Starting phenix.real_space_refine on Tue Jun 17 21:29:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gas_29905/06_2025/8gas_29905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gas_29905/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gas_29905/06_2025/8gas_29905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gas_29905/06_2025/8gas_29905.map" model { file = "/net/cci-nas-00/data/ceres_data/8gas_29905/06_2025/8gas_29905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gas_29905/06_2025/8gas_29905.cif" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.87, per 1000 atoms: 0.64 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: 5.92 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.95 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: 7.66 Time building geometry restraints manager: 6.94 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: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.040 Extract box with map and model: 0.730 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 49.070 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (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 TRP 0.022 0.001 TRP I 100D HIS 0.006 0.000 HIS D 85 PHE 0.016 0.001 PHE D 391 TYR 0.030 0.001 TYR J 435 ARG 0.010 0.000 ARG J 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 57) link_NAG-ASN : angle 2.63966 ( 171) link_BETA1-4 : bond 0.00349 ( 33) link_BETA1-4 : angle 1.98172 ( 99) link_ALPHA1-3 : bond 0.00432 ( 3) link_ALPHA1-3 : angle 1.52130 ( 9) hydrogen bonds : bond 0.25150 ( 578) hydrogen bonds : angle 8.60803 ( 1470) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.22248 ( 84) covalent geometry : bond 0.00416 (20658) covalent geometry : angle 0.68339 (28056) *********************** 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 : 2.261 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: 0.3543 time to fit residues: 146.1716 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 : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN G 99 ASN G 249 HIS G 330 HIS B 652 GLN A 17 GLN C 81 GLN D 99 ASN D 249 HIS D 330 HIS F 96 GLN I 81 GLN J 99 ASN J 103 GLN J 249 HIS J 330 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.066962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.048550 restraints weight = 101511.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.050663 restraints weight = 57808.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.051456 restraints weight = 36121.329| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20793 Z= 0.238 Angle : 0.857 16.012 28419 Z= 0.406 Chirality : 0.052 0.520 3423 Planarity : 0.005 0.081 3444 Dihedral : 11.831 65.805 4515 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.18 % Favored : 92.70 % Rotamer: Outliers : 0.14 % Allowed : 5.07 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.18), residues: 2382 helix: 1.17 (0.28), residues: 351 sheet: -0.84 (0.18), residues: 780 loop : -0.99 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 571 HIS 0.006 0.001 HIS D 85 PHE 0.024 0.003 PHE D 361 TYR 0.029 0.002 TYR I 91 ARG 0.011 0.001 ARG L 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 57) link_NAG-ASN : angle 3.56352 ( 171) link_BETA1-4 : bond 0.00624 ( 33) link_BETA1-4 : angle 2.53799 ( 99) link_ALPHA1-3 : bond 0.01252 ( 3) link_ALPHA1-3 : angle 3.29576 ( 9) hydrogen bonds : bond 0.04782 ( 578) hydrogen bonds : angle 6.15525 ( 1470) SS BOND : bond 0.00508 ( 42) SS BOND : angle 1.55219 ( 84) covalent geometry : bond 0.00535 (20658) covalent geometry : angle 0.79518 (28056) *********************** 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 189 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 186 time to evaluate : 2.107 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: 0.8084 (t0) cc_final: 0.7699 (t70) REVERT: L 81 GLU cc_start: 0.8479 (mp0) cc_final: 0.8047 (mp0) REVERT: H 32 TYR cc_start: 0.9106 (m-80) cc_final: 0.8092 (m-80) REVERT: H 34 ILE cc_start: 0.9136 (mm) cc_final: 0.8875 (mm) REVERT: G 104 MET cc_start: 0.9401 (ttm) cc_final: 0.9049 (ttm) REVERT: G 271 MET cc_start: 0.8130 (mmp) cc_final: 0.7861 (mmm) REVERT: B 518 VAL cc_start: 0.9573 (m) cc_final: 0.9369 (p) REVERT: B 543 ASN cc_start: 0.8828 (t0) cc_final: 0.8521 (t0) REVERT: B 643 TYR cc_start: 0.8488 (m-10) cc_final: 0.8093 (m-10) REVERT: C 23 LYS cc_start: 0.8654 (mptt) cc_final: 0.8421 (tptp) REVERT: C 32 TYR cc_start: 0.8653 (m-10) cc_final: 0.8352 (m-10) REVERT: C 34 ILE cc_start: 0.8928 (mm) cc_final: 0.8589 (mm) REVERT: C 105 GLN cc_start: 0.9422 (tp40) cc_final: 0.9181 (tp40) REVERT: D 271 MET cc_start: 0.7597 (mmp) cc_final: 0.7274 (mmm) REVERT: E 543 ASN cc_start: 0.9043 (t0) cc_final: 0.8555 (t0) REVERT: F 4 MET cc_start: 0.5663 (mmt) cc_final: 0.5095 (mmp) REVERT: I 5 GLN cc_start: 0.8439 (mm110) cc_final: 0.8154 (mm110) REVERT: J 271 MET cc_start: 0.7513 (mmm) cc_final: 0.7228 (mmm) outliers start: 3 outliers final: 2 residues processed: 189 average time/residue: 0.3429 time to fit residues: 97.8172 Evaluate side-chains 124 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 121 optimal weight: 0.0060 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 348 GLN A 17 GLN C 3 GLN D 99 ASN D 348 GLN F 96 GLN J 348 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.064907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.046724 restraints weight = 101855.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.048939 restraints weight = 57746.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.049663 restraints weight = 36066.962| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20793 Z= 0.219 Angle : 0.778 15.277 28419 Z= 0.373 Chirality : 0.050 0.501 3423 Planarity : 0.005 0.049 3444 Dihedral : 8.881 59.385 4515 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.59 % Favored : 93.28 % Rotamer: Outliers : 0.19 % Allowed : 4.92 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2382 helix: 1.01 (0.28), residues: 351 sheet: -0.96 (0.18), residues: 750 loop : -0.95 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 628 HIS 0.006 0.001 HIS D 85 PHE 0.021 0.002 PHE G 383 TYR 0.018 0.002 TYR I 91 ARG 0.007 0.001 ARG L 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 57) link_NAG-ASN : angle 3.05489 ( 171) link_BETA1-4 : bond 0.00519 ( 33) link_BETA1-4 : angle 2.28288 ( 99) link_ALPHA1-3 : bond 0.01433 ( 3) link_ALPHA1-3 : angle 1.83726 ( 9) hydrogen bonds : bond 0.04633 ( 578) hydrogen bonds : angle 5.60623 ( 1470) SS BOND : bond 0.00349 ( 42) SS BOND : angle 1.40993 ( 84) covalent geometry : bond 0.00491 (20658) covalent geometry : angle 0.72876 (28056) *********************** 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 164 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 160 time to evaluate : 2.321 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: 0.8123 (t0) cc_final: 0.7680 (t70) REVERT: L 74 LYS cc_start: 0.9069 (mmpt) cc_final: 0.8799 (mmmt) REVERT: L 81 GLU cc_start: 0.8424 (mp0) cc_final: 0.7987 (mp0) REVERT: H 32 TYR cc_start: 0.9179 (m-80) cc_final: 0.8221 (m-80) REVERT: H 34 ILE cc_start: 0.9242 (mm) cc_final: 0.8924 (mm) REVERT: G 271 MET cc_start: 0.8209 (mmp) cc_final: 0.7785 (mmm) REVERT: B 543 ASN cc_start: 0.9057 (t0) cc_final: 0.8513 (t0) REVERT: B 584 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8422 (tm-30) REVERT: B 626 MET cc_start: 0.8780 (ppp) cc_final: 0.8494 (ppp) REVERT: A 77 ARG cc_start: 0.8753 (mtp-110) cc_final: 0.8520 (tmm160) REVERT: C 23 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8472 (tptp) REVERT: C 32 TYR cc_start: 0.8784 (m-10) cc_final: 0.8447 (m-10) REVERT: C 34 ILE cc_start: 0.8997 (mm) cc_final: 0.8637 (mm) REVERT: D 95 MET cc_start: 0.8147 (ttm) cc_final: 0.7887 (ttm) REVERT: D 271 MET cc_start: 0.7725 (mmp) cc_final: 0.7314 (mmm) REVERT: E 543 ASN cc_start: 0.9197 (t0) cc_final: 0.8623 (t0) REVERT: E 647 GLU cc_start: 0.9068 (pm20) cc_final: 0.8734 (pm20) REVERT: F 21 ILE cc_start: 0.8706 (mm) cc_final: 0.8041 (pt) REVERT: I 5 GLN cc_start: 0.8365 (mm110) cc_final: 0.7570 (mp10) REVERT: I 100 LEU cc_start: 0.7815 (mt) cc_final: 0.7547 (mt) REVERT: J 52 LEU cc_start: 0.9078 (mt) cc_final: 0.8626 (mp) REVERT: J 271 MET cc_start: 0.7472 (mmm) cc_final: 0.7187 (mmm) REVERT: J 479 TRP cc_start: 0.8070 (m-10) cc_final: 0.7724 (m-10) REVERT: K 535 MET cc_start: 0.9332 (mpp) cc_final: 0.8881 (mpp) REVERT: K 543 ASN cc_start: 0.9065 (t0) cc_final: 0.8852 (t0) outliers start: 4 outliers final: 0 residues processed: 163 average time/residue: 0.3476 time to fit residues: 86.9980 Evaluate side-chains 118 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 100 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 198 optimal weight: 0.3980 chunk 157 optimal weight: 0.4980 chunk 200 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN G 103 GLN A 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.066599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.048062 restraints weight = 100415.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.050121 restraints weight = 59056.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.051309 restraints weight = 35389.924| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20793 Z= 0.120 Angle : 0.686 14.746 28419 Z= 0.327 Chirality : 0.048 0.493 3423 Planarity : 0.004 0.047 3444 Dihedral : 7.408 57.227 4515 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.34 % Favored : 93.53 % Rotamer: Outliers : 0.14 % Allowed : 3.50 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.18), residues: 2382 helix: 1.42 (0.29), residues: 351 sheet: -1.02 (0.18), residues: 759 loop : -0.79 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 628 HIS 0.007 0.001 HIS D 85 PHE 0.015 0.001 PHE D 376 TYR 0.016 0.001 TYR E 643 ARG 0.005 0.000 ARG K 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 57) link_NAG-ASN : angle 2.81817 ( 171) link_BETA1-4 : bond 0.00495 ( 33) link_BETA1-4 : angle 2.14407 ( 99) link_ALPHA1-3 : bond 0.01265 ( 3) link_ALPHA1-3 : angle 2.31176 ( 9) hydrogen bonds : bond 0.03668 ( 578) hydrogen bonds : angle 5.26906 ( 1470) SS BOND : bond 0.00295 ( 42) SS BOND : angle 0.96891 ( 84) covalent geometry : bond 0.00266 (20658) covalent geometry : angle 0.63885 (28056) *********************** 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 187 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 2.405 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: 0.8271 (t0) cc_final: 0.7797 (t70) REVERT: L 74 LYS cc_start: 0.9075 (mmpt) cc_final: 0.8786 (mmmt) REVERT: L 81 GLU cc_start: 0.8357 (mp0) cc_final: 0.7893 (mp0) REVERT: H 32 TYR cc_start: 0.9170 (m-80) cc_final: 0.8222 (m-80) REVERT: H 34 ILE cc_start: 0.9280 (mm) cc_final: 0.8970 (mm) REVERT: G 271 MET cc_start: 0.7967 (mmp) cc_final: 0.7591 (mmm) REVERT: G 285 LEU cc_start: 0.8557 (tp) cc_final: 0.8209 (mp) REVERT: B 535 MET cc_start: 0.9224 (mtm) cc_final: 0.8601 (mpp) REVERT: B 543 ASN cc_start: 0.8996 (t0) cc_final: 0.8548 (t0) REVERT: B 584 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8447 (tm-30) REVERT: B 643 TYR cc_start: 0.8455 (m-10) cc_final: 0.8073 (m-10) REVERT: C 32 TYR cc_start: 0.8694 (m-10) cc_final: 0.8429 (m-10) REVERT: C 34 ILE cc_start: 0.9083 (mm) cc_final: 0.8728 (mm) REVERT: E 543 ASN cc_start: 0.9145 (t0) cc_final: 0.8720 (t0) REVERT: E 584 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8839 (tm-30) REVERT: E 647 GLU cc_start: 0.8981 (pm20) cc_final: 0.8696 (pm20) REVERT: F 4 MET cc_start: 0.6127 (mmt) cc_final: 0.5433 (mmp) REVERT: F 21 ILE cc_start: 0.8711 (mm) cc_final: 0.8103 (pt) REVERT: F 27 ASP cc_start: 0.7954 (t70) cc_final: 0.7579 (t70) REVERT: I 5 GLN cc_start: 0.8343 (mm110) cc_final: 0.7548 (mp10) REVERT: J 52 LEU cc_start: 0.9138 (mt) cc_final: 0.8523 (mp) REVERT: J 95 MET cc_start: 0.8010 (ttm) cc_final: 0.7254 (ttp) REVERT: J 107 ASP cc_start: 0.8785 (t70) cc_final: 0.8369 (t70) REVERT: J 271 MET cc_start: 0.7089 (mmm) cc_final: 0.6885 (mmm) REVERT: J 434 MET cc_start: 0.7979 (ptm) cc_final: 0.7632 (ptp) REVERT: K 535 MET cc_start: 0.9246 (mpp) cc_final: 0.8871 (mpp) outliers start: 3 outliers final: 0 residues processed: 187 average time/residue: 0.3444 time to fit residues: 97.7650 Evaluate side-chains 125 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 30 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 230 optimal weight: 0.0070 chunk 71 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 overall best weight: 4.0006 ------------------------------------------------------------------------------- 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** G 103 GLN G 203 GLN ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 618 ASN F 96 GLN J 103 GLN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.064566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.046349 restraints weight = 102833.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.048538 restraints weight = 58779.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.049323 restraints weight = 35993.219| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20793 Z= 0.237 Angle : 0.790 15.053 28419 Z= 0.376 Chirality : 0.050 0.491 3423 Planarity : 0.004 0.051 3444 Dihedral : 7.304 57.490 4515 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.98 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2382 helix: 1.10 (0.29), residues: 345 sheet: -1.23 (0.17), residues: 798 loop : -0.74 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 479 HIS 0.006 0.001 HIS D 85 PHE 0.027 0.002 PHE D 361 TYR 0.015 0.002 TYR G 318 ARG 0.007 0.001 ARG A 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 57) link_NAG-ASN : angle 3.19469 ( 171) link_BETA1-4 : bond 0.00514 ( 33) link_BETA1-4 : angle 2.14682 ( 99) link_ALPHA1-3 : bond 0.01415 ( 3) link_ALPHA1-3 : angle 2.37156 ( 9) hydrogen bonds : bond 0.04162 ( 578) hydrogen bonds : angle 5.41802 ( 1470) SS BOND : bond 0.00524 ( 42) SS BOND : angle 1.29638 ( 84) covalent geometry : bond 0.00536 (20658) covalent geometry : angle 0.73965 (28056) *********************** 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 158 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 2.250 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: 0.8278 (t0) cc_final: 0.7848 (t70) REVERT: L 74 LYS cc_start: 0.9092 (mmpt) cc_final: 0.8842 (mmmt) REVERT: L 81 GLU cc_start: 0.8417 (mp0) cc_final: 0.8023 (mp0) REVERT: H 32 TYR cc_start: 0.9269 (m-80) cc_final: 0.8419 (m-80) REVERT: G 104 MET cc_start: 0.9462 (ttm) cc_final: 0.9250 (ttm) REVERT: G 271 MET cc_start: 0.8231 (mmp) cc_final: 0.7819 (mmm) REVERT: G 426 MET cc_start: 0.8949 (tpp) cc_final: 0.8518 (tpp) REVERT: B 535 MET cc_start: 0.9262 (mtm) cc_final: 0.8924 (mtm) REVERT: B 584 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8441 (tm-30) REVERT: B 643 TYR cc_start: 0.8452 (m-10) cc_final: 0.8023 (m-10) REVERT: B 647 GLU cc_start: 0.9160 (pm20) cc_final: 0.8868 (pm20) REVERT: C 23 LYS cc_start: 0.9080 (tppt) cc_final: 0.8870 (tptp) REVERT: C 32 TYR cc_start: 0.8827 (m-10) cc_final: 0.8500 (m-10) REVERT: D 271 MET cc_start: 0.7883 (mmp) cc_final: 0.7589 (mmm) REVERT: D 426 MET cc_start: 0.9086 (tpp) cc_final: 0.8515 (tpp) REVERT: E 543 ASN cc_start: 0.9309 (t0) cc_final: 0.8750 (t0) REVERT: E 647 GLU cc_start: 0.9093 (pm20) cc_final: 0.8794 (pm20) REVERT: F 4 MET cc_start: 0.6336 (mmt) cc_final: 0.5695 (mmp) REVERT: F 21 ILE cc_start: 0.8740 (mm) cc_final: 0.8126 (pt) REVERT: F 27 ASP cc_start: 0.7933 (t70) cc_final: 0.7685 (t0) REVERT: J 107 ASP cc_start: 0.8756 (t70) cc_final: 0.8307 (t70) REVERT: J 271 MET cc_start: 0.7545 (mmm) cc_final: 0.7232 (mmm) REVERT: K 535 MET cc_start: 0.9275 (mpp) cc_final: 0.8893 (mpp) REVERT: K 543 ASN cc_start: 0.9153 (t0) cc_final: 0.8926 (t0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.3519 time to fit residues: 85.2888 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 : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 164 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 203 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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** G 99 ASN A 17 GLN A 96 GLN C 5 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.064668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.046546 restraints weight = 102833.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.048489 restraints weight = 60137.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.049360 restraints weight = 37614.317| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20793 Z= 0.194 Angle : 0.738 14.546 28419 Z= 0.356 Chirality : 0.049 0.483 3423 Planarity : 0.004 0.050 3444 Dihedral : 7.020 56.697 4515 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.14 % Favored : 92.74 % Rotamer: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 2382 helix: 1.39 (0.29), residues: 333 sheet: -1.18 (0.17), residues: 828 loop : -0.81 (0.19), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP J 479 HIS 0.005 0.001 HIS D 85 PHE 0.019 0.002 PHE G 361 TYR 0.013 0.001 TYR J 318 ARG 0.006 0.000 ARG A 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 57) link_NAG-ASN : angle 2.93302 ( 171) link_BETA1-4 : bond 0.00460 ( 33) link_BETA1-4 : angle 2.03532 ( 99) link_ALPHA1-3 : bond 0.01064 ( 3) link_ALPHA1-3 : angle 1.78687 ( 9) hydrogen bonds : bond 0.03811 ( 578) hydrogen bonds : angle 5.28420 ( 1470) SS BOND : bond 0.00411 ( 42) SS BOND : angle 1.27257 ( 84) covalent geometry : bond 0.00438 (20658) covalent geometry : angle 0.69222 (28056) *********************** 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 153 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 2.140 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: 0.8217 (t0) cc_final: 0.7862 (t70) REVERT: L 74 LYS cc_start: 0.9091 (mmpt) cc_final: 0.8880 (mmmt) REVERT: L 81 GLU cc_start: 0.8436 (mp0) cc_final: 0.8068 (mp0) REVERT: H 32 TYR cc_start: 0.9278 (m-80) cc_final: 0.8387 (m-80) REVERT: H 34 ILE cc_start: 0.9248 (mm) cc_final: 0.8979 (mm) REVERT: G 271 MET cc_start: 0.8263 (mmp) cc_final: 0.7898 (mmm) REVERT: G 426 MET cc_start: 0.9093 (tpp) cc_final: 0.8830 (tpp) REVERT: B 535 MET cc_start: 0.9304 (mtm) cc_final: 0.8684 (mpp) REVERT: B 543 ASN cc_start: 0.8999 (t0) cc_final: 0.8427 (t0) REVERT: B 548 ILE cc_start: 0.7069 (mm) cc_final: 0.6853 (mm) REVERT: B 584 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8455 (tm-30) REVERT: B 647 GLU cc_start: 0.9151 (pm20) cc_final: 0.8830 (pm20) REVERT: B 654 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8319 (mt-10) REVERT: C 23 LYS cc_start: 0.9057 (tppt) cc_final: 0.8659 (tptp) REVERT: C 32 TYR cc_start: 0.8897 (m-10) cc_final: 0.8506 (m-10) REVERT: C 34 ILE cc_start: 0.9118 (mm) cc_final: 0.8819 (mm) REVERT: D 271 MET cc_start: 0.7899 (mmp) cc_final: 0.7686 (mmm) REVERT: D 426 MET cc_start: 0.8988 (tpp) cc_final: 0.8392 (tpp) REVERT: E 535 MET cc_start: 0.9311 (mtm) cc_final: 0.9010 (mtm) REVERT: E 543 ASN cc_start: 0.9329 (t0) cc_final: 0.8783 (t0) REVERT: E 647 GLU cc_start: 0.9113 (pm20) cc_final: 0.8814 (pm20) REVERT: F 4 MET cc_start: 0.6593 (mmt) cc_final: 0.5935 (mmm) REVERT: F 21 ILE cc_start: 0.8701 (mm) cc_final: 0.8046 (pt) REVERT: F 24 LYS cc_start: 0.8766 (tmmt) cc_final: 0.8508 (tmtt) REVERT: F 27 ASP cc_start: 0.7955 (t70) cc_final: 0.7687 (t0) REVERT: I 5 GLN cc_start: 0.8270 (mm-40) cc_final: 0.8020 (mm-40) REVERT: J 52 LEU cc_start: 0.9147 (mt) cc_final: 0.8519 (mm) REVERT: J 107 ASP cc_start: 0.8772 (t70) cc_final: 0.8341 (t70) REVERT: J 271 MET cc_start: 0.7584 (mmm) cc_final: 0.7312 (mmm) REVERT: K 535 MET cc_start: 0.9230 (mpp) cc_final: 0.8779 (mpp) REVERT: K 543 ASN cc_start: 0.9095 (t0) cc_final: 0.8820 (t0) REVERT: K 647 GLU cc_start: 0.8904 (pm20) cc_final: 0.8316 (pm20) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.3443 time to fit residues: 81.7798 Evaluate side-chains 114 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 212 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 119 optimal weight: 0.0970 chunk 113 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 96 GLN ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 170 GLN D 328 GLN F 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.065474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.046984 restraints weight = 101739.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.048534 restraints weight = 57918.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.049576 restraints weight = 40754.233| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 20793 Z= 0.135 Angle : 0.705 14.247 28419 Z= 0.337 Chirality : 0.048 0.479 3423 Planarity : 0.004 0.041 3444 Dihedral : 6.694 56.802 4515 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.59 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.18), residues: 2382 helix: 1.63 (0.29), residues: 333 sheet: -1.02 (0.18), residues: 792 loop : -0.83 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 628 HIS 0.004 0.001 HIS G 85 PHE 0.015 0.002 PHE G 376 TYR 0.013 0.001 TYR B 638 ARG 0.009 0.000 ARG D 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 57) link_NAG-ASN : angle 3.14677 ( 171) link_BETA1-4 : bond 0.00429 ( 33) link_BETA1-4 : angle 1.98567 ( 99) link_ALPHA1-3 : bond 0.01007 ( 3) link_ALPHA1-3 : angle 1.65948 ( 9) hydrogen bonds : bond 0.03485 ( 578) hydrogen bonds : angle 5.12100 ( 1470) SS BOND : bond 0.00324 ( 42) SS BOND : angle 1.20508 ( 84) covalent geometry : bond 0.00312 (20658) covalent geometry : angle 0.65145 (28056) *********************** 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 159 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 2.342 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: 0.8258 (t0) cc_final: 0.7896 (t70) REVERT: L 74 LYS cc_start: 0.9087 (mmpt) cc_final: 0.8879 (mmmt) REVERT: L 81 GLU cc_start: 0.8450 (mp0) cc_final: 0.8078 (mp0) REVERT: H 32 TYR cc_start: 0.9254 (m-80) cc_final: 0.8358 (m-80) REVERT: H 34 ILE cc_start: 0.9237 (mm) cc_final: 0.8954 (mm) REVERT: G 104 MET cc_start: 0.9385 (ttm) cc_final: 0.8964 (ttm) REVERT: G 271 MET cc_start: 0.8203 (mmp) cc_final: 0.7871 (mmm) REVERT: B 535 MET cc_start: 0.9258 (mtm) cc_final: 0.8626 (mpp) REVERT: B 543 ASN cc_start: 0.9010 (t0) cc_final: 0.8469 (t0) REVERT: B 584 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8402 (tm-30) REVERT: B 647 GLU cc_start: 0.9108 (pm20) cc_final: 0.8816 (pm20) REVERT: B 654 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8332 (mt-10) REVERT: C 23 LYS cc_start: 0.9024 (tppt) cc_final: 0.8696 (tptp) REVERT: C 32 TYR cc_start: 0.8797 (m-10) cc_final: 0.8446 (m-10) REVERT: C 34 ILE cc_start: 0.9126 (mm) cc_final: 0.8810 (mm) REVERT: D 434 MET cc_start: 0.7919 (ptm) cc_final: 0.7697 (ptm) REVERT: E 535 MET cc_start: 0.9333 (mtm) cc_final: 0.9009 (mtm) REVERT: E 543 ASN cc_start: 0.9274 (t0) cc_final: 0.8820 (t0) REVERT: E 647 GLU cc_start: 0.9100 (pm20) cc_final: 0.8781 (pm20) REVERT: F 4 MET cc_start: 0.6598 (mmt) cc_final: 0.5801 (mmp) REVERT: F 21 ILE cc_start: 0.8697 (mm) cc_final: 0.8054 (pt) REVERT: F 24 LYS cc_start: 0.8703 (tmmt) cc_final: 0.8428 (tmtt) REVERT: F 27 ASP cc_start: 0.7857 (t70) cc_final: 0.7596 (t0) REVERT: I 5 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7958 (mm-40) REVERT: J 95 MET cc_start: 0.8031 (ttm) cc_final: 0.7721 (ttp) REVERT: J 107 ASP cc_start: 0.8756 (t70) cc_final: 0.8330 (t70) REVERT: J 271 MET cc_start: 0.7647 (mmm) cc_final: 0.7399 (mmm) REVERT: J 426 MET cc_start: 0.8883 (tpp) cc_final: 0.8635 (tpp) REVERT: K 535 MET cc_start: 0.9162 (mpp) cc_final: 0.8650 (mpp) REVERT: K 543 ASN cc_start: 0.9109 (t0) cc_final: 0.8852 (t0) REVERT: K 647 GLU cc_start: 0.8849 (pm20) cc_final: 0.8307 (pm20) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3428 time to fit residues: 84.8979 Evaluate side-chains 120 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 31 optimal weight: 0.7980 chunk 157 optimal weight: 7.9990 chunk 60 optimal weight: 0.0970 chunk 193 optimal weight: 9.9990 chunk 190 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 213 optimal weight: 0.0870 chunk 121 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 overall best weight: 1.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.065821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047533 restraints weight = 102521.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.049902 restraints weight = 57921.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050877 restraints weight = 34444.383| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20793 Z= 0.127 Angle : 0.686 13.903 28419 Z= 0.328 Chirality : 0.047 0.474 3423 Planarity : 0.004 0.041 3444 Dihedral : 6.448 56.982 4515 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.47 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2382 helix: 1.29 (0.29), residues: 333 sheet: -0.95 (0.18), residues: 792 loop : -0.74 (0.19), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 479 HIS 0.004 0.001 HIS G 85 PHE 0.013 0.001 PHE J 376 TYR 0.023 0.001 TYR I 91 ARG 0.006 0.000 ARG I 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 57) link_NAG-ASN : angle 2.97383 ( 171) link_BETA1-4 : bond 0.00435 ( 33) link_BETA1-4 : angle 1.94036 ( 99) link_ALPHA1-3 : bond 0.00791 ( 3) link_ALPHA1-3 : angle 1.52144 ( 9) hydrogen bonds : bond 0.03398 ( 578) hydrogen bonds : angle 5.05017 ( 1470) SS BOND : bond 0.00296 ( 42) SS BOND : angle 1.00930 ( 84) covalent geometry : bond 0.00290 (20658) covalent geometry : angle 0.63660 (28056) *********************** 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 154 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 2.339 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: symmetry clash REVERT: L 27 ASP cc_start: 0.8176 (t0) cc_final: 0.7809 (t70) REVERT: L 74 LYS cc_start: 0.9104 (mmpt) cc_final: 0.8893 (mmmt) REVERT: L 81 GLU cc_start: 0.8449 (mp0) cc_final: 0.8077 (mp0) REVERT: H 32 TYR cc_start: 0.9250 (m-80) cc_final: 0.8385 (m-80) REVERT: H 34 ILE cc_start: 0.9299 (mm) cc_final: 0.9017 (mm) REVERT: G 95 MET cc_start: 0.7812 (ttp) cc_final: 0.7313 (ttm) REVERT: G 104 MET cc_start: 0.9283 (ttm) cc_final: 0.8927 (ttm) REVERT: G 271 MET cc_start: 0.8129 (mmp) cc_final: 0.7801 (mmm) REVERT: G 426 MET cc_start: 0.8874 (tpp) cc_final: 0.8557 (tpp) REVERT: B 535 MET cc_start: 0.9283 (mtm) cc_final: 0.8582 (mpp) REVERT: B 543 ASN cc_start: 0.8981 (t0) cc_final: 0.8500 (t0) REVERT: B 584 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8367 (tm-30) REVERT: B 595 ILE cc_start: 0.9101 (tp) cc_final: 0.8811 (tp) REVERT: B 647 GLU cc_start: 0.9119 (pm20) cc_final: 0.8794 (pm20) REVERT: B 654 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8372 (mt-10) REVERT: A 27 ASP cc_start: 0.8689 (t70) cc_final: 0.8457 (t70) REVERT: C 23 LYS cc_start: 0.9019 (tppt) cc_final: 0.8633 (tptp) REVERT: C 32 TYR cc_start: 0.8751 (m-10) cc_final: 0.8398 (m-10) REVERT: C 34 ILE cc_start: 0.9158 (mm) cc_final: 0.8833 (mm) REVERT: D 161 MET cc_start: 0.8627 (tpp) cc_final: 0.8403 (tpp) REVERT: D 426 MET cc_start: 0.8805 (tpp) cc_final: 0.7834 (ttm) REVERT: D 434 MET cc_start: 0.7906 (ptm) cc_final: 0.7659 (ptm) REVERT: E 535 MET cc_start: 0.9344 (mtm) cc_final: 0.9005 (mtm) REVERT: E 543 ASN cc_start: 0.9249 (t0) cc_final: 0.8817 (t0) REVERT: F 4 MET cc_start: 0.6704 (mmt) cc_final: 0.5864 (mmp) REVERT: F 21 ILE cc_start: 0.8760 (mm) cc_final: 0.8158 (pt) REVERT: F 24 LYS cc_start: 0.8750 (tmmt) cc_final: 0.8479 (tmtt) REVERT: F 27 ASP cc_start: 0.7838 (t70) cc_final: 0.7554 (t0) REVERT: I 5 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7949 (mm-40) REVERT: I 91 TYR cc_start: 0.7124 (m-80) cc_final: 0.6129 (m-80) REVERT: J 107 ASP cc_start: 0.8687 (t70) cc_final: 0.8261 (t70) REVERT: J 271 MET cc_start: 0.7573 (mmm) cc_final: 0.7318 (mmm) REVERT: K 535 MET cc_start: 0.9223 (mpp) cc_final: 0.8644 (mpp) REVERT: K 543 ASN cc_start: 0.9037 (t0) cc_final: 0.8731 (t0) REVERT: K 647 GLU cc_start: 0.8897 (pm20) cc_final: 0.8391 (pm20) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3319 time to fit residues: 80.2411 Evaluate side-chains 122 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 126 optimal weight: 8.9990 chunk 225 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 160 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN E 618 ASN F 96 GLN J 203 GLN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.063602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.045564 restraints weight = 103775.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.047744 restraints weight = 59161.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.048568 restraints weight = 35700.138| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 20793 Z= 0.240 Angle : 0.788 14.093 28419 Z= 0.378 Chirality : 0.050 0.478 3423 Planarity : 0.004 0.047 3444 Dihedral : 6.934 57.032 4515 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.89 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2382 helix: 1.14 (0.29), residues: 333 sheet: -1.10 (0.17), residues: 822 loop : -0.75 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 479 HIS 0.005 0.001 HIS D 374 PHE 0.023 0.002 PHE G 361 TYR 0.025 0.002 TYR L 49 ARG 0.004 0.000 ARG J 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00644 ( 57) link_NAG-ASN : angle 3.11221 ( 171) link_BETA1-4 : bond 0.00480 ( 33) link_BETA1-4 : angle 2.06445 ( 99) link_ALPHA1-3 : bond 0.00733 ( 3) link_ALPHA1-3 : angle 1.58458 ( 9) hydrogen bonds : bond 0.04051 ( 578) hydrogen bonds : angle 5.29398 ( 1470) SS BOND : bond 0.00417 ( 42) SS BOND : angle 1.54771 ( 84) covalent geometry : bond 0.00543 (20658) covalent geometry : angle 0.73982 (28056) *********************** 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 150 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 2.400 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: 0.8199 (t0) cc_final: 0.7883 (t70) REVERT: L 74 LYS cc_start: 0.9131 (mmpt) cc_final: 0.8915 (mmmt) REVERT: L 81 GLU cc_start: 0.8646 (mp0) cc_final: 0.8315 (mp0) REVERT: H 34 ILE cc_start: 0.9261 (mm) cc_final: 0.8964 (mm) REVERT: G 104 MET cc_start: 0.9445 (ttm) cc_final: 0.9115 (ttm) REVERT: G 271 MET cc_start: 0.8225 (mmp) cc_final: 0.7822 (mmm) REVERT: G 427 TRP cc_start: 0.7439 (m-90) cc_final: 0.7216 (m100) REVERT: B 530 MET cc_start: 0.8105 (mmm) cc_final: 0.7564 (mmm) REVERT: B 535 MET cc_start: 0.9309 (mtm) cc_final: 0.8649 (mpp) REVERT: B 584 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8425 (tm-30) REVERT: B 647 GLU cc_start: 0.9132 (pm20) cc_final: 0.8776 (pm20) REVERT: B 654 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8372 (mt-10) REVERT: A 27 ASP cc_start: 0.8715 (t70) cc_final: 0.8502 (t70) REVERT: C 23 LYS cc_start: 0.8990 (tppt) cc_final: 0.8658 (tptp) REVERT: C 32 TYR cc_start: 0.8949 (m-10) cc_final: 0.8740 (m-10) REVERT: C 34 ILE cc_start: 0.9147 (mm) cc_final: 0.8818 (mm) REVERT: D 107 ASP cc_start: 0.8926 (t0) cc_final: 0.8357 (t70) REVERT: D 426 MET cc_start: 0.8561 (tpp) cc_final: 0.8040 (ttm) REVERT: E 535 MET cc_start: 0.9376 (mtm) cc_final: 0.9027 (mtm) REVERT: F 4 MET cc_start: 0.6860 (mmt) cc_final: 0.6132 (mmm) REVERT: F 21 ILE cc_start: 0.8762 (mm) cc_final: 0.8163 (pt) REVERT: F 24 LYS cc_start: 0.8741 (tmmt) cc_final: 0.8466 (tmtt) REVERT: F 27 ASP cc_start: 0.7872 (t70) cc_final: 0.7459 (t70) REVERT: I 5 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7984 (mm-40) REVERT: J 107 ASP cc_start: 0.8686 (t70) cc_final: 0.8263 (t70) REVERT: J 271 MET cc_start: 0.7601 (mmm) cc_final: 0.7293 (mmm) REVERT: K 535 MET cc_start: 0.9337 (mpp) cc_final: 0.8726 (mpp) REVERT: K 647 GLU cc_start: 0.9027 (pm20) cc_final: 0.8602 (pm20) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3466 time to fit residues: 81.8299 Evaluate side-chains 116 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 17 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN 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 = 0.3539 r_free = 0.3539 target = 0.065013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.046928 restraints weight = 102062.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.049267 restraints weight = 56999.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.050156 restraints weight = 33757.334| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20793 Z= 0.131 Angle : 0.709 13.570 28419 Z= 0.339 Chirality : 0.048 0.476 3423 Planarity : 0.004 0.041 3444 Dihedral : 6.574 56.857 4515 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.03 % Rotamer: Outliers : 0.05 % Allowed : 0.24 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2382 helix: 1.15 (0.29), residues: 351 sheet: -1.05 (0.18), residues: 828 loop : -0.60 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 479 HIS 0.004 0.001 HIS G 85 PHE 0.015 0.001 PHE D 376 TYR 0.019 0.001 TYR E 638 ARG 0.005 0.000 ARG K 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 57) link_NAG-ASN : angle 2.86875 ( 171) link_BETA1-4 : bond 0.00432 ( 33) link_BETA1-4 : angle 1.92626 ( 99) link_ALPHA1-3 : bond 0.00755 ( 3) link_ALPHA1-3 : angle 1.44451 ( 9) hydrogen bonds : bond 0.03511 ( 578) hydrogen bonds : angle 5.06123 ( 1470) SS BOND : bond 0.00259 ( 42) SS BOND : angle 1.34661 ( 84) covalent geometry : bond 0.00301 (20658) covalent geometry : angle 0.66282 (28056) ********************** 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 157 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 2.275 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: 0.8146 (t0) cc_final: 0.7829 (t70) REVERT: L 74 LYS cc_start: 0.9130 (mmpt) cc_final: 0.8921 (mmmt) REVERT: L 81 GLU cc_start: 0.8519 (mp0) cc_final: 0.8146 (mp0) REVERT: H 32 TYR cc_start: 0.9310 (m-80) cc_final: 0.8414 (m-80) REVERT: H 34 ILE cc_start: 0.9307 (mm) cc_final: 0.9027 (mm) REVERT: G 95 MET cc_start: 0.7848 (ttp) cc_final: 0.7276 (ttm) REVERT: G 271 MET cc_start: 0.8146 (mmp) cc_final: 0.7796 (mmm) REVERT: G 426 MET cc_start: 0.8803 (tpp) cc_final: 0.8047 (tpp) REVERT: B 530 MET cc_start: 0.7921 (mmm) cc_final: 0.7511 (mmm) REVERT: B 535 MET cc_start: 0.9277 (mtm) cc_final: 0.8584 (mpp) REVERT: B 543 ASN cc_start: 0.9010 (t0) cc_final: 0.8516 (t0) REVERT: B 584 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8386 (tm-30) REVERT: B 633 LYS cc_start: 0.9599 (tptp) cc_final: 0.9308 (pptt) REVERT: B 647 GLU cc_start: 0.9126 (pm20) cc_final: 0.8762 (pm20) REVERT: B 654 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8383 (mt-10) REVERT: C 23 LYS cc_start: 0.9009 (tppt) cc_final: 0.8622 (tptp) REVERT: C 32 TYR cc_start: 0.8855 (m-10) cc_final: 0.8469 (m-10) REVERT: C 34 ILE cc_start: 0.9176 (mm) cc_final: 0.8849 (mm) REVERT: D 107 ASP cc_start: 0.8742 (t0) cc_final: 0.8191 (t70) REVERT: D 426 MET cc_start: 0.8488 (tpp) cc_final: 0.7952 (ttm) REVERT: E 535 MET cc_start: 0.9386 (mtm) cc_final: 0.9032 (mtm) REVERT: E 543 ASN cc_start: 0.9240 (t0) cc_final: 0.8786 (t0) REVERT: E 647 GLU cc_start: 0.9165 (pm20) cc_final: 0.8939 (pm20) REVERT: F 4 MET cc_start: 0.6920 (mmt) cc_final: 0.6170 (mmm) REVERT: F 21 ILE cc_start: 0.8773 (mm) cc_final: 0.8199 (pt) REVERT: F 24 LYS cc_start: 0.8785 (tmmt) cc_final: 0.8579 (tmtt) REVERT: F 27 ASP cc_start: 0.7949 (t70) cc_final: 0.7686 (t0) REVERT: I 5 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7879 (mm-40) REVERT: I 91 TYR cc_start: 0.7784 (m-80) cc_final: 0.6221 (m-80) REVERT: J 107 ASP cc_start: 0.8623 (t70) cc_final: 0.8206 (t70) REVERT: J 271 MET cc_start: 0.7521 (mmm) cc_final: 0.7265 (mmm) REVERT: J 426 MET cc_start: 0.8969 (tpp) cc_final: 0.8701 (tpp) REVERT: K 535 MET cc_start: 0.9413 (mpp) cc_final: 0.8675 (mpp) REVERT: K 543 ASN cc_start: 0.9057 (t0) cc_final: 0.8787 (t0) REVERT: K 647 GLU cc_start: 0.8968 (pm20) cc_final: 0.8579 (pm20) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.3306 time to fit residues: 80.5032 Evaluate side-chains 122 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 118 optimal weight: 0.1980 chunk 204 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 167 optimal weight: 30.0000 chunk 89 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 618 ASN F 96 GLN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.063983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046015 restraints weight = 103581.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.048196 restraints weight = 58216.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.049052 restraints weight = 34937.202| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20793 Z= 0.187 Angle : 0.732 13.565 28419 Z= 0.351 Chirality : 0.048 0.465 3423 Planarity : 0.004 0.044 3444 Dihedral : 6.670 56.944 4515 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.64 % Favored : 92.23 % Rotamer: Outliers : 0.09 % Allowed : 0.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 2382 helix: 1.30 (0.29), residues: 333 sheet: -1.06 (0.18), residues: 822 loop : -0.70 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 479 HIS 0.004 0.001 HIS G 85 PHE 0.017 0.002 PHE G 361 TYR 0.017 0.001 TYR K 643 ARG 0.006 0.000 ARG K 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 57) link_NAG-ASN : angle 2.91802 ( 171) link_BETA1-4 : bond 0.00422 ( 33) link_BETA1-4 : angle 1.98157 ( 99) link_ALPHA1-3 : bond 0.00697 ( 3) link_ALPHA1-3 : angle 1.48151 ( 9) hydrogen bonds : bond 0.03751 ( 578) hydrogen bonds : angle 5.09434 ( 1470) SS BOND : bond 0.00303 ( 42) SS BOND : angle 1.56723 ( 84) covalent geometry : bond 0.00430 (20658) covalent geometry : angle 0.68478 (28056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5653.54 seconds wall clock time: 99 minutes 47.33 seconds (5987.33 seconds total)