.7333 (t) REVERT: E 643 TYR cc_start: 0.8067 (m-10) cc_final: 0.7774 (m-10) REVERT: F 4 MET cc_start: 0.5591 (mmt) cc_final: 0.5379 (mmm) REVERT: I 5 GLN cc_start: 0.8356 (mm110) cc_final: 0.8094 (mm-40) REVERT: I 32 TYR cc_start: 0.8577 (m-80) cc_final: 0.7659 (m-80) REVERT: I 34 ILE cc_start: 0.8481 (tp) cc_final: 0.8232 (tp) REVERT: J 210 PHE cc_start: 0.8773 (m-80) cc_final: 0.8571 (m-10) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.1688 time to fit residues: 53.4015 Evaluate side-chains 135 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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: 9.9990 chunk 7 optimal weight: 20.0000 chunk 188 optimal weight: 8.9990 chunk 121 optimal weight: 0.3980 chunk 86 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 162 optimal weight: 40.0000 chunk 102 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN G 103 GLN G 203 GLN G 249 HIS G 348 GLN B 652 GLN A 17 GLN D 249 HIS D 348 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 HIS J 348 GLN K 591 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.063290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.045667 restraints weight = 103993.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.047214 restraints weight = 56641.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.047944 restraints weight = 38985.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048475 restraints weight = 31329.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048688 restraints weight = 27801.553| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 20793 Z= 0.321 Angle : 0.927 15.738 28419 Z= 0.444 Chirality : 0.054 0.513 3423 Planarity : 0.005 0.053 3444 Dihedral : 9.453 59.993 4515 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.98 % Favored : 91.90 % Rotamer: Outliers : 0.28 % Allowed : 5.82 % Favored : 93.89 % 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 aren not related in a simple way. whole: -1.27 (0.17), residues: 2382 helix: 0.49 (0.27), residues: 351 sheet: -1.12 (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 D 456 TYR 0.019 0.002 TYR E 638 PHE 0.032 0.003 PHE D 361 TRP 0.024 0.002 TRP B 628 HIS 0.007 0.002 HIS J 374 Details of bonding type rmsd covalent geometry : bond 0.00713 (20658) covalent geometry : angle 0.87524 (28056) SS BOND : bond 0.00477 ( 42) SS BOND : angle 1.70216 ( 84) hydrogen bonds : bond 0.05149 ( 578) hydrogen bonds : angle 5.96413 ( 1470) link_ALPHA1-3 : bond 0.01312 ( 3) link_ALPHA1-3 : angle 2.28616 ( 9) link_BETA1-4 : bond 0.00694 ( 33) link_BETA1-4 : angle 2.49923 ( 99) link_NAG-ASN : bond 0.00865 ( 57) link_NAG-ASN : angle 3.44599 ( 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 152 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.856 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: L 27 ASP cc_start: 0.8179 (t0) cc_final: 0.7728 (t70) REVERT: L 74 LYS cc_start: 0.9042 (mmpt) cc_final: 0.8758 (mmmt) REVERT: L 81 GLU cc_start: 0.8637 (mp0) cc_final: 0.8364 (mp0) REVERT: H 5 GLN cc_start: 0.8182 (mm110) cc_final: 0.7913 (mm-40) REVERT: H 23 LYS cc_start: 0.8857 (mttt) cc_final: 0.8616 (tptp) REVERT: H 32 TYR cc_start: 0.9210 (m-80) cc_final: 0.8390 (m-80) REVERT: G 95 MET cc_start: 0.8051 (ttm) cc_final: 0.7753 (ttp) REVERT: G 103 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: G 104 MET cc_start: 0.9400 (ttm) cc_final: 0.8987 (ttm) REVERT: G 210 PHE cc_start: 0.8749 (m-10) cc_final: 0.8470 (m-10) REVERT: G 271 MET cc_start: 0.8094 (mmp) cc_final: 0.7589 (mmm) REVERT: B 626 MET cc_start: 0.8840 (ppp) cc_final: 0.8458 (ppp) REVERT: A 77 ARG cc_start: 0.8667 (mtp-110) cc_final: 0.8423 (tmm160) REVERT: C 23 LYS cc_start: 0.8702 (mptt) cc_final: 0.8478 (tppp) REVERT: C 32 TYR cc_start: 0.8670 (m-10) cc_final: 0.8157 (m-10) REVERT: C 34 ILE cc_start: 0.8959 (mm) cc_final: 0.8556 (mm) REVERT: D 95 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8138 (ttp) REVERT: D 271 MET cc_start: 0.7134 (mmm) cc_final: 0.6775 (mmm) REVERT: E 626 MET cc_start: 0.7868 (ppp) cc_final: 0.7635 (ppp) REVERT: E 647 GLU cc_start: 0.9109 (pm20) cc_final: 0.8773 (pm20) REVERT: F 21 ILE cc_start: 0.8778 (mm) cc_final: 0.8174 (pt) REVERT: I 5 GLN cc_start: 0.8429 (mm110) cc_final: 0.7659 (mp10) REVERT: I 23 LYS cc_start: 0.8770 (mttt) cc_final: 0.8323 (tptp) REVERT: K 535 MET cc_start: 0.9362 (mpp) cc_final: 0.8938 (mpp) REVERT: K 543 ASN cc_start: 0.9060 (t0) cc_final: 0.8856 (t0) outliers start: 6 outliers final: 2 residues processed: 151 average time/residue: 0.1652 time to fit residues: 37.6313 Evaluate side-chains 111 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 237 optimal weight: 4.9990 chunk 129 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN B 591 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** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.065136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.047267 restraints weight = 102242.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.049164 restraints weight = 56322.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.050017 restraints weight = 36122.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.050324 restraints weight = 31350.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.050395 restraints weight = 26621.210| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20793 Z= 0.159 Angle : 0.732 14.853 28419 Z= 0.351 Chirality : 0.049 0.492 3423 Planarity : 0.004 0.043 3444 Dihedral : 7.938 56.859 4515 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.21 % Favored : 93.66 % Rotamer: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % 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 aren not related in a simple way. whole: -1.01 (0.17), residues: 2382 helix: 1.22 (0.29), residues: 351 sheet: -1.13 (0.18), residues: 759 loop : -0.84 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 542 TYR 0.015 0.002 TYR H 102 PHE 0.018 0.002 PHE G 383 TRP 0.021 0.002 TRP B 628 HIS 0.008 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00356 (20658) covalent geometry : angle 0.68124 (28056) SS BOND : bond 0.00347 ( 42) SS BOND : angle 1.39561 ( 84) hydrogen bonds : bond 0.04057 ( 578) hydrogen bonds : angle 5.43696 ( 1470) link_ALPHA1-3 : bond 0.01366 ( 3) link_ALPHA1-3 : angle 2.41839 ( 9) link_BETA1-4 : bond 0.00460 ( 33) link_BETA1-4 : angle 2.20161 ( 99) link_NAG-ASN : bond 0.00546 ( 57) link_NAG-ASN : angle 2.96456 ( 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 171 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 0.791 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: 0.8232 (t0) cc_final: 0.7805 (t70) REVERT: L 74 LYS cc_start: 0.9047 (mmpt) cc_final: 0.8766 (mmmt) REVERT: L 81 GLU cc_start: 0.8416 (mp0) cc_final: 0.8101 (mp0) REVERT: H 32 TYR cc_start: 0.9169 (m-80) cc_final: 0.8223 (m-80) REVERT: H 34 ILE cc_start: 0.9204 (mm) cc_final: 0.8917 (mm) REVERT: G 53 PHE cc_start: 0.6435 (t80) cc_final: 0.6133 (t80) REVERT: G 271 MET cc_start: 0.8150 (mmp) cc_final: 0.7749 (mmm) REVERT: B 535 MET cc_start: 0.9259 (mtm) cc_final: 0.8707 (mpp) REVERT: B 543 ASN cc_start: 0.9044 (t0) cc_final: 0.8492 (t0) REVERT: B 584 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8386 (tm-30) REVERT: B 643 TYR cc_start: 0.8499 (m-10) cc_final: 0.8182 (m-10) REVERT: A 77 ARG cc_start: 0.8760 (mtp-110) cc_final: 0.8529 (tmm160) REVERT: A 81 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6709 (tp30) REVERT: C 32 TYR cc_start: 0.8592 (m-10) cc_final: 0.8167 (m-10) REVERT: C 34 ILE cc_start: 0.9078 (mm) cc_final: 0.8708 (mm) REVERT: D 271 MET cc_start: 0.7343 (mmm) cc_final: 0.6964 (mmm) REVERT: E 543 ASN cc_start: 0.9203 (t0) cc_final: 0.8711 (t0) REVERT: E 626 MET cc_start: 0.8060 (ppp) cc_final: 0.7799 (ppp) REVERT: E 647 GLU cc_start: 0.9030 (pm20) cc_final: 0.8754 (pm20) REVERT: F 4 MET cc_start: 0.6363 (mmt) cc_final: 0.5741 (mmp) REVERT: F 21 ILE cc_start: 0.8755 (mm) cc_final: 0.8099 (pt) REVERT: F 27 ASP cc_start: 0.7157 (m-30) cc_final: 0.6775 (m-30) REVERT: I 5 GLN cc_start: 0.8327 (mm110) cc_final: 0.8122 (tp40) REVERT: I 91 TYR cc_start: 0.7398 (m-10) cc_final: 0.6960 (m-80) REVERT: J 107 ASP cc_start: 0.8782 (t70) cc_final: 0.8392 (t70) REVERT: J 426 MET cc_start: 0.8483 (tpp) cc_final: 0.7935 (ttm) REVERT: K 535 MET cc_start: 0.9231 (mpp) cc_final: 0.8843 (mpp) REVERT: K 543 ASN cc_start: 0.9050 (t0) cc_final: 0.8790 (t0) outliers start: 2 outliers final: 0 residues processed: 171 average time/residue: 0.1691 time to fit residues: 43.7408 Evaluate side-chains 121 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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: 6.9990 chunk 41 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 96 GLN G 99 ASN G 103 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN A 17 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.061329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.044065 restraints weight = 106558.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.045549 restraints weight = 58887.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045918 restraints weight = 41126.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046204 restraints weight = 36386.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.046814 restraints weight = 32320.580| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.097 20793 Z= 0.427 Angle : 1.035 15.678 28419 Z= 0.496 Chirality : 0.056 0.510 3423 Planarity : 0.006 0.056 3444 Dihedral : 8.820 58.862 4515 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.99 % Favored : 89.88 % Rotamer: Outliers : 0.09 % Allowed : 5.54 % Favored : 94.37 % 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 aren not related in a simple way. whole: -1.69 (0.17), residues: 2382 helix: 0.41 (0.27), residues: 333 sheet: -1.42 (0.18), residues: 747 loop : -1.30 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 503 TYR 0.019 0.003 TYR L 32 PHE 0.043 0.003 PHE D 361 TRP 0.056 0.003 TRP A 35 HIS 0.013 0.002 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00956 (20658) covalent geometry : angle 0.98004 (28056) SS BOND : bond 0.00816 ( 42) SS BOND : angle 2.03322 ( 84) hydrogen bonds : bond 0.05333 ( 578) hydrogen bonds : angle 6.13792 ( 1470) link_ALPHA1-3 : bond 0.00913 ( 3) link_ALPHA1-3 : angle 2.68737 ( 9) link_BETA1-4 : bond 0.00860 ( 33) link_BETA1-4 : angle 2.51933 ( 99) link_NAG-ASN : bond 0.01012 ( 57) link_NAG-ASN : angle 3.78942 ( 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 132 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.677 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: 0.8232 (t0) cc_final: 0.7893 (t70) REVERT: L 74 LYS cc_start: 0.9099 (mmpt) cc_final: 0.8861 (mmmt) REVERT: L 81 GLU cc_start: 0.8587 (mp0) cc_final: 0.8368 (mp0) REVERT: G 271 MET cc_start: 0.8276 (mmp) cc_final: 0.7876 (mmm) REVERT: B 535 MET cc_start: 0.9310 (mtm) cc_final: 0.9050 (mtm) REVERT: B 584 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 77 ARG cc_start: 0.8748 (mtp-110) cc_final: 0.8522 (tmm160) REVERT: C 23 LYS cc_start: 0.8936 (tptp) cc_final: 0.8665 (tptp) REVERT: C 32 TYR cc_start: 0.8888 (m-10) cc_final: 0.8663 (m-10) REVERT: D 271 MET cc_start: 0.7464 (mmm) cc_final: 0.7136 (mmm) REVERT: D 426 MET cc_start: 0.9126 (tpp) cc_final: 0.8843 (tpp) REVERT: E 647 GLU cc_start: 0.9228 (pm20) cc_final: 0.8879 (pm20) REVERT: F 21 ILE cc_start: 0.8832 (mm) cc_final: 0.8239 (pt) REVERT: F 27 ASP cc_start: 0.7172 (m-30) cc_final: 0.6948 (m-30) REVERT: I 5 GLN cc_start: 0.8335 (mm110) cc_final: 0.8122 (mm-40) REVERT: J 271 MET cc_start: 0.7338 (mmm) cc_final: 0.7075 (mmm) REVERT: J 426 MET cc_start: 0.8744 (tpp) cc_final: 0.8010 (ttm) REVERT: K 535 MET cc_start: 0.9335 (mpp) cc_final: 0.8832 (mpp) outliers start: 2 outliers final: 0 residues processed: 131 average time/residue: 0.1504 time to fit residues: 29.8409 Evaluate side-chains 96 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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: 7.9990 chunk 20 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 328 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.062974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045166 restraints weight = 103200.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.047447 restraints weight = 58775.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.048144 restraints weight = 35256.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.048454 restraints weight = 28879.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.048591 restraints weight = 26643.584| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20793 Z= 0.224 Angle : 0.806 15.071 28419 Z= 0.387 Chirality : 0.050 0.487 3423 Planarity : 0.004 0.042 3444 Dihedral : 8.103 58.780 4515 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.93 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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 aren not related in a simple way. whole: -1.44 (0.17), residues: 2382 helix: 1.09 (0.28), residues: 333 sheet: -1.54 (0.17), residues: 789 loop : -1.05 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.025 0.002 TYR A 86 PHE 0.021 0.002 PHE D 361 TRP 0.028 0.002 TRP K 628 HIS 0.007 0.002 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00506 (20658) covalent geometry : angle 0.75308 (28056) SS BOND : bond 0.00377 ( 42) SS BOND : angle 1.65173 ( 84) hydrogen bonds : bond 0.04261 ( 578) hydrogen bonds : angle 5.55313 ( 1470) link_ALPHA1-3 : bond 0.01296 ( 3) link_ALPHA1-3 : angle 1.84040 ( 9) link_BETA1-4 : bond 0.00495 ( 33) link_BETA1-4 : angle 2.12159 ( 99) link_NAG-ASN : bond 0.00630 ( 57) link_NAG-ASN : angle 3.27056 ( 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 143 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.830 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: 0.8168 (t0) cc_final: 0.7856 (t70) REVERT: L 74 LYS cc_start: 0.9106 (mmpt) cc_final: 0.8895 (mmmt) REVERT: G 271 MET cc_start: 0.8307 (mmp) cc_final: 0.7896 (mmm) REVERT: B 535 MET cc_start: 0.9280 (mtm) cc_final: 0.8997 (mtm) REVERT: B 584 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8306 (tm-30) REVERT: B 643 TYR cc_start: 0.8437 (m-10) cc_final: 0.8023 (m-10) REVERT: B 654 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8247 (mt-10) REVERT: A 77 ARG cc_start: 0.8877 (mtp-110) cc_final: 0.8578 (tmm160) REVERT: C 32 TYR cc_start: 0.8785 (m-10) cc_final: 0.8555 (m-10) REVERT: C 34 ILE cc_start: 0.9149 (mm) cc_final: 0.8836 (mm) REVERT: D 271 MET cc_start: 0.7616 (mmm) cc_final: 0.7058 (mmm) REVERT: E 535 MET cc_start: 0.9312 (mtm) cc_final: 0.9003 (mtm) REVERT: E 626 MET cc_start: 0.8734 (ppp) cc_final: 0.8384 (ppp) REVERT: E 647 GLU cc_start: 0.9190 (pm20) cc_final: 0.8851 (pm20) REVERT: F 21 ILE cc_start: 0.8767 (mm) cc_final: 0.8142 (pt) REVERT: J 107 ASP cc_start: 0.8861 (t70) cc_final: 0.8405 (t70) REVERT: J 271 MET cc_start: 0.7709 (mmm) cc_final: 0.7467 (mmm) REVERT: K 535 MET cc_start: 0.9236 (mpp) cc_final: 0.8709 (mpp) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1584 time to fit residues: 34.4872 Evaluate side-chains 105 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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: 4.9990 chunk 74 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 96 GLN A 96 GLN ** 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 = 0.3508 r_free = 0.3508 target = 0.063882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.046013 restraints weight = 102509.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.048181 restraints weight = 57926.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.048894 restraints weight = 34707.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.049305 restraints weight = 29060.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.049460 restraints weight = 26589.176| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20793 Z= 0.155 Angle : 0.747 14.797 28419 Z= 0.359 Chirality : 0.049 0.486 3423 Planarity : 0.004 0.037 3444 Dihedral : 7.602 57.972 4515 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.64 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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 aren not related in a simple way. whole: -1.16 (0.18), residues: 2382 helix: 1.31 (0.29), residues: 351 sheet: -1.36 (0.18), residues: 759 loop : -0.91 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 542 TYR 0.020 0.002 TYR C 102 PHE 0.017 0.002 PHE J 376 TRP 0.028 0.002 TRP J 427 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00354 (20658) covalent geometry : angle 0.69767 (28056) SS BOND : bond 0.00359 ( 42) SS BOND : angle 1.29441 ( 84) hydrogen bonds : bond 0.03821 ( 578) hydrogen bonds : angle 5.30713 ( 1470) link_ALPHA1-3 : bond 0.01022 ( 3) link_ALPHA1-3 : angle 1.73427 ( 9) link_BETA1-4 : bond 0.00423 ( 33) link_BETA1-4 : angle 2.06506 ( 99) link_NAG-ASN : bond 0.00559 ( 57) link_NAG-ASN : angle 3.05587 ( 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 154 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.815 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: 0.8105 (t0) cc_final: 0.7758 (t70) REVERT: L 74 LYS cc_start: 0.9108 (mmpt) cc_final: 0.8906 (mmmt) REVERT: H 32 TYR cc_start: 0.9282 (m-80) cc_final: 0.8416 (m-80) REVERT: H 34 ILE cc_start: 0.9327 (mm) cc_final: 0.9018 (mm) REVERT: G 271 MET cc_start: 0.8143 (mmp) cc_final: 0.7793 (mmm) REVERT: B 535 MET cc_start: 0.9274 (mtm) cc_final: 0.8946 (mtm) REVERT: B 548 ILE cc_start: 0.7163 (mm) cc_final: 0.6941 (mm) REVERT: B 584 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8381 (tm-30) REVERT: B 643 TYR cc_start: 0.8478 (m-10) cc_final: 0.8047 (m-10) REVERT: B 654 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8315 (mt-10) REVERT: A 77 ARG cc_start: 0.8850 (mtp-110) cc_final: 0.8572 (tmm160) REVERT: C 32 TYR cc_start: 0.8726 (m-10) cc_final: 0.8295 (m-10) REVERT: C 34 ILE cc_start: 0.9149 (mm) cc_final: 0.8850 (mm) REVERT: D 271 MET cc_start: 0.7594 (mmm) cc_final: 0.7032 (mmm) REVERT: D 426 MET cc_start: 0.8262 (tpp) cc_final: 0.7984 (ttm) REVERT: E 535 MET cc_start: 0.9330 (mtm) cc_final: 0.9008 (mtm) REVERT: E 626 MET cc_start: 0.8645 (ppp) cc_final: 0.8363 (ppp) REVERT: E 647 GLU cc_start: 0.9172 (pm20) cc_final: 0.8826 (pm20) REVERT: F 21 ILE cc_start: 0.8832 (mm) cc_final: 0.8227 (pt) REVERT: J 107 ASP cc_start: 0.8910 (t70) cc_final: 0.8485 (t70) REVERT: J 271 MET cc_start: 0.7509 (mmm) cc_final: 0.7286 (mmm) REVERT: K 535 MET cc_start: 0.9218 (mpp) cc_final: 0.8608 (mpp) REVERT: K 647 GLU cc_start: 0.8973 (pm20) cc_final: 0.8359 (pm20) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1526 time to fit residues: 36.5164 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 : 0.655 ------------------------------------------------------------------------------- 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: 9.9990 chunk 182 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 232 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 96 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.045523 restraints weight = 102997.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.047749 restraints weight = 58514.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.048491 restraints weight = 34780.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.049044 restraints weight = 28552.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.049140 restraints weight = 25577.723| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20793 Z= 0.186 Angle : 0.753 14.711 28419 Z= 0.362 Chirality : 0.048 0.484 3423 Planarity : 0.004 0.040 3444 Dihedral : 7.430 56.946 4515 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.98 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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 aren not related in a simple way. whole: -1.13 (0.18), residues: 2382 helix: 1.66 (0.29), residues: 333 sheet: -1.33 (0.18), residues: 756 loop : -0.98 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 542 TYR 0.013 0.001 TYR C 91 PHE 0.017 0.002 PHE G 361 TRP 0.052 0.002 TRP G 479 HIS 0.005 0.001 HIS G 85 Details of bonding type rmsd covalent geometry : bond 0.00424 (20658) covalent geometry : angle 0.70510 (28056) SS BOND : bond 0.00341 ( 42) SS BOND : angle 1.48285 ( 84) hydrogen bonds : bond 0.03850 ( 578) hydrogen bonds : angle 5.31070 ( 1470) link_ALPHA1-3 : bond 0.00628 ( 3) link_ALPHA1-3 : angle 1.51759 ( 9) link_BETA1-4 : bond 0.00427 ( 33) link_BETA1-4 : angle 2.06095 ( 99) link_NAG-ASN : bond 0.00565 ( 57) link_NAG-ASN : angle 3.00169 ( 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 147 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.795 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: 0.8253 (t0) cc_final: 0.7943 (t70) REVERT: L 74 LYS cc_start: 0.9117 (mmpt) cc_final: 0.8906 (mmmt) REVERT: G 104 MET cc_start: 0.9420 (ttm) cc_final: 0.9207 (ttm) REVERT: G 271 MET cc_start: 0.8221 (mmp) cc_final: 0.7845 (mmm) REVERT: B 535 MET cc_start: 0.9274 (mtm) cc_final: 0.8939 (mtm) REVERT: B 548 ILE cc_start: 0.7119 (mm) cc_final: 0.6910 (mm) REVERT: B 584 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8382 (tm-30) REVERT: B 643 TYR cc_start: 0.8465 (m-10) cc_final: 0.8030 (m-10) REVERT: B 654 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8361 (mt-10) REVERT: A 27 ASP cc_start: 0.8702 (t70) cc_final: 0.8499 (t70) REVERT: A 77 ARG cc_start: 0.8870 (mtp-110) cc_final: 0.8586 (tmm160) REVERT: C 23 LYS cc_start: 0.9019 (tptt) cc_final: 0.8559 (tppt) REVERT: C 32 TYR cc_start: 0.8745 (m-10) cc_final: 0.8294 (m-10) REVERT: C 34 ILE cc_start: 0.9161 (mm) cc_final: 0.8858 (mm) REVERT: D 271 MET cc_start: 0.7668 (mmm) cc_final: 0.7160 (mmm) REVERT: E 535 MET cc_start: 0.9347 (mtm) cc_final: 0.8995 (mtm) REVERT: E 584 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8806 (tm-30) REVERT: E 626 MET cc_start: 0.8633 (ppp) cc_final: 0.8384 (ppp) REVERT: E 647 GLU cc_start: 0.9179 (pm20) cc_final: 0.8833 (pm20) REVERT: F 21 ILE cc_start: 0.8806 (mm) cc_final: 0.8150 (pt) REVERT: J 95 MET cc_start: 0.8486 (ttp) cc_final: 0.7332 (ttp) REVERT: J 107 ASP cc_start: 0.8846 (t70) cc_final: 0.8465 (t70) REVERT: J 271 MET cc_start: 0.7515 (mmm) cc_final: 0.7272 (mmm) REVERT: K 535 MET cc_start: 0.9303 (mpp) cc_final: 0.8679 (mpp) REVERT: K 647 GLU cc_start: 0.9016 (pm20) cc_final: 0.8418 (pm20) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1603 time to fit residues: 36.5603 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 : 0.783 ------------------------------------------------------------------------------- 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: 9.9990 chunk 156 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 139 optimal weight: 0.3980 chunk 161 optimal weight: 30.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 96 GLN G 328 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 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 203 GLN ** 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 = 0.3490 r_free = 0.3490 target = 0.063079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.045231 restraints weight = 103098.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.047395 restraints weight = 58854.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048208 restraints weight = 35353.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.048512 restraints weight = 29185.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.048707 restraints weight = 26794.116| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20793 Z= 0.206 Angle : 0.772 14.401 28419 Z= 0.372 Chirality : 0.049 0.491 3423 Planarity : 0.004 0.044 3444 Dihedral : 7.433 56.912 4515 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.48 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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 aren not related in a simple way. whole: -1.17 (0.17), residues: 2382 helix: 1.57 (0.29), residues: 333 sheet: -1.34 (0.18), residues: 750 loop : -1.00 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 542 TYR 0.026 0.002 TYR K 638 PHE 0.019 0.002 PHE G 361 TRP 0.047 0.002 TRP D 479 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00469 (20658) covalent geometry : angle 0.72529 (28056) SS BOND : bond 0.00360 ( 42) SS BOND : angle 1.60281 ( 84) hydrogen bonds : bond 0.03931 ( 578) hydrogen bonds : angle 5.35653 ( 1470) link_ALPHA1-3 : bond 0.00877 ( 3) link_ALPHA1-3 : angle 1.64333 ( 9) link_BETA1-4 : bond 0.00459 ( 33) link_BETA1-4 : angle 2.06060 ( 99) link_NAG-ASN : bond 0.00593 ( 57) link_NAG-ASN : angle 2.96890 ( 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 145 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.815 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: 0.8290 (t0) cc_final: 0.7981 (t70) REVERT: L 74 LYS cc_start: 0.9109 (mmpt) cc_final: 0.8904 (mmmt) REVERT: H 34 ILE cc_start: 0.9255 (mm) cc_final: 0.9021 (mm) REVERT: G 271 MET cc_start: 0.8254 (mmp) cc_final: 0.7870 (mmm) REVERT: G 426 MET cc_start: 0.8970 (tpp) cc_final: 0.8731 (tpp) REVERT: B 535 MET cc_start: 0.9291 (mtm) cc_final: 0.8963 (mtm) REVERT: B 584 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8334 (tm-30) REVERT: B 643 TYR cc_start: 0.8479 (m-10) cc_final: 0.8035 (m-10) REVERT: B 654 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8344 (mt-10) REVERT: A 77 ARG cc_start: 0.8853 (mtp-110) cc_final: 0.8561 (tmm160) REVERT: C 23 LYS cc_start: 0.9029 (tptt) cc_final: 0.8763 (tptp) REVERT: C 32 TYR cc_start: 0.8798 (m-10) cc_final: 0.8308 (m-10) REVERT: C 34 ILE cc_start: 0.9175 (mm) cc_final: 0.8877 (mm) REVERT: D 271 MET cc_start: 0.7670 (mmm) cc_final: 0.7145 (mmm) REVERT: E 584 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8797 (tm-30) REVERT: F 21 ILE cc_start: 0.8798 (mm) cc_final: 0.8467 (tp) REVERT: I 5 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7764 (mm-40) REVERT: J 95 MET cc_start: 0.8485 (ttp) cc_final: 0.7276 (ttp) REVERT: J 107 ASP cc_start: 0.8852 (t70) cc_final: 0.8469 (t70) REVERT: J 271 MET cc_start: 0.7491 (mmm) cc_final: 0.7247 (mmm) REVERT: K 535 MET cc_start: 0.9290 (mpp) cc_final: 0.8755 (mpp) REVERT: K 647 GLU cc_start: 0.9102 (pm20) cc_final: 0.8557 (pm20) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1626 time to fit residues: 36.3697 Evaluate side-chains 109 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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: 0.9980 chunk 189 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 180 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 96 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN F 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.064237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.046429 restraints weight = 102378.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.048608 restraints weight = 56747.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.049405 restraints weight = 34215.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.050034 restraints weight = 27704.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.050229 restraints weight = 24362.132| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20793 Z= 0.129 Angle : 0.719 13.982 28419 Z= 0.346 Chirality : 0.048 0.463 3423 Planarity : 0.004 0.042 3444 Dihedral : 6.908 56.881 4515 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.22 % Favored : 92.65 % 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 : 0.13 % 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 aren not related in a simple way. whole: -0.98 (0.18), residues: 2382 helix: 1.82 (0.29), residues: 333 sheet: -1.22 (0.18), residues: 756 loop : -0.90 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 77 TYR 0.023 0.001 TYR B 638 PHE 0.019 0.002 PHE J 317 TRP 0.042 0.002 TRP G 479 HIS 0.005 0.001 HIS G 85 Details of bonding type rmsd covalent geometry : bond 0.00294 (20658) covalent geometry : angle 0.67586 (28056) SS BOND : bond 0.00302 ( 42) SS BOND : angle 1.42099 ( 84) hydrogen bonds : bond 0.03457 ( 578) hydrogen bonds : angle 5.17104 ( 1470) link_ALPHA1-3 : bond 0.00763 ( 3) link_ALPHA1-3 : angle 1.45044 ( 9) link_BETA1-4 : bond 0.00444 ( 33) link_BETA1-4 : angle 1.97751 ( 99) link_NAG-ASN : bond 0.00505 ( 57) link_NAG-ASN : angle 2.76099 ( 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 153 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.559 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: 0.8253 (t0) cc_final: 0.7921 (t70) REVERT: L 74 LYS cc_start: 0.9151 (mmpt) cc_final: 0.8929 (mmmt) REVERT: H 32 TYR cc_start: 0.9319 (m-80) cc_final: 0.8371 (m-80) REVERT: H 34 ILE cc_start: 0.9264 (mm) cc_final: 0.9034 (mm) REVERT: G 271 MET cc_start: 0.8304 (mmp) cc_final: 0.7870 (mmm) REVERT: G 426 MET cc_start: 0.8953 (tpp) cc_final: 0.8741 (tpp) REVERT: B 535 MET cc_start: 0.9257 (mtm) cc_final: 0.8886 (mtm) REVERT: B 574 LYS cc_start: 0.8272 (mppt) cc_final: 0.7951 (mtpp) REVERT: B 584 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8222 (tm-30) REVERT: B 633 LYS cc_start: 0.9601 (tptp) cc_final: 0.9292 (tppt) REVERT: B 643 TYR cc_start: 0.8471 (m-10) cc_final: 0.8025 (m-10) REVERT: B 654 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8345 (mt-10) REVERT: A 27 ASP cc_start: 0.8782 (t70) cc_final: 0.8578 (t70) REVERT: A 77 ARG cc_start: 0.8857 (mtp-110) cc_final: 0.8529 (tmm160) REVERT: C 23 LYS cc_start: 0.9004 (tptt) cc_final: 0.8706 (tptp) REVERT: C 32 TYR cc_start: 0.8664 (m-10) cc_final: 0.8307 (m-10) REVERT: C 34 ILE cc_start: 0.9184 (mm) cc_final: 0.8890 (mm) REVERT: D 95 MET cc_start: 0.7325 (ttm) cc_final: 0.6924 (ttm) REVERT: D 271 MET cc_start: 0.7624 (mmm) cc_final: 0.7134 (mmm) REVERT: D 426 MET cc_start: 0.8467 (tpp) cc_final: 0.8241 (tpp) REVERT: E 530 MET cc_start: 0.7804 (mmm) cc_final: 0.7364 (mmm) REVERT: E 543 ASN cc_start: 0.9211 (t0) cc_final: 0.8841 (t0) REVERT: E 584 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8773 (tm-30) REVERT: E 595 ILE cc_start: 0.9121 (tp) cc_final: 0.8908 (tp) REVERT: F 21 ILE cc_start: 0.8868 (mm) cc_final: 0.8275 (pt) REVERT: I 5 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7722 (mm-40) REVERT: I 71 VAL cc_start: 0.8354 (m) cc_final: 0.8113 (t) REVERT: J 107 ASP cc_start: 0.8786 (t70) cc_final: 0.8525 (t70) REVERT: J 271 MET cc_start: 0.7460 (mmm) cc_final: 0.7228 (mmm) REVERT: K 535 MET cc_start: 0.9190 (mpp) cc_final: 0.8577 (mpp) REVERT: K 647 GLU cc_start: 0.9061 (pm20) cc_final: 0.8577 (pm20) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.1437 time to fit residues: 34.2454 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 : 0.651 ------------------------------------------------------------------------------- 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: 8.9990 chunk 80 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 193 optimal weight: 0.0070 chunk 43 optimal weight: 0.9980 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 HIS ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 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 = 0.3512 r_free = 0.3512 target = 0.064019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.046146 restraints weight = 102376.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.048482 restraints weight = 57746.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.049250 restraints weight = 34060.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.049745 restraints weight = 27451.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.049867 restraints weight = 24832.096| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20793 Z= 0.147 Angle : 0.718 13.803 28419 Z= 0.346 Chirality : 0.048 0.467 3423 Planarity : 0.004 0.042 3444 Dihedral : 6.768 56.917 4515 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.81 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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 aren not related in a simple way. whole: -1.00 (0.18), residues: 2382 helix: 1.69 (0.29), residues: 333 sheet: -1.18 (0.18), residues: 750 loop : -0.92 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 588 TYR 0.019 0.001 TYR B 638 PHE 0.018 0.002 PHE A 62 TRP 0.039 0.002 TRP G 479 HIS 0.005 0.001 HIS G 85 Details of bonding type rmsd covalent geometry : bond 0.00340 (20658) covalent geometry : angle 0.67525 (28056) SS BOND : bond 0.00305 ( 42) SS BOND : angle 1.41997 ( 84) hydrogen bonds : bond 0.03464 ( 578) hydrogen bonds : angle 5.11231 ( 1470) link_ALPHA1-3 : bond 0.00696 ( 3) link_ALPHA1-3 : angle 1.49326 ( 9) link_BETA1-4 : bond 0.00416 ( 33) link_BETA1-4 : angle 1.97151 ( 99) link_NAG-ASN : bond 0.00497 ( 57) link_NAG-ASN : angle 2.75405 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2978.44 seconds wall clock time: 52 minutes 56.07 seconds (3176.07 seconds total)