Starting phenix.real_space_refine on Wed Jul 30 13:17:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sgf_25109/07_2025/7sgf_25109.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgf_25109/07_2025/7sgf_25109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sgf_25109/07_2025/7sgf_25109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgf_25109/07_2025/7sgf_25109.map" model { file = "/net/cci-nas-00/data/ceres_data/7sgf_25109/07_2025/7sgf_25109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgf_25109/07_2025/7sgf_25109.cif" } resolution = 4.41 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= 0.000 sd= 0.001 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 90 5.16 5 C 7404 2.51 5 N 2031 2.21 5 O 2553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12078 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "a" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 595 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 231 Chain: "L" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "b" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "J" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 595 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 231 Chain: "K" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "C" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "c" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "M" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 595 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 231 Chain: "N" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 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: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 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: "Y" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 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: "g" 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 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: "k" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "l" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 Time building chain proxies: 8.60, per 1000 atoms: 0.71 Number of scatterers: 12078 At special positions: 0 Unit cell: (143.17, 135.96, 95.79, 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 90 16.00 O 2553 8.00 N 2031 7.00 C 7404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.08 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.01 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.04 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.08 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.01 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.04 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.04 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.08 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.01 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.04 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA U 3 " - " MAN U 4 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA U 3 " - " MAN U 5 " " BMA g 3 " - " MAN g 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 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 f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " BETA1-6 " NAG P 1 " - " FUC P 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 3 " " NAG Y 1 " - " FUC Y 4 " " NAG Z 1 " - " FUC Z 3 " " NAG k 1 " - " FUC k 4 " " NAG l 1 " - " FUC l 3 " NAG-ASN " NAG A 701 " - " ASN A 99 " " NAG A 702 " - " ASN A 224 " " NAG B 701 " - " ASN B 99 " " NAG B 702 " - " ASN B 224 " " NAG C 701 " - " ASN C 99 " " NAG C 702 " - " ASN C 224 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 109 " " NAG G 1 " - " ASN A 119 " " NAG I 1 " - " ASN A 167 " " NAG O 1 " - " ASN a 373 " " NAG P 1 " - " ASN a 390 " " NAG Q 1 " - " ASN a 395 " " NAG R 1 " - " ASN a 365 " " NAG S 1 " - " ASN B 79 " " NAG T 1 " - " ASN B 89 " " NAG U 1 " - " ASN B 109 " " NAG V 1 " - " ASN B 119 " " NAG W 1 " - " ASN B 167 " " NAG X 1 " - " ASN b 373 " " NAG Y 1 " - " ASN b 390 " " NAG Z 1 " - " ASN b 395 " " NAG d 1 " - " ASN b 365 " " NAG e 1 " - " ASN C 79 " " NAG f 1 " - " ASN C 89 " " NAG g 1 " - " ASN C 109 " " NAG h 1 " - " ASN C 119 " " NAG i 1 " - " ASN C 167 " " NAG j 1 " - " ASN c 373 " " NAG k 1 " - " ASN c 390 " " NAG l 1 " - " ASN c 395 " " NAG m 1 " - " ASN c 365 " Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 1.7 seconds 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 27 sheets defined 23.9% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'a' and resid 294 through 304 removed outlier: 4.105A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 327 removed outlier: 3.762A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 345 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.539A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 415 Processing helix chain 'H' and resid 64 through 67 removed outlier: 3.520A pdb=" N ASP H 67 " --> pdb=" O TRP H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'b' and resid 294 through 304 removed outlier: 4.105A pdb=" N VAL b 298 " --> pdb=" O GLY b 294 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 327 removed outlier: 3.762A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 345 Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.538A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 415 Processing helix chain 'J' and resid 64 through 67 removed outlier: 3.520A pdb=" N ASP J 67 " --> pdb=" O TRP J 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 64 through 67' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'c' and resid 294 through 304 removed outlier: 4.105A pdb=" N VAL c 298 " --> pdb=" O GLY c 294 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 327 removed outlier: 3.762A pdb=" N ASP c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 345 Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.538A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 415 Processing helix chain 'M' and resid 64 through 67 removed outlier: 3.520A pdb=" N ASP M 67 " --> pdb=" O TRP M 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 64 through 67' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 4.441A pdb=" N ASN a 365 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP a 386 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER a 367 " --> pdb=" O LYS a 384 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N LYS a 384 " --> pdb=" O SER a 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 7 removed outlier: 5.409A pdb=" N GLY H 16 " --> pdb=" O GLY H 85 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR H 78 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR H 74 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR H 80 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER H 72 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN H 82 " --> pdb=" O SER H 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.944A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.287A pdb=" N CYS H 96 " --> pdb=" O TRP H 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP H 116 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS H 98 " --> pdb=" O ASP H 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.567A pdb=" N ARG H 109 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.595A pdb=" N VAL L 11 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 62 removed outlier: 4.441A pdb=" N ASN b 365 " --> pdb=" O TRP b 386 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP b 386 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER b 367 " --> pdb=" O LYS b 384 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N LYS b 384 " --> pdb=" O SER b 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AB4, first strand: chain 'J' and resid 4 through 7 removed outlier: 5.409A pdb=" N GLY J 16 " --> pdb=" O GLY J 85 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR J 78 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR J 74 " --> pdb=" O THR J 78 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR J 80 " --> pdb=" O SER J 72 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER J 72 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN J 82 " --> pdb=" O SER J 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 10 through 11 removed outlier: 5.944A pdb=" N ARG J 39 " --> pdb=" O TRP J 48 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TRP J 48 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 10 through 11 removed outlier: 7.287A pdb=" N CYS J 96 " --> pdb=" O TRP J 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP J 116 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS J 98 " --> pdb=" O ASP J 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 102 through 103 removed outlier: 3.567A pdb=" N ARG J 109 " --> pdb=" O ARG J 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 12 removed outlier: 7.595A pdb=" N VAL K 11 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU K 48 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AC2, first strand: chain 'C' and resid 61 through 62 removed outlier: 4.441A pdb=" N ASN c 365 " --> pdb=" O TRP c 386 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP c 386 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER c 367 " --> pdb=" O LYS c 384 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N LYS c 384 " --> pdb=" O SER c 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AC4, first strand: chain 'M' and resid 4 through 7 removed outlier: 5.409A pdb=" N GLY M 16 " --> pdb=" O GLY M 85 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR M 78 " --> pdb=" O THR M 74 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR M 74 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR M 80 " --> pdb=" O SER M 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER M 72 " --> pdb=" O THR M 80 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN M 82 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 10 through 11 removed outlier: 5.944A pdb=" N ARG M 39 " --> pdb=" O TRP M 48 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TRP M 48 " --> pdb=" O ARG M 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.286A pdb=" N CYS M 96 " --> pdb=" O TRP M 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP M 116 " --> pdb=" O CYS M 96 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS M 98 " --> pdb=" O ASP M 114 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 102 through 103 removed outlier: 3.568A pdb=" N ARG M 109 " --> pdb=" O ARG M 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.595A pdb=" N VAL N 11 " --> pdb=" O VAL N 109 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN N 39 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1458 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: 4.02 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3101 1.33 - 1.47: 3750 1.47 - 1.60: 5224 1.60 - 1.74: 24 1.74 - 1.88: 132 Bond restraints: 12231 Sorted by residual: bond pdb=" CB TYR C 94 " pdb=" CG TYR C 94 " ideal model delta sigma weight residual 1.512 1.390 0.122 2.20e-02 2.07e+03 3.06e+01 bond pdb=" CB TYR A 94 " pdb=" CG TYR A 94 " ideal model delta sigma weight residual 1.512 1.390 0.122 2.20e-02 2.07e+03 3.06e+01 bond pdb=" CB TYR B 94 " pdb=" CG TYR B 94 " ideal model delta sigma weight residual 1.512 1.391 0.121 2.20e-02 2.07e+03 3.05e+01 bond pdb=" CB LEU a 415 " pdb=" CG LEU a 415 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" CB LEU b 415 " pdb=" CG LEU b 415 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 12226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13416 2.38 - 4.77: 2660 4.77 - 7.15: 458 7.15 - 9.54: 87 9.54 - 11.92: 29 Bond angle restraints: 16650 Sorted by residual: angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 112.90 121.94 -9.04 9.60e-01 1.09e+00 8.86e+01 angle pdb=" N VAL B 65 " pdb=" CA VAL B 65 " pdb=" C VAL B 65 " ideal model delta sigma weight residual 112.90 121.92 -9.02 9.60e-01 1.09e+00 8.84e+01 angle pdb=" N VAL C 65 " pdb=" CA VAL C 65 " pdb=" C VAL C 65 " ideal model delta sigma weight residual 112.90 121.92 -9.02 9.60e-01 1.09e+00 8.83e+01 angle pdb=" N PHE M 104 " pdb=" CA PHE M 104 " pdb=" C PHE M 104 " ideal model delta sigma weight residual 112.92 124.32 -11.40 1.23e+00 6.61e-01 8.59e+01 angle pdb=" N PHE J 104 " pdb=" CA PHE J 104 " pdb=" C PHE J 104 " ideal model delta sigma weight residual 112.92 124.31 -11.39 1.23e+00 6.61e-01 8.58e+01 ... (remaining 16645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 7881 21.23 - 42.46: 240 42.46 - 63.69: 36 63.69 - 84.92: 87 84.92 - 106.16: 75 Dihedral angle restraints: 8319 sinusoidal: 3639 harmonic: 4680 Sorted by residual: dihedral pdb=" CB CYS a 301 " pdb=" SG CYS a 301 " pdb=" SG CYS a 310 " pdb=" CB CYS a 310 " ideal model delta sinusoidal sigma weight residual -86.00 -171.62 85.62 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS c 301 " pdb=" SG CYS c 301 " pdb=" SG CYS c 310 " pdb=" CB CYS c 310 " ideal model delta sinusoidal sigma weight residual -86.00 -171.62 85.62 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS b 301 " pdb=" SG CYS b 301 " pdb=" SG CYS b 310 " pdb=" CB CYS b 310 " ideal model delta sinusoidal sigma weight residual -86.00 -171.60 85.60 1 1.00e+01 1.00e-02 8.86e+01 ... (remaining 8316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1390 0.105 - 0.209: 495 0.209 - 0.314: 186 0.314 - 0.418: 71 0.418 - 0.523: 60 Chirality restraints: 2202 Sorted by residual: chirality pdb=" C1 BMA e 3 " pdb=" O4 NAG e 2 " pdb=" C2 BMA e 3 " pdb=" O5 BMA e 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.39e+02 ... (remaining 2199 not shown) Planarity restraints: 2103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.297 2.00e-02 2.50e+03 2.50e-01 7.82e+02 pdb=" C7 NAG W 1 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 1 " 0.297 2.00e-02 2.50e+03 2.50e-01 7.82e+02 pdb=" C7 NAG i 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG i 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG i 1 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG i 1 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.297 2.00e-02 2.50e+03 2.50e-01 7.81e+02 pdb=" C7 NAG I 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.020 2.00e-02 2.50e+03 ... (remaining 2100 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4235 2.86 - 3.37: 11353 3.37 - 3.88: 19394 3.88 - 4.39: 22062 4.39 - 4.90: 34281 Nonbonded interactions: 91325 Sorted by model distance: nonbonded pdb=" O3 NAG S 2 " pdb=" O7 NAG S 2 " model vdw 2.354 3.040 nonbonded pdb=" O3 NAG D 2 " pdb=" O7 NAG D 2 " model vdw 2.355 3.040 nonbonded pdb=" O3 NAG e 2 " pdb=" O7 NAG e 2 " model vdw 2.355 3.040 nonbonded pdb=" N TYR C 200 " pdb=" N ILE C 201 " model vdw 2.381 2.560 nonbonded pdb=" N TYR B 200 " pdb=" N ILE B 201 " model vdw 2.382 2.560 ... (remaining 91320 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'O' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'f' selection = chain 'h' selection = chain 'j' } ncs_group { reference = chain 'F' selection = chain 'U' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'P' selection = chain 'Y' selection = chain 'k' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 4.170 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.390 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 0.022 0.149 12339 Z= 1.225 Angle : 2.116 13.698 16953 Z= 1.328 Chirality : 0.151 0.523 2202 Planarity : 0.014 0.250 2070 Dihedral : 17.976 106.156 5244 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 1605 helix: 0.11 (0.24), residues: 315 sheet: 0.86 (0.27), residues: 333 loop : -0.33 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.008 TRP a 370 HIS 0.008 0.002 HIS a 354 PHE 0.031 0.006 PHE b 309 TYR 0.079 0.010 TYR b 363 ARG 0.002 0.001 ARG c 314 Details of bonding type rmsd link_NAG-ASN : bond 0.07030 ( 33) link_NAG-ASN : angle 3.35269 ( 99) link_ALPHA1-6 : bond 0.06533 ( 3) link_ALPHA1-6 : angle 2.34277 ( 9) link_BETA1-4 : bond 0.06311 ( 42) link_BETA1-4 : angle 5.06774 ( 126) link_ALPHA1-3 : bond 0.08879 ( 3) link_ALPHA1-3 : angle 7.95870 ( 9) hydrogen bonds : bond 0.16954 ( 531) hydrogen bonds : angle 8.18612 ( 1458) link_BETA1-6 : bond 0.06288 ( 6) link_BETA1-6 : angle 7.27622 ( 18) SS BOND : bond 0.01984 ( 21) SS BOND : angle 3.06152 ( 42) covalent geometry : bond 0.02183 (12231) covalent geometry : angle 2.04419 (16650) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.6735 (mttt) cc_final: 0.6479 (mmtt) REVERT: A 144 ILE cc_start: 0.8021 (mt) cc_final: 0.7700 (mt) REVERT: A 200 TYR cc_start: 0.8807 (p90) cc_final: 0.8545 (p90) REVERT: A 217 TYR cc_start: 0.7930 (m-80) cc_final: 0.6916 (m-80) REVERT: A 227 TRP cc_start: 0.7889 (p90) cc_final: 0.7245 (p-90) REVERT: A 228 GLU cc_start: 0.8290 (pm20) cc_final: 0.7973 (pp20) REVERT: A 236 PRO cc_start: 0.8505 (Cg_endo) cc_final: 0.7930 (Cg_exo) REVERT: a 308 GLU cc_start: 0.8539 (mp0) cc_final: 0.8275 (mm-30) REVERT: a 371 TYR cc_start: 0.7382 (m-80) cc_final: 0.7112 (m-80) REVERT: a 396 GLU cc_start: 0.8773 (mp0) cc_final: 0.8567 (mp0) REVERT: B 144 ILE cc_start: 0.8029 (mt) cc_final: 0.7744 (mt) REVERT: B 217 TYR cc_start: 0.7811 (m-80) cc_final: 0.6836 (m-80) REVERT: B 227 TRP cc_start: 0.7911 (p90) cc_final: 0.7378 (p-90) REVERT: B 228 GLU cc_start: 0.8067 (pm20) cc_final: 0.7751 (pp20) REVERT: B 236 PRO cc_start: 0.8579 (Cg_endo) cc_final: 0.8051 (Cg_exo) REVERT: b 311 ASP cc_start: 0.8674 (m-30) cc_final: 0.8204 (t0) REVERT: b 371 TYR cc_start: 0.7389 (m-80) cc_final: 0.7024 (m-80) REVERT: b 396 GLU cc_start: 0.8700 (mp0) cc_final: 0.8468 (mp0) REVERT: C 78 LEU cc_start: 0.8753 (mt) cc_final: 0.8470 (mp) REVERT: C 144 ILE cc_start: 0.8057 (mt) cc_final: 0.7749 (mt) REVERT: C 211 ASP cc_start: 0.8000 (p0) cc_final: 0.7613 (p0) REVERT: C 217 TYR cc_start: 0.7983 (m-80) cc_final: 0.7076 (m-80) REVERT: C 236 PRO cc_start: 0.8575 (Cg_endo) cc_final: 0.7970 (Cg_exo) REVERT: c 311 ASP cc_start: 0.8598 (m-30) cc_final: 0.8211 (t0) REVERT: c 316 PHE cc_start: 0.8584 (m-80) cc_final: 0.8191 (m-10) REVERT: c 321 GLN cc_start: 0.8332 (mt0) cc_final: 0.7953 (mm-40) REVERT: c 396 GLU cc_start: 0.8699 (mp0) cc_final: 0.8497 (mp0) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.2598 time to fit residues: 126.7542 Evaluate side-chains 188 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 141 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 321 GLN a 331 GLN B 92 HIS B 141 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 321 GLN b 338 ASN b 405 GLN C 92 HIS C 141 HIS ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.074457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.063248 restraints weight = 81106.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.064551 restraints weight = 55364.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.065459 restraints weight = 41745.544| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 12339 Z= 0.319 Angle : 1.133 13.419 16953 Z= 0.544 Chirality : 0.057 0.403 2202 Planarity : 0.005 0.040 2070 Dihedral : 15.416 105.787 3450 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.70 % Allowed : 7.25 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.46 (0.19), residues: 1605 helix: 0.23 (0.27), residues: 345 sheet: 0.54 (0.28), residues: 318 loop : -0.80 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 210 HIS 0.015 0.003 HIS B 230 PHE 0.028 0.003 PHE A 233 TYR 0.036 0.004 TYR B 66 ARG 0.007 0.001 ARG b 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00896 ( 33) link_NAG-ASN : angle 2.70635 ( 99) link_ALPHA1-6 : bond 0.01593 ( 3) link_ALPHA1-6 : angle 1.28536 ( 9) link_BETA1-4 : bond 0.00609 ( 42) link_BETA1-4 : angle 3.27877 ( 126) link_ALPHA1-3 : bond 0.00375 ( 3) link_ALPHA1-3 : angle 4.58984 ( 9) hydrogen bonds : bond 0.06132 ( 531) hydrogen bonds : angle 6.30621 ( 1458) link_BETA1-6 : bond 0.03308 ( 6) link_BETA1-6 : angle 6.57616 ( 18) SS BOND : bond 0.00562 ( 21) SS BOND : angle 1.39803 ( 42) covalent geometry : bond 0.00659 (12231) covalent geometry : angle 1.05715 (16650) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 239 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.7312 (t0) cc_final: 0.6713 (t70) REVERT: A 161 LYS cc_start: 0.8725 (ptpp) cc_final: 0.8252 (pttt) REVERT: A 200 TYR cc_start: 0.8322 (p90) cc_final: 0.8043 (p90) REVERT: A 217 TYR cc_start: 0.7449 (m-80) cc_final: 0.7209 (m-80) REVERT: A 228 GLU cc_start: 0.8429 (pm20) cc_final: 0.7680 (pp20) REVERT: a 311 ASP cc_start: 0.9127 (m-30) cc_final: 0.8911 (m-30) REVERT: a 335 GLN cc_start: 0.9118 (pm20) cc_final: 0.8578 (pm20) REVERT: a 336 LEU cc_start: 0.9243 (tp) cc_final: 0.8740 (tp) REVERT: a 339 LYS cc_start: 0.9317 (mppt) cc_final: 0.9100 (mptt) REVERT: a 363 TYR cc_start: 0.7518 (p90) cc_final: 0.7097 (p90) REVERT: a 371 TYR cc_start: 0.6724 (m-80) cc_final: 0.6495 (m-80) REVERT: a 396 GLU cc_start: 0.8711 (mp0) cc_final: 0.8379 (mp0) REVERT: a 408 ASP cc_start: 0.7662 (t0) cc_final: 0.7401 (t70) REVERT: a 410 MET cc_start: 0.9043 (mtt) cc_final: 0.8774 (mtp) REVERT: B 156 ASP cc_start: 0.7161 (t0) cc_final: 0.6799 (t70) REVERT: B 161 LYS cc_start: 0.8616 (ptpp) cc_final: 0.8230 (pttt) REVERT: B 193 ARG cc_start: 0.8383 (mtm180) cc_final: 0.8165 (mtm-85) REVERT: B 200 TYR cc_start: 0.8345 (p90) cc_final: 0.8145 (p90) REVERT: B 205 SER cc_start: 0.8586 (p) cc_final: 0.8339 (t) REVERT: B 217 TYR cc_start: 0.7492 (m-80) cc_final: 0.7221 (m-80) REVERT: B 228 GLU cc_start: 0.8441 (pm20) cc_final: 0.7894 (pp20) REVERT: B 236 PRO cc_start: 0.9142 (Cg_endo) cc_final: 0.8400 (Cg_exo) REVERT: b 308 GLU cc_start: 0.8700 (mp0) cc_final: 0.8470 (pm20) REVERT: b 311 ASP cc_start: 0.9069 (m-30) cc_final: 0.8863 (m-30) REVERT: b 335 GLN cc_start: 0.9036 (pm20) cc_final: 0.8439 (pm20) REVERT: b 396 GLU cc_start: 0.8734 (mp0) cc_final: 0.8259 (mp0) REVERT: b 408 ASP cc_start: 0.7557 (t0) cc_final: 0.7279 (t70) REVERT: b 410 MET cc_start: 0.9233 (mtt) cc_final: 0.8925 (mtp) REVERT: C 116 LYS cc_start: 0.8091 (mttt) cc_final: 0.7530 (tptt) REVERT: C 134 MET cc_start: 0.7332 (ttp) cc_final: 0.5482 (mtt) REVERT: C 156 ASP cc_start: 0.7115 (t0) cc_final: 0.6617 (t70) REVERT: C 161 LYS cc_start: 0.8641 (ptpp) cc_final: 0.8198 (pttt) REVERT: C 194 MET cc_start: 0.8225 (ptp) cc_final: 0.7897 (ptp) REVERT: C 236 PRO cc_start: 0.9010 (Cg_endo) cc_final: 0.8234 (Cg_exo) REVERT: c 311 ASP cc_start: 0.9037 (m-30) cc_final: 0.8641 (m-30) REVERT: c 396 GLU cc_start: 0.8780 (mp0) cc_final: 0.8466 (mp0) REVERT: c 408 ASP cc_start: 0.7681 (t0) cc_final: 0.7480 (t70) REVERT: c 410 MET cc_start: 0.9039 (mtt) cc_final: 0.8746 (mtp) outliers start: 6 outliers final: 2 residues processed: 243 average time/residue: 0.2475 time to fit residues: 85.0459 Evaluate side-chains 181 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 30.0000 chunk 96 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 30.0000 chunk 3 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 123 optimal weight: 0.0070 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN a 331 GLN a 374 HIS B 230 HIS b 338 ASN b 374 HIS c 354 HIS c 374 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.076376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.064982 restraints weight = 81401.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.066304 restraints weight = 55506.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.067228 restraints weight = 42054.281| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12339 Z= 0.185 Angle : 0.916 13.595 16953 Z= 0.427 Chirality : 0.050 0.457 2202 Planarity : 0.004 0.054 2070 Dihedral : 12.401 92.200 3450 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.58 % Allowed : 4.33 % Favored : 95.09 % 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: -0.37 (0.20), residues: 1605 helix: 0.75 (0.29), residues: 342 sheet: 0.43 (0.28), residues: 315 loop : -0.86 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP a 386 HIS 0.006 0.001 HIS A 141 PHE 0.013 0.002 PHE c 399 TYR 0.029 0.003 TYR C 66 ARG 0.005 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 33) link_NAG-ASN : angle 2.63233 ( 99) link_ALPHA1-6 : bond 0.01961 ( 3) link_ALPHA1-6 : angle 2.10358 ( 9) link_BETA1-4 : bond 0.00722 ( 42) link_BETA1-4 : angle 2.84258 ( 126) link_ALPHA1-3 : bond 0.00210 ( 3) link_ALPHA1-3 : angle 4.51813 ( 9) hydrogen bonds : bond 0.04927 ( 531) hydrogen bonds : angle 5.71262 ( 1458) link_BETA1-6 : bond 0.02593 ( 6) link_BETA1-6 : angle 6.27472 ( 18) SS BOND : bond 0.00865 ( 21) SS BOND : angle 1.50591 ( 42) covalent geometry : bond 0.00387 (12231) covalent geometry : angle 0.83034 (16650) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 254 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9356 (mp) cc_final: 0.8962 (tt) REVERT: A 96 MET cc_start: 0.7146 (ppp) cc_final: 0.6572 (ppp) REVERT: A 156 ASP cc_start: 0.7301 (t0) cc_final: 0.6899 (t70) REVERT: A 161 LYS cc_start: 0.8531 (ptpp) cc_final: 0.8232 (pttm) REVERT: A 200 TYR cc_start: 0.8115 (p90) cc_final: 0.7882 (p90) REVERT: A 217 TYR cc_start: 0.7364 (m-80) cc_final: 0.7030 (m-80) REVERT: A 228 GLU cc_start: 0.7991 (pm20) cc_final: 0.7781 (pp20) REVERT: a 311 ASP cc_start: 0.9082 (m-30) cc_final: 0.8681 (t0) REVERT: a 335 GLN cc_start: 0.9103 (pm20) cc_final: 0.8901 (pm20) REVERT: a 336 LEU cc_start: 0.9210 (tp) cc_final: 0.9002 (tp) REVERT: a 363 TYR cc_start: 0.7551 (p90) cc_final: 0.7324 (p90) REVERT: a 408 ASP cc_start: 0.7707 (t0) cc_final: 0.7444 (t70) REVERT: B 72 GLU cc_start: 0.7847 (mp0) cc_final: 0.7626 (mp0) REVERT: B 96 MET cc_start: 0.7265 (ppp) cc_final: 0.6644 (ppp) REVERT: B 156 ASP cc_start: 0.7339 (t0) cc_final: 0.6831 (t70) REVERT: B 161 LYS cc_start: 0.8547 (ptpp) cc_final: 0.8155 (pttt) REVERT: B 193 ARG cc_start: 0.8304 (mtm180) cc_final: 0.7904 (mtm-85) REVERT: B 200 TYR cc_start: 0.8135 (p90) cc_final: 0.7908 (p90) REVERT: B 205 SER cc_start: 0.8511 (p) cc_final: 0.8263 (t) REVERT: B 217 TYR cc_start: 0.7259 (m-80) cc_final: 0.6939 (m-80) REVERT: B 228 GLU cc_start: 0.7857 (pm20) cc_final: 0.7498 (pp20) REVERT: b 308 GLU cc_start: 0.8705 (mp0) cc_final: 0.8252 (pm20) REVERT: b 325 ARG cc_start: 0.8905 (mmt180) cc_final: 0.8704 (mmt180) REVERT: C 116 LYS cc_start: 0.8066 (mttt) cc_final: 0.7546 (tptt) REVERT: C 134 MET cc_start: 0.7375 (ttp) cc_final: 0.5916 (mtt) REVERT: C 156 ASP cc_start: 0.7066 (t0) cc_final: 0.5962 (t70) REVERT: C 161 LYS cc_start: 0.8474 (ptpp) cc_final: 0.7859 (pttt) REVERT: C 200 TYR cc_start: 0.8025 (p90) cc_final: 0.7820 (p90) REVERT: C 217 TYR cc_start: 0.7024 (m-80) cc_final: 0.6785 (m-80) REVERT: C 236 PRO cc_start: 0.8945 (Cg_endo) cc_final: 0.8313 (Cg_exo) REVERT: c 321 GLN cc_start: 0.8342 (mt0) cc_final: 0.8028 (mm-40) REVERT: c 325 ARG cc_start: 0.8662 (mpt180) cc_final: 0.8173 (mmt-90) REVERT: c 363 TYR cc_start: 0.7090 (p90) cc_final: 0.6628 (p90) REVERT: c 408 ASP cc_start: 0.7589 (t0) cc_final: 0.7376 (t70) outliers start: 5 outliers final: 1 residues processed: 255 average time/residue: 0.3020 time to fit residues: 108.6139 Evaluate side-chains 183 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 56 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS b 331 GLN C 141 HIS ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 331 GLN c 353 ASN c 354 HIS ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.074318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062964 restraints weight = 81254.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.064221 restraints weight = 55611.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.065121 restraints weight = 42209.744| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12339 Z= 0.242 Angle : 0.948 12.720 16953 Z= 0.441 Chirality : 0.049 0.351 2202 Planarity : 0.004 0.051 2070 Dihedral : 10.917 86.137 3450 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.53 (0.20), residues: 1605 helix: 0.76 (0.29), residues: 324 sheet: 0.23 (0.29), residues: 318 loop : -0.96 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP a 386 HIS 0.011 0.002 HIS c 354 PHE 0.012 0.002 PHE A 157 TYR 0.031 0.003 TYR c 366 ARG 0.004 0.001 ARG C 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 33) link_NAG-ASN : angle 2.79030 ( 99) link_ALPHA1-6 : bond 0.01920 ( 3) link_ALPHA1-6 : angle 3.22706 ( 9) link_BETA1-4 : bond 0.00591 ( 42) link_BETA1-4 : angle 2.80259 ( 126) link_ALPHA1-3 : bond 0.00217 ( 3) link_ALPHA1-3 : angle 4.23511 ( 9) hydrogen bonds : bond 0.04939 ( 531) hydrogen bonds : angle 5.73675 ( 1458) link_BETA1-6 : bond 0.03003 ( 6) link_BETA1-6 : angle 6.47578 ( 18) SS BOND : bond 0.00514 ( 21) SS BOND : angle 1.23169 ( 42) covalent geometry : bond 0.00502 (12231) covalent geometry : angle 0.86280 (16650) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8821 (mp) cc_final: 0.8621 (mt) REVERT: A 96 MET cc_start: 0.7298 (ppp) cc_final: 0.6547 (ppp) REVERT: A 189 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8696 (tp-100) REVERT: A 200 TYR cc_start: 0.8281 (p90) cc_final: 0.7955 (p90) REVERT: A 217 TYR cc_start: 0.7410 (m-80) cc_final: 0.6941 (m-80) REVERT: a 331 GLN cc_start: 0.7729 (mp10) cc_final: 0.6853 (tt0) REVERT: a 333 SER cc_start: 0.9137 (p) cc_final: 0.8694 (m) REVERT: a 363 TYR cc_start: 0.7764 (p90) cc_final: 0.7550 (p90) REVERT: a 408 ASP cc_start: 0.7659 (t0) cc_final: 0.7344 (t70) REVERT: a 410 MET cc_start: 0.9070 (mtt) cc_final: 0.8807 (mtp) REVERT: B 72 GLU cc_start: 0.7687 (mp0) cc_final: 0.7257 (mp0) REVERT: B 96 MET cc_start: 0.7679 (ppp) cc_final: 0.7158 (ppp) REVERT: B 193 ARG cc_start: 0.8345 (mtm180) cc_final: 0.8101 (mtm-85) REVERT: B 200 TYR cc_start: 0.8406 (p90) cc_final: 0.8155 (p90) REVERT: B 205 SER cc_start: 0.8594 (p) cc_final: 0.8335 (t) REVERT: B 217 TYR cc_start: 0.7752 (m-80) cc_final: 0.7369 (m-80) REVERT: b 308 GLU cc_start: 0.8550 (mp0) cc_final: 0.8006 (mp0) REVERT: b 363 TYR cc_start: 0.7398 (p90) cc_final: 0.7182 (p90) REVERT: b 410 MET cc_start: 0.9116 (mtt) cc_final: 0.8823 (mtp) REVERT: C 73 LEU cc_start: 0.9174 (tt) cc_final: 0.8597 (mm) REVERT: C 75 MET cc_start: 0.7724 (mmm) cc_final: 0.7192 (mmt) REVERT: C 96 MET cc_start: 0.7845 (ppp) cc_final: 0.7070 (ppp) REVERT: C 116 LYS cc_start: 0.8127 (mttt) cc_final: 0.7550 (tptt) REVERT: C 134 MET cc_start: 0.7276 (ttp) cc_final: 0.5834 (mtt) REVERT: C 217 TYR cc_start: 0.7494 (m-80) cc_final: 0.7268 (m-80) REVERT: c 284 MET cc_start: 0.7963 (ptp) cc_final: 0.7382 (ptp) REVERT: c 311 ASP cc_start: 0.9027 (m-30) cc_final: 0.8759 (m-30) REVERT: c 321 GLN cc_start: 0.8416 (mt0) cc_final: 0.7863 (mm-40) REVERT: c 363 TYR cc_start: 0.7172 (p90) cc_final: 0.6775 (p90) REVERT: c 408 ASP cc_start: 0.7524 (t0) cc_final: 0.7273 (t70) REVERT: c 410 MET cc_start: 0.8927 (mtt) cc_final: 0.8725 (mtp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2962 time to fit residues: 93.5749 Evaluate side-chains 170 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 90 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 40.0000 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS a 406 GLN B 230 HIS b 406 GLN c 406 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.073856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062508 restraints weight = 81337.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.063825 restraints weight = 54613.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064689 restraints weight = 41306.612| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12339 Z= 0.221 Angle : 0.907 12.390 16953 Z= 0.423 Chirality : 0.048 0.352 2202 Planarity : 0.004 0.044 2070 Dihedral : 9.870 74.177 3450 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.83 (0.20), residues: 1605 helix: 0.58 (0.28), residues: 324 sheet: 0.07 (0.29), residues: 318 loop : -1.21 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 386 HIS 0.010 0.002 HIS B 141 PHE 0.026 0.002 PHE B 191 TYR 0.019 0.002 TYR c 371 ARG 0.008 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 33) link_NAG-ASN : angle 2.59543 ( 99) link_ALPHA1-6 : bond 0.02159 ( 3) link_ALPHA1-6 : angle 4.24783 ( 9) link_BETA1-4 : bond 0.00572 ( 42) link_BETA1-4 : angle 2.50483 ( 126) link_ALPHA1-3 : bond 0.00134 ( 3) link_ALPHA1-3 : angle 4.24694 ( 9) hydrogen bonds : bond 0.04768 ( 531) hydrogen bonds : angle 5.76573 ( 1458) link_BETA1-6 : bond 0.02983 ( 6) link_BETA1-6 : angle 6.39176 ( 18) SS BOND : bond 0.00585 ( 21) SS BOND : angle 1.48051 ( 42) covalent geometry : bond 0.00452 (12231) covalent geometry : angle 0.82545 (16650) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7641 (ttm) cc_final: 0.7135 (ttm) REVERT: A 96 MET cc_start: 0.7669 (ppp) cc_final: 0.7004 (ppp) REVERT: A 217 TYR cc_start: 0.7432 (m-80) cc_final: 0.6875 (m-80) REVERT: a 284 MET cc_start: 0.7945 (pmm) cc_final: 0.7517 (pmm) REVERT: a 308 GLU cc_start: 0.8461 (pm20) cc_final: 0.7653 (mm-30) REVERT: a 311 ASP cc_start: 0.9183 (m-30) cc_final: 0.8926 (m-30) REVERT: a 325 ARG cc_start: 0.8663 (mmt-90) cc_final: 0.8455 (mmt-90) REVERT: a 333 SER cc_start: 0.8936 (p) cc_final: 0.8710 (m) REVERT: a 334 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8039 (mp) REVERT: a 351 MET cc_start: 0.8929 (mmp) cc_final: 0.8635 (tpp) REVERT: a 363 TYR cc_start: 0.7378 (p90) cc_final: 0.7008 (p90) REVERT: a 408 ASP cc_start: 0.7633 (t0) cc_final: 0.7294 (t70) REVERT: B 72 GLU cc_start: 0.7517 (mp0) cc_final: 0.7187 (mp0) REVERT: B 73 LEU cc_start: 0.9063 (mm) cc_final: 0.8733 (mm) REVERT: B 75 MET cc_start: 0.7734 (mmm) cc_final: 0.7105 (tpp) REVERT: B 96 MET cc_start: 0.7815 (ppp) cc_final: 0.7231 (ppp) REVERT: B 193 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7985 (mtm-85) REVERT: B 194 MET cc_start: 0.8163 (ptp) cc_final: 0.7926 (ptp) REVERT: B 200 TYR cc_start: 0.8314 (p90) cc_final: 0.8048 (p90) REVERT: B 205 SER cc_start: 0.8697 (p) cc_final: 0.8464 (t) REVERT: B 217 TYR cc_start: 0.7686 (m-80) cc_final: 0.7296 (m-80) REVERT: b 308 GLU cc_start: 0.8657 (mp0) cc_final: 0.8162 (mp0) REVERT: b 333 SER cc_start: 0.9325 (p) cc_final: 0.8853 (m) REVERT: b 410 MET cc_start: 0.9139 (mtt) cc_final: 0.8874 (mtp) REVERT: C 96 MET cc_start: 0.8176 (ppp) cc_final: 0.7492 (ppp) REVERT: C 116 LYS cc_start: 0.8130 (mttt) cc_final: 0.7445 (tptt) REVERT: C 134 MET cc_start: 0.7380 (ttp) cc_final: 0.6060 (mtt) REVERT: C 193 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.8230 (mtm-85) REVERT: c 284 MET cc_start: 0.7847 (ptp) cc_final: 0.7534 (ptp) REVERT: c 311 ASP cc_start: 0.9105 (m-30) cc_final: 0.8876 (m-30) REVERT: c 321 GLN cc_start: 0.8373 (mt0) cc_final: 0.7815 (mm-40) REVERT: c 408 ASP cc_start: 0.7465 (t0) cc_final: 0.7201 (t70) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.2748 time to fit residues: 85.7752 Evaluate side-chains 169 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 108 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 40.0000 chunk 65 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.074854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.063460 restraints weight = 81448.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.064771 restraints weight = 54510.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.065712 restraints weight = 40948.595| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12339 Z= 0.177 Angle : 0.875 12.403 16953 Z= 0.403 Chirality : 0.048 0.339 2202 Planarity : 0.004 0.043 2070 Dihedral : 9.375 66.763 3450 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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: -0.93 (0.20), residues: 1605 helix: 0.33 (0.27), residues: 351 sheet: -0.11 (0.29), residues: 318 loop : -1.19 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 210 HIS 0.009 0.001 HIS A 141 PHE 0.018 0.002 PHE C 157 TYR 0.016 0.002 TYR A 66 ARG 0.006 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 33) link_NAG-ASN : angle 2.64190 ( 99) link_ALPHA1-6 : bond 0.01943 ( 3) link_ALPHA1-6 : angle 4.12953 ( 9) link_BETA1-4 : bond 0.00533 ( 42) link_BETA1-4 : angle 2.33846 ( 126) link_ALPHA1-3 : bond 0.00150 ( 3) link_ALPHA1-3 : angle 4.24999 ( 9) hydrogen bonds : bond 0.04445 ( 531) hydrogen bonds : angle 5.61882 ( 1458) link_BETA1-6 : bond 0.02995 ( 6) link_BETA1-6 : angle 6.34806 ( 18) SS BOND : bond 0.00414 ( 21) SS BOND : angle 1.34910 ( 42) covalent geometry : bond 0.00364 (12231) covalent geometry : angle 0.79334 (16650) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7629 (ttm) cc_final: 0.7308 (ttm) REVERT: A 96 MET cc_start: 0.7618 (ppp) cc_final: 0.6852 (ppp) REVERT: A 189 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8623 (tp40) REVERT: A 193 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.8007 (mmm-85) REVERT: A 194 MET cc_start: 0.7776 (ptp) cc_final: 0.7572 (ptp) REVERT: A 217 TYR cc_start: 0.7379 (m-80) cc_final: 0.6820 (m-80) REVERT: a 284 MET cc_start: 0.7938 (pmm) cc_final: 0.7533 (pmm) REVERT: a 308 GLU cc_start: 0.8353 (mp0) cc_final: 0.7466 (mp0) REVERT: a 334 ILE cc_start: 0.8142 (mp) cc_final: 0.7709 (mp) REVERT: a 351 MET cc_start: 0.8869 (mmp) cc_final: 0.8526 (tpp) REVERT: a 363 TYR cc_start: 0.7430 (p90) cc_final: 0.7156 (p90) REVERT: a 408 ASP cc_start: 0.7630 (t0) cc_final: 0.7325 (t70) REVERT: a 410 MET cc_start: 0.9182 (mtt) cc_final: 0.8897 (mtp) REVERT: B 75 MET cc_start: 0.7537 (mmm) cc_final: 0.7150 (tpp) REVERT: B 96 MET cc_start: 0.8098 (ppp) cc_final: 0.7535 (ppp) REVERT: B 193 ARG cc_start: 0.8463 (mtm180) cc_final: 0.7961 (mtm-85) REVERT: B 200 TYR cc_start: 0.8237 (p90) cc_final: 0.8031 (p90) REVERT: B 205 SER cc_start: 0.8549 (p) cc_final: 0.8317 (t) REVERT: B 217 TYR cc_start: 0.7664 (m-80) cc_final: 0.7209 (m-80) REVERT: b 308 GLU cc_start: 0.8657 (mp0) cc_final: 0.8162 (mp0) REVERT: b 333 SER cc_start: 0.9325 (p) cc_final: 0.8890 (m) REVERT: b 334 ILE cc_start: 0.8851 (mm) cc_final: 0.8606 (mm) REVERT: b 363 TYR cc_start: 0.7515 (p90) cc_final: 0.7258 (p90) REVERT: C 96 MET cc_start: 0.8236 (ppp) cc_final: 0.7532 (ppp) REVERT: C 116 LYS cc_start: 0.8116 (mttt) cc_final: 0.7419 (tptt) REVERT: C 134 MET cc_start: 0.7270 (ttp) cc_final: 0.5938 (mtt) REVERT: c 284 MET cc_start: 0.7839 (ptp) cc_final: 0.7510 (ptp) REVERT: c 311 ASP cc_start: 0.9096 (m-30) cc_final: 0.8844 (m-30) REVERT: c 321 GLN cc_start: 0.8349 (mt0) cc_final: 0.7808 (mm-40) REVERT: c 363 TYR cc_start: 0.7389 (p90) cc_final: 0.6793 (p90) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2509 time to fit residues: 78.9680 Evaluate side-chains 165 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 152 optimal weight: 40.0000 chunk 114 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.074612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.063188 restraints weight = 80446.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064489 restraints weight = 54157.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.065409 restraints weight = 40720.413| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12339 Z= 0.182 Angle : 0.872 12.518 16953 Z= 0.401 Chirality : 0.047 0.350 2202 Planarity : 0.004 0.055 2070 Dihedral : 9.141 61.277 3450 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: -1.03 (0.20), residues: 1605 helix: 0.40 (0.28), residues: 345 sheet: -0.25 (0.28), residues: 318 loop : -1.28 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 210 HIS 0.011 0.001 HIS A 141 PHE 0.027 0.002 PHE B 191 TYR 0.032 0.002 TYR c 366 ARG 0.007 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 33) link_NAG-ASN : angle 2.84592 ( 99) link_ALPHA1-6 : bond 0.01812 ( 3) link_ALPHA1-6 : angle 4.21037 ( 9) link_BETA1-4 : bond 0.00498 ( 42) link_BETA1-4 : angle 2.24860 ( 126) link_ALPHA1-3 : bond 0.00143 ( 3) link_ALPHA1-3 : angle 4.26955 ( 9) hydrogen bonds : bond 0.04332 ( 531) hydrogen bonds : angle 5.62803 ( 1458) link_BETA1-6 : bond 0.03047 ( 6) link_BETA1-6 : angle 6.39060 ( 18) SS BOND : bond 0.00383 ( 21) SS BOND : angle 1.08214 ( 42) covalent geometry : bond 0.00373 (12231) covalent geometry : angle 0.78765 (16650) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7635 (ppp) cc_final: 0.6898 (ppp) REVERT: A 189 GLN cc_start: 0.8853 (tp-100) cc_final: 0.8568 (tp40) REVERT: A 217 TYR cc_start: 0.7308 (m-80) cc_final: 0.6724 (m-80) REVERT: A 218 GLN cc_start: 0.7283 (pp30) cc_final: 0.7039 (pp30) REVERT: a 284 MET cc_start: 0.7934 (pmm) cc_final: 0.7468 (pmm) REVERT: a 308 GLU cc_start: 0.8476 (mp0) cc_final: 0.7600 (mm-30) REVERT: a 311 ASP cc_start: 0.9168 (m-30) cc_final: 0.8905 (m-30) REVERT: a 334 ILE cc_start: 0.8111 (mp) cc_final: 0.7591 (mp) REVERT: a 351 MET cc_start: 0.8926 (mmp) cc_final: 0.8452 (tpp) REVERT: a 363 TYR cc_start: 0.7450 (p90) cc_final: 0.7176 (p90) REVERT: a 408 ASP cc_start: 0.7606 (t0) cc_final: 0.7347 (t70) REVERT: a 410 MET cc_start: 0.9085 (mtt) cc_final: 0.8841 (mtp) REVERT: B 96 MET cc_start: 0.8104 (ppp) cc_final: 0.7552 (ppp) REVERT: B 193 ARG cc_start: 0.8367 (mtm180) cc_final: 0.7908 (mtm-85) REVERT: B 200 TYR cc_start: 0.8185 (p90) cc_final: 0.7982 (p90) REVERT: B 205 SER cc_start: 0.8611 (p) cc_final: 0.8345 (t) REVERT: B 217 TYR cc_start: 0.7526 (m-80) cc_final: 0.7064 (m-80) REVERT: b 284 MET cc_start: 0.8076 (ptp) cc_final: 0.7603 (ptp) REVERT: b 308 GLU cc_start: 0.8773 (mp0) cc_final: 0.8220 (mp0) REVERT: b 332 MET cc_start: 0.7697 (mmm) cc_final: 0.7296 (mmt) REVERT: b 333 SER cc_start: 0.9038 (p) cc_final: 0.8572 (m) REVERT: b 334 ILE cc_start: 0.8926 (mm) cc_final: 0.8659 (mm) REVERT: b 363 TYR cc_start: 0.7490 (p90) cc_final: 0.7193 (p90) REVERT: b 410 MET cc_start: 0.9123 (mtt) cc_final: 0.8900 (mtp) REVERT: C 96 MET cc_start: 0.8275 (ppp) cc_final: 0.7566 (ppp) REVERT: C 116 LYS cc_start: 0.8043 (mttt) cc_final: 0.7374 (tptt) REVERT: C 134 MET cc_start: 0.7341 (ttp) cc_final: 0.6074 (mtt) REVERT: c 284 MET cc_start: 0.7706 (ptp) cc_final: 0.7415 (ptp) REVERT: c 311 ASP cc_start: 0.9091 (m-30) cc_final: 0.8839 (m-30) REVERT: c 321 GLN cc_start: 0.8363 (mt0) cc_final: 0.7830 (mm-40) REVERT: c 332 MET cc_start: 0.7700 (mmm) cc_final: 0.7398 (mmt) REVERT: c 334 ILE cc_start: 0.8900 (mm) cc_final: 0.8510 (mm) REVERT: c 410 MET cc_start: 0.9038 (mtt) cc_final: 0.8750 (mtp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2641 time to fit residues: 81.0509 Evaluate side-chains 166 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 15 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 155 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 43 optimal weight: 0.0170 chunk 70 optimal weight: 0.0670 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.075936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.064389 restraints weight = 80388.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.065722 restraints weight = 53764.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.066641 restraints weight = 40286.515| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12339 Z= 0.151 Angle : 0.843 12.197 16953 Z= 0.389 Chirality : 0.047 0.346 2202 Planarity : 0.004 0.046 2070 Dihedral : 8.677 59.734 3450 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: -0.96 (0.20), residues: 1605 helix: 0.55 (0.28), residues: 345 sheet: -0.24 (0.28), residues: 318 loop : -1.26 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 227 HIS 0.004 0.001 HIS C 124 PHE 0.016 0.002 PHE C 157 TYR 0.019 0.002 TYR a 371 ARG 0.008 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 33) link_NAG-ASN : angle 2.59146 ( 99) link_ALPHA1-6 : bond 0.01779 ( 3) link_ALPHA1-6 : angle 4.06747 ( 9) link_BETA1-4 : bond 0.00518 ( 42) link_BETA1-4 : angle 2.08650 ( 126) link_ALPHA1-3 : bond 0.00111 ( 3) link_ALPHA1-3 : angle 4.24803 ( 9) hydrogen bonds : bond 0.04019 ( 531) hydrogen bonds : angle 5.42944 ( 1458) link_BETA1-6 : bond 0.03002 ( 6) link_BETA1-6 : angle 6.25529 ( 18) SS BOND : bond 0.00495 ( 21) SS BOND : angle 1.93491 ( 42) covalent geometry : bond 0.00314 (12231) covalent geometry : angle 0.76149 (16650) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7756 (ttm) cc_final: 0.7482 (ttm) REVERT: A 96 MET cc_start: 0.7576 (ppp) cc_final: 0.6911 (ppp) REVERT: A 161 LYS cc_start: 0.8046 (pttm) cc_final: 0.7804 (pttp) REVERT: A 193 ARG cc_start: 0.8142 (mmm-85) cc_final: 0.7920 (mmm-85) REVERT: A 217 TYR cc_start: 0.7306 (m-80) cc_final: 0.6634 (m-80) REVERT: A 218 GLN cc_start: 0.7132 (pp30) cc_final: 0.6838 (pp30) REVERT: a 284 MET cc_start: 0.7862 (pmm) cc_final: 0.7408 (pmm) REVERT: a 308 GLU cc_start: 0.8373 (mp0) cc_final: 0.7435 (mm-30) REVERT: a 311 ASP cc_start: 0.9131 (m-30) cc_final: 0.8862 (m-30) REVERT: a 325 ARG cc_start: 0.8465 (mmt-90) cc_final: 0.8264 (mmt-90) REVERT: a 334 ILE cc_start: 0.8186 (mp) cc_final: 0.7882 (mp) REVERT: a 351 MET cc_start: 0.8870 (mmp) cc_final: 0.8467 (tpp) REVERT: a 363 TYR cc_start: 0.7387 (p90) cc_final: 0.7145 (p90) REVERT: a 410 MET cc_start: 0.9047 (mtt) cc_final: 0.8792 (mtp) REVERT: B 80 MET cc_start: 0.8418 (mtm) cc_final: 0.8104 (mtt) REVERT: B 82 MET cc_start: 0.8888 (ptp) cc_final: 0.8294 (pmm) REVERT: B 96 MET cc_start: 0.8104 (ppp) cc_final: 0.7595 (ppp) REVERT: B 205 SER cc_start: 0.8486 (p) cc_final: 0.8217 (t) REVERT: B 217 TYR cc_start: 0.7625 (m-80) cc_final: 0.7126 (m-80) REVERT: b 284 MET cc_start: 0.8060 (ptp) cc_final: 0.7495 (ptp) REVERT: b 308 GLU cc_start: 0.8736 (mp0) cc_final: 0.8141 (mp0) REVERT: b 363 TYR cc_start: 0.7541 (p90) cc_final: 0.7227 (p90) REVERT: C 96 MET cc_start: 0.8069 (ppp) cc_final: 0.7426 (ppp) REVERT: C 116 LYS cc_start: 0.8095 (mttt) cc_final: 0.7373 (tptt) REVERT: C 134 MET cc_start: 0.7193 (ttp) cc_final: 0.5971 (mtt) REVERT: C 193 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7768 (mmm-85) REVERT: c 284 MET cc_start: 0.7764 (ptp) cc_final: 0.7501 (ptp) REVERT: c 311 ASP cc_start: 0.9047 (m-30) cc_final: 0.8817 (m-30) REVERT: c 321 GLN cc_start: 0.8328 (mt0) cc_final: 0.7817 (mm-40) REVERT: c 334 ILE cc_start: 0.8875 (mm) cc_final: 0.8585 (mm) REVERT: c 410 MET cc_start: 0.8996 (mtt) cc_final: 0.8779 (mtp) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2403 time to fit residues: 77.9418 Evaluate side-chains 171 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 106 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 40.0000 chunk 128 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 338 ASN B 218 GLN ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.070632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.059630 restraints weight = 82313.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060861 restraints weight = 54592.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.061733 restraints weight = 40948.592| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.6741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 12339 Z= 0.332 Angle : 1.076 13.948 16953 Z= 0.511 Chirality : 0.054 0.374 2202 Planarity : 0.005 0.063 2070 Dihedral : 9.936 59.909 3450 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.19), residues: 1605 helix: -0.71 (0.25), residues: 345 sheet: -0.65 (0.26), residues: 342 loop : -1.64 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 210 HIS 0.019 0.003 HIS C 230 PHE 0.033 0.003 PHE A 157 TYR 0.025 0.003 TYR b 371 ARG 0.005 0.001 ARG c 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 33) link_NAG-ASN : angle 3.25229 ( 99) link_ALPHA1-6 : bond 0.01421 ( 3) link_ALPHA1-6 : angle 5.41878 ( 9) link_BETA1-4 : bond 0.00631 ( 42) link_BETA1-4 : angle 2.47643 ( 126) link_ALPHA1-3 : bond 0.00098 ( 3) link_ALPHA1-3 : angle 4.22328 ( 9) hydrogen bonds : bond 0.05390 ( 531) hydrogen bonds : angle 6.50932 ( 1458) link_BETA1-6 : bond 0.03635 ( 6) link_BETA1-6 : angle 6.81593 ( 18) SS BOND : bond 0.00631 ( 21) SS BOND : angle 1.92897 ( 42) covalent geometry : bond 0.00691 (12231) covalent geometry : angle 0.99255 (16650) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.265 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 96 MET cc_start: 0.7857 (ppp) cc_final: 0.7125 (ppp) REVERT: A 217 TYR cc_start: 0.7594 (m-80) cc_final: 0.6874 (m-80) REVERT: a 284 MET cc_start: 0.7939 (pmm) cc_final: 0.7431 (pmm) REVERT: a 308 GLU cc_start: 0.8708 (mp0) cc_final: 0.7687 (mp0) REVERT: a 311 ASP cc_start: 0.9224 (m-30) cc_final: 0.8896 (m-30) REVERT: a 341 VAL cc_start: 0.9473 (t) cc_final: 0.9248 (t) REVERT: a 351 MET cc_start: 0.9070 (mmp) cc_final: 0.8627 (tpp) REVERT: a 410 MET cc_start: 0.9146 (mtt) cc_final: 0.8921 (mtp) REVERT: B 82 MET cc_start: 0.8920 (ptp) cc_final: 0.8357 (pmm) REVERT: B 96 MET cc_start: 0.8215 (ppp) cc_final: 0.7550 (ppp) REVERT: B 217 TYR cc_start: 0.7813 (m-80) cc_final: 0.7225 (m-80) REVERT: b 284 MET cc_start: 0.8089 (ptp) cc_final: 0.7593 (ptp) REVERT: b 308 GLU cc_start: 0.8849 (mp0) cc_final: 0.8368 (mp0) REVERT: b 311 ASP cc_start: 0.9069 (m-30) cc_final: 0.8713 (m-30) REVERT: b 410 MET cc_start: 0.9186 (mtt) cc_final: 0.8911 (mtp) REVERT: C 96 MET cc_start: 0.8181 (ppp) cc_final: 0.7515 (ppp) REVERT: C 116 LYS cc_start: 0.8047 (mttt) cc_final: 0.7372 (tptt) REVERT: C 134 MET cc_start: 0.7409 (ttp) cc_final: 0.6201 (mtt) REVERT: c 311 ASP cc_start: 0.9160 (m-30) cc_final: 0.8828 (m-30) REVERT: c 321 GLN cc_start: 0.8402 (mt0) cc_final: 0.7811 (mm-40) REVERT: c 325 ARG cc_start: 0.8613 (mpt180) cc_final: 0.7597 (mpt180) REVERT: c 333 SER cc_start: 0.9179 (p) cc_final: 0.8679 (m) REVERT: c 410 MET cc_start: 0.9152 (mtt) cc_final: 0.8934 (mtp) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2360 time to fit residues: 68.8120 Evaluate side-chains 161 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 35 optimal weight: 30.0000 chunk 147 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 338 ASN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.072298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.061033 restraints weight = 79699.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.062349 restraints weight = 52150.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.063229 restraints weight = 38665.243| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 12339 Z= 0.232 Angle : 0.978 13.282 16953 Z= 0.465 Chirality : 0.051 0.394 2202 Planarity : 0.005 0.049 2070 Dihedral : 9.584 57.309 3450 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.19), residues: 1605 helix: -0.50 (0.26), residues: 345 sheet: -0.73 (0.26), residues: 339 loop : -1.66 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 227 HIS 0.013 0.002 HIS C 230 PHE 0.037 0.003 PHE A 233 TYR 0.047 0.003 TYR c 371 ARG 0.009 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 33) link_NAG-ASN : angle 2.90189 ( 99) link_ALPHA1-6 : bond 0.01358 ( 3) link_ALPHA1-6 : angle 5.00766 ( 9) link_BETA1-4 : bond 0.00536 ( 42) link_BETA1-4 : angle 2.18394 ( 126) link_ALPHA1-3 : bond 0.00087 ( 3) link_ALPHA1-3 : angle 4.20565 ( 9) hydrogen bonds : bond 0.04867 ( 531) hydrogen bonds : angle 6.30880 ( 1458) link_BETA1-6 : bond 0.03127 ( 6) link_BETA1-6 : angle 6.63125 ( 18) SS BOND : bond 0.00413 ( 21) SS BOND : angle 1.70733 ( 42) covalent geometry : bond 0.00487 (12231) covalent geometry : angle 0.90023 (16650) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7427 (ttm) cc_final: 0.7215 (ttm) REVERT: A 96 MET cc_start: 0.7784 (ppp) cc_final: 0.7110 (ppp) REVERT: A 217 TYR cc_start: 0.7333 (m-80) cc_final: 0.6729 (m-80) REVERT: a 284 MET cc_start: 0.7979 (pmm) cc_final: 0.7507 (pmm) REVERT: a 308 GLU cc_start: 0.8647 (mp0) cc_final: 0.7671 (mp0) REVERT: a 311 ASP cc_start: 0.9203 (m-30) cc_final: 0.8817 (m-30) REVERT: B 82 MET cc_start: 0.8953 (ptp) cc_final: 0.8208 (pmm) REVERT: B 96 MET cc_start: 0.8086 (ppp) cc_final: 0.7507 (ppp) REVERT: b 284 MET cc_start: 0.8164 (ptp) cc_final: 0.7714 (ptp) REVERT: b 308 GLU cc_start: 0.8830 (mp0) cc_final: 0.8278 (mp0) REVERT: b 311 ASP cc_start: 0.8990 (m-30) cc_final: 0.8633 (m-30) REVERT: b 363 TYR cc_start: 0.7669 (p90) cc_final: 0.7303 (p90) REVERT: b 410 MET cc_start: 0.9111 (mtt) cc_final: 0.8895 (mtp) REVERT: C 96 MET cc_start: 0.8219 (ppp) cc_final: 0.7539 (ppp) REVERT: C 116 LYS cc_start: 0.8038 (mttt) cc_final: 0.7370 (tptt) REVERT: C 134 MET cc_start: 0.7249 (ttp) cc_final: 0.6060 (mtt) REVERT: C 191 PHE cc_start: 0.8232 (t80) cc_final: 0.8006 (t80) REVERT: c 311 ASP cc_start: 0.9130 (m-30) cc_final: 0.8760 (m-30) REVERT: c 321 GLN cc_start: 0.8387 (mt0) cc_final: 0.7674 (mm-40) REVERT: c 325 ARG cc_start: 0.8511 (mpt180) cc_final: 0.7448 (mpt180) REVERT: c 331 GLN cc_start: 0.7566 (tt0) cc_final: 0.7232 (tt0) REVERT: c 333 SER cc_start: 0.9197 (p) cc_final: 0.8766 (m) REVERT: c 410 MET cc_start: 0.9151 (mtt) cc_final: 0.8931 (mtp) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2595 time to fit residues: 77.1941 Evaluate side-chains 171 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 49 optimal weight: 30.0000 chunk 93 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 80 optimal weight: 0.0010 chunk 145 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.073692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.062477 restraints weight = 80161.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.063813 restraints weight = 52688.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.064683 restraints weight = 39227.457| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.6950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12339 Z= 0.173 Angle : 0.897 12.837 16953 Z= 0.423 Chirality : 0.048 0.338 2202 Planarity : 0.004 0.056 2070 Dihedral : 9.008 57.938 3450 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -1.64 (0.19), residues: 1605 helix: -0.25 (0.27), residues: 348 sheet: -0.70 (0.26), residues: 339 loop : -1.61 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 210 HIS 0.007 0.001 HIS C 230 PHE 0.034 0.002 PHE A 233 TYR 0.023 0.002 TYR b 371 ARG 0.007 0.001 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 33) link_NAG-ASN : angle 2.68153 ( 99) link_ALPHA1-6 : bond 0.01282 ( 3) link_ALPHA1-6 : angle 4.60177 ( 9) link_BETA1-4 : bond 0.00508 ( 42) link_BETA1-4 : angle 2.02534 ( 126) link_ALPHA1-3 : bond 0.00045 ( 3) link_ALPHA1-3 : angle 4.14403 ( 9) hydrogen bonds : bond 0.04319 ( 531) hydrogen bonds : angle 6.03421 ( 1458) link_BETA1-6 : bond 0.02971 ( 6) link_BETA1-6 : angle 6.43799 ( 18) SS BOND : bond 0.00296 ( 21) SS BOND : angle 1.58261 ( 42) covalent geometry : bond 0.00367 (12231) covalent geometry : angle 0.82022 (16650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3896.71 seconds wall clock time: 69 minutes 11.62 seconds (4151.62 seconds total)