Starting phenix.real_space_refine on Sun Jun 15 09:20:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fl1_29264/06_2025/8fl1_29264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fl1_29264/06_2025/8fl1_29264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fl1_29264/06_2025/8fl1_29264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fl1_29264/06_2025/8fl1_29264.map" model { file = "/net/cci-nas-00/data/ceres_data/8fl1_29264/06_2025/8fl1_29264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fl1_29264/06_2025/8fl1_29264.cif" } resolution = 3.75 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= 0.004 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 10538 2.51 5 N 2808 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16951 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "G" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3543 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3544 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1094 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} 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: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "I" 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 Time building chain proxies: 12.28, per 1000 atoms: 0.72 Number of scatterers: 16951 At special positions: 0 Unit cell: (132.126, 129.96, 168.948, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 3488 8.00 N 2808 7.00 C 10538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " 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=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 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 I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN Q 4 " - " MAN Q 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 7 " " MAN e 4 " - " MAN e 5 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 6 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " 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 Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG A 703 " - " ASN A 618 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG C 611 " - " ASN C 137 " " NAG D 1 " - " ASN C 160 " " NAG E 1 " - " ASN C 197 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 618 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 332 " " NAG G 607 " - " ASN G 339 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 137 " " NAG G 611 " - " ASN G 276 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 234 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 332 " " NAG I 606 " - " ASN I 339 " " NAG I 607 " - " ASN I 355 " " NAG I 608 " - " ASN I 392 " " NAG I 609 " - " ASN I 137 " " NAG I 610 " - " ASN I 462 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 276 " " NAG M 1 " - " ASN C 295 " " NAG N 1 " - " ASN C 363 " " NAG O 1 " - " ASN C 386 " " NAG P 1 " - " ASN G 197 " " NAG Q 1 " - " ASN G 262 " " NAG R 1 " - " ASN G 295 " " NAG S 1 " - " ASN G 363 " " NAG T 1 " - " ASN G 386 " " NAG U 1 " - " ASN G 448 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN I 197 " " NAG X 1 " - " ASN I 262 " " NAG Y 1 " - " ASN I 276 " " NAG Z 1 " - " ASN I 295 " " NAG a 1 " - " ASN I 363 " " NAG b 1 " - " ASN I 386 " " NAG c 1 " - " ASN I 448 " " NAG d 1 " - " ASN I 156 " " NAG e 1 " - " ASN I 160 " Time building additional restraints: 5.57 Conformation dependent library (CDL) restraints added in 2.2 seconds 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 29 sheets defined 23.4% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 4.530A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 542 " --> pdb=" O THR A 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 536 through 542' Processing helix chain 'A' and resid 570 through 596 removed outlier: 3.626A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.647A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 664 removed outlier: 3.508A pdb=" N LEU A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.077A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 3.556A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.767A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.810A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.927A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.580A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.697A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 4.248A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 352 removed outlier: 3.736A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.390A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 536 through 543' Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.987A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 593 " --> pdb=" O ASP F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.562A pdb=" N ASP F 632 " --> pdb=" O TRP F 628 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.594A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 98 through 116 removed outlier: 4.163A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.575A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.541A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 474 through 481 removed outlier: 4.174A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 removed outlier: 3.521A pdb=" N THR I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 59 through 64' Processing helix chain 'I' and resid 99 through 115 removed outlier: 3.634A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 3.837A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.613A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 removed outlier: 4.329A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.796A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 28 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 4.614A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.528A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP G 35 " --> pdb=" O THR G 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.650A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.932A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.154A pdb=" N CYS C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA8, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 309 removed outlier: 6.700A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 309 " --> pdb=" O GLN C 315 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 322 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'F' and resid 603 through 609 removed outlier: 4.549A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.316A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 55 through 56 removed outlier: 3.611A pdb=" N SER G 56 " --> pdb=" O VAL G 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 91 through 94 removed outlier: 4.081A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.505A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 287 current: chain 'G' and resid 330 through 334 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 330 through 334 current: chain 'G' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 381 through 385 current: chain 'G' and resid 465 through 470 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.862A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AB8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.577A pdb=" N LYS I 46 " --> pdb=" O LYS I 490 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'I' and resid 92 through 94 removed outlier: 3.786A pdb=" N PHE I 93 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY I 237 " --> pdb=" O PHE I 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'I' and resid 130 through 133 removed outlier: 7.024A pdb=" N LYS I 169 " --> pdb=" O TYS H 100H" (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE H 100J" --> pdb=" O LYS I 169 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS I 171 " --> pdb=" O PHE H 100J" (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'I' and resid 202 through 203 removed outlier: 7.178A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 298 removed outlier: 3.685A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 329 through 333 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 381 through 385 current: chain 'I' and resid 466 through 470 Processing sheet with id=AC6, first strand: chain 'I' and resid 302 through 312 removed outlier: 6.664A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.752A pdb=" N ARG H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER H 25 " --> pdb=" O ARG H 3 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.045A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'H' and resid 34 through 39 removed outlier: 7.088A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100O through 103 Processing sheet with id=AD1, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 46 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.526A pdb=" N ILE L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE L 75 " --> pdb=" O ILE L 19 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1149 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: 5.11 Time building geometry restraints manager: 6.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5004 1.34 - 1.46: 4416 1.46 - 1.59: 7694 1.59 - 1.71: 1 1.71 - 1.83: 154 Bond restraints: 17269 Sorted by residual: bond pdb=" O3 TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.458 1.635 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.535 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" OH TYS H 100G" pdb=" S TYS H 100G" ideal model delta sigma weight residual 1.679 1.546 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C3 MAN e 4 " pdb=" O3 MAN e 4 " ideal model delta sigma weight residual 1.408 1.474 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CZ TYS H 100G" pdb=" OH TYS H 100G" ideal model delta sigma weight residual 1.371 1.425 -0.054 2.00e-02 2.50e+03 7.28e+00 ... (remaining 17264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 22939 2.20 - 4.40: 414 4.40 - 6.60: 80 6.60 - 8.80: 1 8.80 - 11.00: 3 Bond angle restraints: 23437 Sorted by residual: angle pdb=" CA TYS H 100G" pdb=" C TYS H 100G" pdb=" O TYS H 100G" ideal model delta sigma weight residual 120.80 113.83 6.97 1.70e+00 3.46e-01 1.68e+01 angle pdb=" C CYS I 218 " pdb=" N ALA I 219 " pdb=" CA ALA I 219 " ideal model delta sigma weight residual 120.97 131.74 -10.77 2.84e+00 1.24e-01 1.44e+01 angle pdb=" C2 MAN e 4 " pdb=" C3 MAN e 4 " pdb=" O3 MAN e 4 " ideal model delta sigma weight residual 107.58 118.58 -11.00 3.00e+00 1.11e-01 1.34e+01 angle pdb=" OH TYS H 100H" pdb=" S TYS H 100H" pdb=" O3 TYS H 100H" ideal model delta sigma weight residual 100.21 109.42 -9.21 3.00e+00 1.11e-01 9.43e+00 angle pdb=" CA GLY G 354 " pdb=" C GLY G 354 " pdb=" O GLY G 354 " ideal model delta sigma weight residual 122.24 119.79 2.45 8.70e-01 1.32e+00 7.91e+00 ... (remaining 23432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.65: 10917 23.65 - 47.30: 663 47.30 - 70.95: 112 70.95 - 94.59: 55 94.59 - 118.24: 27 Dihedral angle restraints: 11774 sinusoidal: 6094 harmonic: 5680 Sorted by residual: dihedral pdb=" CB CYS A 605 " pdb=" SG CYS A 605 " pdb=" SG CYS C 501 " pdb=" CB CYS C 501 " ideal model delta sinusoidal sigma weight residual -86.00 -150.38 64.38 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -150.22 64.22 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CB CYS I 378 " pdb=" SG CYS I 378 " pdb=" SG CYS I 445 " pdb=" CB CYS I 445 " ideal model delta sinusoidal sigma weight residual -86.00 -146.05 60.05 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 11771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2480 0.061 - 0.123: 420 0.123 - 0.184: 32 0.184 - 0.246: 0 0.246 - 0.307: 9 Chirality restraints: 2941 Sorted by residual: chirality pdb=" C1 NAG G 608 " pdb=" ND2 ASN G 355 " pdb=" C2 NAG G 608 " pdb=" O5 NAG G 608 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3 MAN e 4 " pdb=" C2 MAN e 4 " pdb=" C4 MAN e 4 " pdb=" O3 MAN e 4 " both_signs ideal model delta sigma weight residual False 2.47 2.17 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2938 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 3 " -0.109 9.50e-02 1.11e+02 4.88e-02 1.47e+00 pdb=" NE ARG H 3 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG H 3 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG H 3 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 3 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 448 " 0.011 2.00e-02 2.50e+03 9.82e-03 1.21e+00 pdb=" CG ASN C 448 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN C 448 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 448 " -0.011 2.00e-02 2.50e+03 pdb=" C1 NAG C 610 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 75 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO I 76 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO I 76 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO I 76 " 0.015 5.00e-02 4.00e+02 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3537 2.79 - 3.32: 15367 3.32 - 3.84: 25820 3.84 - 4.37: 30107 4.37 - 4.90: 52026 Nonbonded interactions: 126857 Sorted by model distance: nonbonded pdb=" OD1 ASN C 137 " pdb=" N2 NAG C 611 " model vdw 2.259 3.120 nonbonded pdb=" NH1 ARG G 298 " pdb=" OD1 ASN G 302 " model vdw 2.273 3.120 nonbonded pdb=" OG1 THR G 163 " pdb=" OE1 GLU G 164 " model vdw 2.274 3.040 nonbonded pdb=" OG SER L 14 " pdb=" OE1 GLN L 17 " model vdw 2.278 3.040 nonbonded pdb=" O LEU L 4 " pdb=" OG1 THR L 100 " model vdw 2.280 3.040 ... (remaining 126852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 519 through 664 or resid 701 through 702)) selection = chain 'B' selection = (chain 'F' and (resid 519 through 546 or resid 569 through 664 or resid 701 thro \ ugh 702)) } ncs_group { reference = (chain 'C' and (resid 33 through 505 or resid 601 through 610)) selection = (chain 'G' and (resid 33 through 185 or resid 189 through 505 or resid 601 throu \ gh 610)) selection = (chain 'I' and (resid 33 through 505 or resid 601 through 610)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'J' and (resid 1 or resid 4 through 6)) selection = (chain 'X' and (resid 1 or resid 4 through 6)) selection = (chain 'e' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'Q' selection = chain 'V' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.030 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.110 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.005 0.177 17415 Z= 0.249 Angle : 0.702 10.997 23837 Z= 0.297 Chirality : 0.048 0.307 2941 Planarity : 0.003 0.049 2846 Dihedral : 16.101 118.243 7992 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.19), residues: 1934 helix: 0.41 (0.28), residues: 362 sheet: 1.01 (0.24), residues: 490 loop : -0.31 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.003 0.000 HIS I 374 PHE 0.010 0.001 PHE C 223 TYR 0.008 0.001 TYR L 49 ARG 0.008 0.000 ARG A 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 63) link_NAG-ASN : angle 1.67990 ( 189) link_ALPHA1-6 : bond 0.00400 ( 6) link_ALPHA1-6 : angle 1.45372 ( 18) link_BETA1-4 : bond 0.00467 ( 29) link_BETA1-4 : angle 1.13501 ( 87) link_ALPHA1-2 : bond 0.00714 ( 3) link_ALPHA1-2 : angle 1.59062 ( 9) link_ALPHA1-3 : bond 0.00622 ( 7) link_ALPHA1-3 : angle 2.75689 ( 21) hydrogen bonds : bond 0.28822 ( 408) hydrogen bonds : angle 8.50327 ( 1149) SS BOND : bond 0.00266 ( 38) SS BOND : angle 1.37668 ( 76) covalent geometry : bond 0.00500 (17269) covalent geometry : angle 0.67685 (23437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.703 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: A 655 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7469 (ptmm) REVERT: B 579 ARG cc_start: 0.8932 (ttm-80) cc_final: 0.8674 (ttm170) REVERT: B 612 SER cc_start: 0.8931 (m) cc_final: 0.8405 (p) REVERT: B 615 SER cc_start: 0.8688 (t) cc_final: 0.8361 (m) REVERT: C 128 THR cc_start: 0.8773 (m) cc_final: 0.8484 (p) REVERT: G 97 LYS cc_start: 0.7919 (mttp) cc_final: 0.7624 (mttp) REVERT: G 246 GLN cc_start: 0.6151 (mp10) cc_final: 0.5516 (mp10) REVERT: G 277 ILE cc_start: 0.8144 (mm) cc_final: 0.7880 (mm) REVERT: I 121 LYS cc_start: 0.8141 (mttp) cc_final: 0.7899 (tttm) REVERT: I 474 ASP cc_start: 0.6285 (t0) cc_final: 0.6079 (t0) REVERT: H 34 MET cc_start: 0.6912 (mmt) cc_final: 0.6343 (mmt) REVERT: H 52 LYS cc_start: 0.7686 (mtpt) cc_final: 0.6705 (mtpp) REVERT: H 70 SER cc_start: 0.8258 (t) cc_final: 0.7944 (p) REVERT: H 100 ASP cc_start: 0.8659 (t0) cc_final: 0.8450 (t70) REVERT: H 100 MET cc_start: 0.8044 (mtt) cc_final: 0.7686 (mtp) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.3149 time to fit residues: 189.4413 Evaluate side-chains 231 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.9990 chunk 147 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 99 optimal weight: 0.0770 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 176 optimal weight: 4.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN C 67 ASN C 195 ASN C 249 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN G 249 HIS ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN L 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.161688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128655 restraints weight = 25147.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.132069 restraints weight = 17218.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134248 restraints weight = 13534.793| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17415 Z= 0.141 Angle : 0.710 17.799 23837 Z= 0.324 Chirality : 0.048 0.392 2941 Planarity : 0.004 0.041 2846 Dihedral : 12.324 110.129 4331 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.31 % Allowed : 9.23 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.12 (0.19), residues: 1934 helix: 0.44 (0.27), residues: 371 sheet: 0.63 (0.23), residues: 529 loop : -0.27 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 35 HIS 0.004 0.001 HIS G 105 PHE 0.028 0.001 PHE C 382 TYR 0.017 0.001 TYR L 36 ARG 0.006 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 63) link_NAG-ASN : angle 3.22966 ( 189) link_ALPHA1-6 : bond 0.00571 ( 6) link_ALPHA1-6 : angle 1.87397 ( 18) link_BETA1-4 : bond 0.00461 ( 29) link_BETA1-4 : angle 1.34544 ( 87) link_ALPHA1-2 : bond 0.00982 ( 3) link_ALPHA1-2 : angle 1.76349 ( 9) link_ALPHA1-3 : bond 0.01178 ( 7) link_ALPHA1-3 : angle 3.71576 ( 21) hydrogen bonds : bond 0.07103 ( 408) hydrogen bonds : angle 5.88937 ( 1149) SS BOND : bond 0.00302 ( 38) SS BOND : angle 1.12545 ( 76) covalent geometry : bond 0.00295 (17269) covalent geometry : angle 0.63331 (23437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 607 ASN cc_start: 0.7567 (p0) cc_final: 0.7142 (p0) REVERT: B 612 SER cc_start: 0.8355 (m) cc_final: 0.8117 (p) REVERT: B 615 SER cc_start: 0.8709 (t) cc_final: 0.8398 (m) REVERT: B 655 LYS cc_start: 0.7906 (ptpt) cc_final: 0.7610 (pptt) REVERT: C 434 MET cc_start: 0.7422 (tmm) cc_final: 0.7002 (tmm) REVERT: F 590 GLN cc_start: 0.9101 (tp40) cc_final: 0.8774 (tp40) REVERT: F 626 MET cc_start: 0.7034 (ttm) cc_final: 0.6802 (ttm) REVERT: G 97 LYS cc_start: 0.8154 (mttp) cc_final: 0.7809 (mttp) REVERT: G 475 MET cc_start: 0.7259 (mmm) cc_final: 0.6996 (mmm) REVERT: I 104 MET cc_start: 0.8374 (ttt) cc_final: 0.8079 (ttt) REVERT: I 121 LYS cc_start: 0.8269 (mttp) cc_final: 0.7970 (tttm) REVERT: H 56 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7687 (pp20) REVERT: H 100 ASP cc_start: 0.8789 (t0) cc_final: 0.8436 (t0) REVERT: L 87 TYR cc_start: 0.6616 (m-80) cc_final: 0.6386 (m-10) outliers start: 40 outliers final: 28 residues processed: 269 average time/residue: 0.2921 time to fit residues: 118.2327 Evaluate side-chains 237 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 640 GLN B 653 GLN C 85 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.162465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.132689 restraints weight = 25786.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.134840 restraints weight = 23826.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136506 restraints weight = 18903.217| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 17415 Z= 0.209 Angle : 0.782 25.535 23837 Z= 0.352 Chirality : 0.057 1.438 2941 Planarity : 0.004 0.042 2846 Dihedral : 11.228 105.375 4331 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.00 % Allowed : 12.52 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.03 (0.19), residues: 1934 helix: 0.62 (0.27), residues: 376 sheet: 0.47 (0.24), residues: 477 loop : -0.34 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 35 HIS 0.006 0.001 HIS I 330 PHE 0.020 0.002 PHE C 382 TYR 0.016 0.002 TYR B 638 ARG 0.014 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 63) link_NAG-ASN : angle 3.96642 ( 189) link_ALPHA1-6 : bond 0.00582 ( 6) link_ALPHA1-6 : angle 1.76757 ( 18) link_BETA1-4 : bond 0.00437 ( 29) link_BETA1-4 : angle 1.30844 ( 87) link_ALPHA1-2 : bond 0.00704 ( 3) link_ALPHA1-2 : angle 1.69617 ( 9) link_ALPHA1-3 : bond 0.01317 ( 7) link_ALPHA1-3 : angle 3.25673 ( 21) hydrogen bonds : bond 0.06170 ( 408) hydrogen bonds : angle 5.39761 ( 1149) SS BOND : bond 0.00385 ( 38) SS BOND : angle 1.66936 ( 76) covalent geometry : bond 0.00488 (17269) covalent geometry : angle 0.68353 (23437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 607 ASN cc_start: 0.7670 (p0) cc_final: 0.7276 (p0) REVERT: B 615 SER cc_start: 0.8765 (t) cc_final: 0.8501 (m) REVERT: C 337 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8502 (m) REVERT: F 590 GLN cc_start: 0.9140 (tp40) cc_final: 0.8855 (tp40) REVERT: F 621 GLU cc_start: 0.6694 (tm-30) cc_final: 0.6307 (tm-30) REVERT: G 97 LYS cc_start: 0.8250 (mttp) cc_final: 0.7815 (mttp) REVERT: I 39 TYR cc_start: 0.8972 (m-80) cc_final: 0.8771 (m-80) REVERT: I 104 MET cc_start: 0.8426 (ttt) cc_final: 0.8217 (ttt) REVERT: I 121 LYS cc_start: 0.8241 (mttp) cc_final: 0.8010 (tttm) REVERT: H 32 GLN cc_start: 0.6969 (mt0) cc_final: 0.6715 (mt0) REVERT: H 56 GLU cc_start: 0.8160 (pm20) cc_final: 0.7925 (pp20) REVERT: H 100 ASP cc_start: 0.8655 (t0) cc_final: 0.8443 (t0) outliers start: 52 outliers final: 39 residues processed: 254 average time/residue: 0.2907 time to fit residues: 111.6433 Evaluate side-chains 227 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 145 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 137 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 117 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.164545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.135331 restraints weight = 25457.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136990 restraints weight = 23433.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138251 restraints weight = 18262.837| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17415 Z= 0.130 Angle : 0.690 21.035 23837 Z= 0.312 Chirality : 0.050 0.807 2941 Planarity : 0.003 0.064 2846 Dihedral : 9.968 100.317 4331 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.12 % Allowed : 14.20 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.19), residues: 1934 helix: 0.79 (0.27), residues: 376 sheet: 0.53 (0.23), residues: 501 loop : -0.30 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP L 35 HIS 0.004 0.001 HIS G 105 PHE 0.021 0.001 PHE C 382 TYR 0.024 0.001 TYR B 638 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 63) link_NAG-ASN : angle 3.42192 ( 189) link_ALPHA1-6 : bond 0.00819 ( 6) link_ALPHA1-6 : angle 1.50248 ( 18) link_BETA1-4 : bond 0.00416 ( 29) link_BETA1-4 : angle 1.18928 ( 87) link_ALPHA1-2 : bond 0.00635 ( 3) link_ALPHA1-2 : angle 1.70830 ( 9) link_ALPHA1-3 : bond 0.01267 ( 7) link_ALPHA1-3 : angle 3.25947 ( 21) hydrogen bonds : bond 0.04825 ( 408) hydrogen bonds : angle 4.94748 ( 1149) SS BOND : bond 0.00365 ( 38) SS BOND : angle 1.80812 ( 76) covalent geometry : bond 0.00293 (17269) covalent geometry : angle 0.60075 (23437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 607 ASN cc_start: 0.7638 (p0) cc_final: 0.7337 (p0) REVERT: B 615 SER cc_start: 0.8847 (t) cc_final: 0.8535 (m) REVERT: B 626 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7480 (mtt) REVERT: C 337 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8314 (m) REVERT: C 434 MET cc_start: 0.7294 (tmm) cc_final: 0.7008 (tmm) REVERT: G 97 LYS cc_start: 0.8228 (mttp) cc_final: 0.7810 (mttp) REVERT: I 121 LYS cc_start: 0.8259 (mttp) cc_final: 0.8036 (tttm) REVERT: H 32 GLN cc_start: 0.6897 (mt0) cc_final: 0.6691 (mt0) REVERT: H 52 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7987 (mtpt) outliers start: 54 outliers final: 38 residues processed: 255 average time/residue: 0.2773 time to fit residues: 107.4364 Evaluate side-chains 228 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.162893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128600 restraints weight = 25824.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131197 restraints weight = 23074.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132106 restraints weight = 17885.870| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17415 Z= 0.194 Angle : 0.724 17.474 23837 Z= 0.333 Chirality : 0.050 0.726 2941 Planarity : 0.003 0.042 2846 Dihedral : 9.413 104.192 4331 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.04 % Allowed : 14.48 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.00 (0.19), residues: 1934 helix: 0.79 (0.28), residues: 376 sheet: 0.31 (0.23), residues: 492 loop : -0.38 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 35 HIS 0.006 0.001 HIS I 330 PHE 0.019 0.002 PHE C 382 TYR 0.020 0.002 TYR H 58 ARG 0.005 0.000 ARG G 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 63) link_NAG-ASN : angle 3.22746 ( 189) link_ALPHA1-6 : bond 0.00725 ( 6) link_ALPHA1-6 : angle 1.45854 ( 18) link_BETA1-4 : bond 0.00434 ( 29) link_BETA1-4 : angle 1.28131 ( 87) link_ALPHA1-2 : bond 0.00540 ( 3) link_ALPHA1-2 : angle 1.80017 ( 9) link_ALPHA1-3 : bond 0.01184 ( 7) link_ALPHA1-3 : angle 3.21683 ( 21) hydrogen bonds : bond 0.05016 ( 408) hydrogen bonds : angle 4.98164 ( 1149) SS BOND : bond 0.00404 ( 38) SS BOND : angle 1.80035 ( 76) covalent geometry : bond 0.00457 (17269) covalent geometry : angle 0.64817 (23437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 200 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 SER cc_start: 0.8940 (t) cc_final: 0.8688 (m) REVERT: C 190 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: C 337 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8502 (m) REVERT: G 97 LYS cc_start: 0.8370 (mttp) cc_final: 0.7897 (mttp) REVERT: G 102 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: G 161 MET cc_start: 0.8055 (tpt) cc_final: 0.7614 (tpt) REVERT: I 121 LYS cc_start: 0.8273 (mttp) cc_final: 0.8037 (tttm) outliers start: 70 outliers final: 53 residues processed: 249 average time/residue: 0.2725 time to fit residues: 104.5549 Evaluate side-chains 239 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 481 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 190 optimal weight: 20.0000 chunk 168 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.160916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126219 restraints weight = 25669.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128737 restraints weight = 20866.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131408 restraints weight = 16873.462| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17415 Z= 0.202 Angle : 0.731 18.433 23837 Z= 0.338 Chirality : 0.048 0.454 2941 Planarity : 0.003 0.042 2846 Dihedral : 9.164 110.281 4331 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.10 % Allowed : 16.10 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.13 (0.19), residues: 1934 helix: 0.68 (0.27), residues: 381 sheet: 0.24 (0.23), residues: 484 loop : -0.46 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 35 HIS 0.006 0.001 HIS L 39 PHE 0.021 0.002 PHE C 382 TYR 0.017 0.002 TYR B 638 ARG 0.006 0.000 ARG I 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 63) link_NAG-ASN : angle 3.07743 ( 189) link_ALPHA1-6 : bond 0.00693 ( 6) link_ALPHA1-6 : angle 1.50092 ( 18) link_BETA1-4 : bond 0.00439 ( 29) link_BETA1-4 : angle 1.26699 ( 87) link_ALPHA1-2 : bond 0.00463 ( 3) link_ALPHA1-2 : angle 1.91362 ( 9) link_ALPHA1-3 : bond 0.01128 ( 7) link_ALPHA1-3 : angle 3.20804 ( 21) hydrogen bonds : bond 0.04851 ( 408) hydrogen bonds : angle 4.93346 ( 1149) SS BOND : bond 0.00401 ( 38) SS BOND : angle 1.78324 ( 76) covalent geometry : bond 0.00475 (17269) covalent geometry : angle 0.66265 (23437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 199 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 SER cc_start: 0.8914 (t) cc_final: 0.8607 (m) REVERT: C 104 MET cc_start: 0.8557 (ttm) cc_final: 0.8269 (ttt) REVERT: C 337 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8496 (m) REVERT: G 97 LYS cc_start: 0.8323 (mttp) cc_final: 0.7865 (mttp) REVERT: G 102 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: G 161 MET cc_start: 0.8241 (tpt) cc_final: 0.7824 (tpt) REVERT: G 215 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8315 (tp) outliers start: 71 outliers final: 53 residues processed: 251 average time/residue: 0.2903 time to fit residues: 110.8761 Evaluate side-chains 235 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 481 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 68 optimal weight: 0.2980 chunk 111 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 653 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS I 105 HIS I 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.162655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128065 restraints weight = 25434.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133355 restraints weight = 19184.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.134593 restraints weight = 14510.961| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17415 Z= 0.136 Angle : 0.721 18.735 23837 Z= 0.326 Chirality : 0.048 0.498 2941 Planarity : 0.003 0.041 2846 Dihedral : 8.758 111.230 4331 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.58 % Allowed : 16.91 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.06 (0.19), residues: 1934 helix: 0.67 (0.28), residues: 388 sheet: 0.27 (0.23), residues: 504 loop : -0.39 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 35 HIS 0.003 0.001 HIS G 105 PHE 0.018 0.001 PHE C 382 TYR 0.015 0.001 TYR H 58 ARG 0.008 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 63) link_NAG-ASN : angle 3.46439 ( 189) link_ALPHA1-6 : bond 0.00715 ( 6) link_ALPHA1-6 : angle 1.47797 ( 18) link_BETA1-4 : bond 0.00428 ( 29) link_BETA1-4 : angle 1.22229 ( 87) link_ALPHA1-2 : bond 0.00497 ( 3) link_ALPHA1-2 : angle 1.86568 ( 9) link_ALPHA1-3 : bond 0.01145 ( 7) link_ALPHA1-3 : angle 3.10871 ( 21) hydrogen bonds : bond 0.04437 ( 408) hydrogen bonds : angle 4.79860 ( 1149) SS BOND : bond 0.00379 ( 38) SS BOND : angle 1.66214 ( 76) covalent geometry : bond 0.00317 (17269) covalent geometry : angle 0.63647 (23437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 GLU cc_start: 0.6846 (pt0) cc_final: 0.6634 (pt0) REVERT: B 615 SER cc_start: 0.8840 (t) cc_final: 0.8527 (m) REVERT: C 104 MET cc_start: 0.8478 (ttm) cc_final: 0.8152 (ttt) REVERT: C 190 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: C 337 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8400 (m) REVERT: F 542 ARG cc_start: 0.7874 (mtp85) cc_final: 0.7667 (mtm180) REVERT: G 97 LYS cc_start: 0.8237 (mttp) cc_final: 0.7817 (mttp) REVERT: G 102 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6140 (mp0) REVERT: G 161 MET cc_start: 0.8363 (tpt) cc_final: 0.7946 (tpt) REVERT: G 215 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8092 (tp) outliers start: 62 outliers final: 45 residues processed: 228 average time/residue: 0.2848 time to fit residues: 98.4078 Evaluate side-chains 222 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 167 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 157 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.162643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128312 restraints weight = 25437.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133337 restraints weight = 19903.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134115 restraints weight = 15386.730| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17415 Z= 0.139 Angle : 0.705 15.642 23837 Z= 0.322 Chirality : 0.047 0.492 2941 Planarity : 0.003 0.042 2846 Dihedral : 8.353 112.471 4331 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.35 % Allowed : 17.43 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.01 (0.19), residues: 1934 helix: 0.83 (0.28), residues: 387 sheet: 0.29 (0.24), residues: 487 loop : -0.40 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 35 HIS 0.003 0.001 HIS G 105 PHE 0.018 0.001 PHE C 382 TYR 0.015 0.001 TYR H 58 ARG 0.005 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 63) link_NAG-ASN : angle 3.22300 ( 189) link_ALPHA1-6 : bond 0.00684 ( 6) link_ALPHA1-6 : angle 1.52370 ( 18) link_BETA1-4 : bond 0.00444 ( 29) link_BETA1-4 : angle 1.21764 ( 87) link_ALPHA1-2 : bond 0.00483 ( 3) link_ALPHA1-2 : angle 1.85202 ( 9) link_ALPHA1-3 : bond 0.01150 ( 7) link_ALPHA1-3 : angle 3.03426 ( 21) hydrogen bonds : bond 0.04181 ( 408) hydrogen bonds : angle 4.75754 ( 1149) SS BOND : bond 0.00387 ( 38) SS BOND : angle 1.61035 ( 76) covalent geometry : bond 0.00324 (17269) covalent geometry : angle 0.63020 (23437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 GLU cc_start: 0.6952 (pt0) cc_final: 0.6747 (pt0) REVERT: B 612 SER cc_start: 0.8676 (m) cc_final: 0.8316 (p) REVERT: B 615 SER cc_start: 0.8869 (t) cc_final: 0.8570 (m) REVERT: C 104 MET cc_start: 0.8541 (ttm) cc_final: 0.8197 (ttt) REVERT: C 190 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: F 542 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7575 (ttm110) REVERT: G 97 LYS cc_start: 0.8304 (mttp) cc_final: 0.7863 (mttp) REVERT: G 102 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: G 161 MET cc_start: 0.8374 (tpt) cc_final: 0.7964 (tpt) REVERT: G 215 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8064 (tp) outliers start: 58 outliers final: 47 residues processed: 235 average time/residue: 0.2848 time to fit residues: 102.7785 Evaluate side-chains 224 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 481 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 75 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 95 optimal weight: 0.0470 chunk 186 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 101 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 103 optimal weight: 7.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.164626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130167 restraints weight = 25670.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134640 restraints weight = 19725.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136165 restraints weight = 14902.960| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17415 Z= 0.116 Angle : 0.700 16.193 23837 Z= 0.317 Chirality : 0.047 0.483 2941 Planarity : 0.003 0.041 2846 Dihedral : 7.911 112.388 4331 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.29 % Allowed : 18.06 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.07 (0.19), residues: 1934 helix: 0.92 (0.28), residues: 388 sheet: 0.39 (0.24), residues: 474 loop : -0.39 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 35 HIS 0.003 0.001 HIS G 105 PHE 0.016 0.001 PHE C 382 TYR 0.049 0.001 TYR A 638 ARG 0.009 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 63) link_NAG-ASN : angle 3.34673 ( 189) link_ALPHA1-6 : bond 0.00717 ( 6) link_ALPHA1-6 : angle 1.49572 ( 18) link_BETA1-4 : bond 0.00448 ( 29) link_BETA1-4 : angle 1.19213 ( 87) link_ALPHA1-2 : bond 0.00505 ( 3) link_ALPHA1-2 : angle 1.80113 ( 9) link_ALPHA1-3 : bond 0.01164 ( 7) link_ALPHA1-3 : angle 2.76843 ( 21) hydrogen bonds : bond 0.03862 ( 408) hydrogen bonds : angle 4.63643 ( 1149) SS BOND : bond 0.00368 ( 38) SS BOND : angle 1.53050 ( 76) covalent geometry : bond 0.00262 (17269) covalent geometry : angle 0.62124 (23437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6706 (p0) REVERT: B 612 SER cc_start: 0.8673 (m) cc_final: 0.8329 (p) REVERT: B 615 SER cc_start: 0.8842 (t) cc_final: 0.8493 (m) REVERT: C 104 MET cc_start: 0.8392 (ttm) cc_final: 0.8092 (ttt) REVERT: C 190 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: C 434 MET cc_start: 0.7353 (tmm) cc_final: 0.7149 (tmm) REVERT: F 542 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7580 (ttm110) REVERT: G 97 LYS cc_start: 0.8277 (mttp) cc_final: 0.7831 (mttp) REVERT: G 102 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.5988 (mp0) REVERT: G 161 MET cc_start: 0.8390 (tpt) cc_final: 0.7989 (tpt) REVERT: G 215 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8010 (tp) outliers start: 57 outliers final: 44 residues processed: 228 average time/residue: 0.2834 time to fit residues: 100.1103 Evaluate side-chains 222 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 71 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 114 optimal weight: 0.4980 chunk 130 optimal weight: 0.0060 chunk 143 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.164111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130450 restraints weight = 25579.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132851 restraints weight = 19756.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.134786 restraints weight = 16871.543| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17415 Z= 0.129 Angle : 0.701 18.450 23837 Z= 0.320 Chirality : 0.047 0.478 2941 Planarity : 0.003 0.038 2846 Dihedral : 7.759 112.737 4331 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.89 % Allowed : 18.87 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.08 (0.19), residues: 1934 helix: 1.01 (0.28), residues: 382 sheet: 0.37 (0.24), residues: 474 loop : -0.39 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 35 HIS 0.003 0.001 HIS G 105 PHE 0.016 0.001 PHE C 382 TYR 0.038 0.001 TYR A 638 ARG 0.009 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 63) link_NAG-ASN : angle 3.43615 ( 189) link_ALPHA1-6 : bond 0.00763 ( 6) link_ALPHA1-6 : angle 1.56289 ( 18) link_BETA1-4 : bond 0.00445 ( 29) link_BETA1-4 : angle 1.20442 ( 87) link_ALPHA1-2 : bond 0.00494 ( 3) link_ALPHA1-2 : angle 1.79611 ( 9) link_ALPHA1-3 : bond 0.01218 ( 7) link_ALPHA1-3 : angle 2.03671 ( 21) hydrogen bonds : bond 0.03909 ( 408) hydrogen bonds : angle 4.62984 ( 1149) SS BOND : bond 0.00411 ( 38) SS BOND : angle 1.59473 ( 76) covalent geometry : bond 0.00299 (17269) covalent geometry : angle 0.62002 (23437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7323 (m-30) cc_final: 0.6706 (p0) REVERT: B 612 SER cc_start: 0.8760 (m) cc_final: 0.8387 (p) REVERT: B 615 SER cc_start: 0.8857 (t) cc_final: 0.8515 (m) REVERT: C 104 MET cc_start: 0.8493 (ttm) cc_final: 0.8114 (ttt) REVERT: C 190 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: C 434 MET cc_start: 0.7418 (tmm) cc_final: 0.7200 (tmm) REVERT: C 484 TYR cc_start: 0.8790 (p90) cc_final: 0.8530 (p90) REVERT: F 542 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7589 (ttm110) REVERT: G 97 LYS cc_start: 0.8331 (mttp) cc_final: 0.7858 (mttp) REVERT: G 102 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6092 (mp0) REVERT: G 161 MET cc_start: 0.8396 (tpt) cc_final: 0.7987 (tpt) REVERT: G 215 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8032 (tp) REVERT: L 89 LYS cc_start: 0.7294 (tmtt) cc_final: 0.6977 (tmtt) outliers start: 50 outliers final: 44 residues processed: 214 average time/residue: 0.2884 time to fit residues: 95.1922 Evaluate side-chains 223 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.162403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128747 restraints weight = 25414.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.131042 restraints weight = 19902.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132749 restraints weight = 17040.691| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17415 Z= 0.139 Angle : 0.689 14.460 23837 Z= 0.319 Chirality : 0.047 0.463 2941 Planarity : 0.003 0.036 2846 Dihedral : 7.752 113.721 4331 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.77 % Allowed : 19.04 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.04 (0.19), residues: 1934 helix: 0.97 (0.28), residues: 388 sheet: 0.27 (0.24), residues: 477 loop : -0.39 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 64 HIS 0.003 0.001 HIS G 105 PHE 0.019 0.001 PHE C 382 TYR 0.030 0.001 TYR A 638 ARG 0.008 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 63) link_NAG-ASN : angle 3.00528 ( 189) link_ALPHA1-6 : bond 0.00654 ( 6) link_ALPHA1-6 : angle 1.52935 ( 18) link_BETA1-4 : bond 0.00434 ( 29) link_BETA1-4 : angle 1.22933 ( 87) link_ALPHA1-2 : bond 0.00465 ( 3) link_ALPHA1-2 : angle 1.83517 ( 9) link_ALPHA1-3 : bond 0.00899 ( 7) link_ALPHA1-3 : angle 1.82882 ( 21) hydrogen bonds : bond 0.04065 ( 408) hydrogen bonds : angle 4.65514 ( 1149) SS BOND : bond 0.00410 ( 38) SS BOND : angle 1.60256 ( 76) covalent geometry : bond 0.00326 (17269) covalent geometry : angle 0.62420 (23437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5164.90 seconds wall clock time: 90 minutes 45.41 seconds (5445.41 seconds total)