Starting phenix.real_space_refine on Thu Mar 5 22:01:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ugn_26490/03_2026/7ugn_26490_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugn_26490/03_2026/7ugn_26490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ugn_26490/03_2026/7ugn_26490_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugn_26490/03_2026/7ugn_26490_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ugn_26490/03_2026/7ugn_26490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugn_26490/03_2026/7ugn_26490.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 153 5.16 5 C 16083 2.51 5 N 4329 2.21 5 O 5133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25698 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3552 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 426} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3552 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 426} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3552 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 426} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 778 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "K" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 778 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 778 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "M" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "N" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "O" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "Q" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.74, per 1000 atoms: 0.22 Number of scatterers: 25698 At special positions: 0 Unit cell: (151.445, 162.695, 157.503, 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 153 16.00 O 5133 8.00 N 4329 7.00 C 16083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM25461 O5 NAG p 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM25461 O5 NAG p 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-3 " BMA U 3 " - " MAN U 4 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 5 " " MAN X 6 " - " MAN X 7 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 6 " " MAN f 4 " - " MAN f 5 " " MAN f 6 " - " MAN Q 201 " " BMA k 3 " - " MAN k 4 " " BMA n 3 " - " MAN n 4 " " MAN n 4 " - " MAN n 5 " " MAN n 6 " - " MAN n 7 " ALPHA1-6 " BMA U 3 " - " MAN U 5 " " BMA X 3 " - " MAN X 6 " " BMA c 3 " - " MAN c 5 " " BMA f 3 " - " MAN f 4 " " BMA k 3 " - " MAN k 5 " " BMA n 3 " - " MAN n 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " 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 X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " 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 h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " 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 n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 392 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 133 " " NAG B 603 " - " ASN B 160 " " NAG B 604 " - " ASN B 392 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG E 701 " - " ASN E 637 " " NAG F 701 " - " ASN F 637 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 234 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN A 363 " " NAG a 1 " - " ASN B 156 " " NAG b 1 " - " ASN B 234 " " NAG c 1 " - " ASN B 262 " " NAG d 1 " - " ASN B 295 " " NAG e 1 " - " ASN B 301 " " NAG f 1 " - " ASN B 332 " " NAG g 1 " - " ASN B 363 " " NAG i 1 " - " ASN C 156 " " NAG j 1 " - " ASN C 234 " " NAG k 1 " - " ASN C 262 " " NAG l 1 " - " ASN C 295 " " NAG m 1 " - " ASN C 301 " " NAG n 1 " - " ASN C 332 " " NAG o 1 " - " ASN C 363 " " NAG p 1 " - " ASN C 448 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5790 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 64 sheets defined 13.0% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.621A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.868A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.565A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.700A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.623A pdb=" N THR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.926A pdb=" N LEU B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 126' Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.569A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 removed outlier: 3.693A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.619A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.565A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.681A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.751A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 574 removed outlier: 3.556A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 595 removed outlier: 3.975A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.691A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 574 removed outlier: 3.564A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 595 removed outlier: 3.974A pdb=" N ARG E 579 " --> pdb=" O GLN E 575 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E 581 " --> pdb=" O GLN E 577 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 588 " --> pdb=" O GLU E 584 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.738A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 574 removed outlier: 3.558A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 595 removed outlier: 3.993A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.533A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 662 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.760A pdb=" N ASP G 86 " --> pdb=" O ARG G 83 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.773A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.766A pdb=" N ASP I 86 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'L' and resid 30 through 34 removed outlier: 3.820A pdb=" N ASN L 33 " --> pdb=" O GLY L 30 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR L 34 " --> pdb=" O GLY L 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 30 through 34' Processing helix chain 'M' and resid 61 through 64 removed outlier: 4.141A pdb=" N ASN M 64 " --> pdb=" O PRO M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 83 through 87 removed outlier: 4.113A pdb=" N THR M 87 " --> pdb=" O PRO M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 64 removed outlier: 4.174A pdb=" N ASN N 64 " --> pdb=" O PRO N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 64' Processing helix chain 'N' and resid 83 through 87 removed outlier: 4.064A pdb=" N THR N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 removed outlier: 4.017A pdb=" N ASN O 64 " --> pdb=" O PRO O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.831A pdb=" N THR O 87 " --> pdb=" O PRO O 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 495 removed outlier: 3.550A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR D 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.877A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.096A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.582A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.811A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 307 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'B' and resid 494 through 495 removed outlier: 3.538A pdb=" N GLY B 495 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.876A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 75 through 76 removed outlier: 7.119A pdb=" N CYS B 54 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.585A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AB7, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'B' and resid 271 through 273 Processing sheet with id=AB9, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.825A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 304 through 307 Processing sheet with id=AC2, first strand: chain 'B' and resid 423 through 424 Processing sheet with id=AC3, first strand: chain 'C' and resid 494 through 495 removed outlier: 3.535A pdb=" N GLY C 495 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 494 through 495 removed outlier: 3.535A pdb=" N GLY C 495 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR F 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.861A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 75 through 76 removed outlier: 7.121A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.607A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AC9, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AD1, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.627A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AD3, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.806A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AD5, first strand: chain 'G' and resid 9 through 10 removed outlier: 3.850A pdb=" N GLU G 10 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 9 through 10 removed outlier: 3.850A pdb=" N GLU G 10 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE G 102 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AD8, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.710A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE H 102 " --> pdb=" O THR H 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.710A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 9 through 10 removed outlier: 3.863A pdb=" N GLU I 10 " --> pdb=" O MET I 108 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 9 through 10 removed outlier: 3.863A pdb=" N GLU I 10 " --> pdb=" O MET I 108 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE I 102 " --> pdb=" O THR I 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AE5, first strand: chain 'J' and resid 18 through 22 Processing sheet with id=AE6, first strand: chain 'J' and resid 47 through 48 Processing sheet with id=AE7, first strand: chain 'K' and resid 18 through 22 Processing sheet with id=AE8, first strand: chain 'K' and resid 47 through 48 Processing sheet with id=AE9, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AF1, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AF2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'M' and resid 58 through 59 removed outlier: 4.168A pdb=" N THR M 58 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR M 50 " --> pdb=" O THR M 58 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 95 through 100A Processing sheet with id=AF6, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AF8, first strand: chain 'N' and resid 58 through 59 removed outlier: 4.150A pdb=" N THR N 58 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR N 50 " --> pdb=" O THR N 58 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 95 through 100A Processing sheet with id=AG1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.689A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'O' and resid 58 through 59 removed outlier: 4.175A pdb=" N THR O 58 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR O 50 " --> pdb=" O THR O 58 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 95 through 100A Processing sheet with id=AG5, first strand: chain 'P' and resid 9 through 14 removed outlier: 6.449A pdb=" N ARG P 9 " --> pdb=" O ARG P 103 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR P 105 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU P 107 " --> pdb=" O LEU P 11 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL P 13 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR P 102 " --> pdb=" O TYR P 86 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR P 86 " --> pdb=" O THR P 102 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 19 through 22 Processing sheet with id=AG7, first strand: chain 'Q' and resid 9 through 14 removed outlier: 6.419A pdb=" N ARG Q 9 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N THR Q 105 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU Q 107 " --> pdb=" O LEU Q 11 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL Q 13 " --> pdb=" O LEU Q 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR Q 102 " --> pdb=" O TYR Q 86 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR Q 86 " --> pdb=" O THR Q 102 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id=AG9, first strand: chain 'R' and resid 9 through 14 removed outlier: 6.450A pdb=" N ARG R 9 " --> pdb=" O ARG R 103 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR R 105 " --> pdb=" O ARG R 9 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU R 107 " --> pdb=" O LEU R 11 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL R 13 " --> pdb=" O LEU R 107 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR R 102 " --> pdb=" O TYR R 86 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR R 86 " --> pdb=" O THR R 102 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'R' and resid 19 through 22 729 hydrogen bonds defined for protein. 1857 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: 4.81 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8146 1.34 - 1.47: 6752 1.47 - 1.59: 11124 1.59 - 1.71: 0 1.71 - 1.84: 216 Bond restraints: 26238 Sorted by residual: bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.18e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" C1 NAG F 701 " pdb=" O5 NAG F 701 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C LYS B 117 " pdb=" N PRO B 118 " ideal model delta sigma weight residual 1.332 1.353 -0.020 8.90e-03 1.26e+04 5.20e+00 bond pdb=" N ASN C 448 " pdb=" CA ASN C 448 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.19e-02 7.06e+03 5.17e+00 ... (remaining 26233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 34990 2.10 - 4.20: 532 4.20 - 6.30: 88 6.30 - 8.40: 12 8.40 - 10.50: 6 Bond angle restraints: 35628 Sorted by residual: angle pdb=" C ARG Q 54 " pdb=" N PRO Q 55 " pdb=" CA PRO Q 55 " ideal model delta sigma weight residual 120.03 129.59 -9.56 9.90e-01 1.02e+00 9.32e+01 angle pdb=" C ARG R 54 " pdb=" N PRO R 55 " pdb=" CA PRO R 55 " ideal model delta sigma weight residual 120.03 128.29 -8.26 9.90e-01 1.02e+00 6.95e+01 angle pdb=" C ARG P 54 " pdb=" N PRO P 55 " pdb=" CA PRO P 55 " ideal model delta sigma weight residual 119.05 126.27 -7.22 1.11e+00 8.12e-01 4.24e+01 angle pdb=" N ASP Q 53 " pdb=" CA ASP Q 53 " pdb=" C ASP Q 53 " ideal model delta sigma weight residual 110.50 116.16 -5.66 1.41e+00 5.03e-01 1.61e+01 angle pdb=" N ASP P 53 " pdb=" CA ASP P 53 " pdb=" C ASP P 53 " ideal model delta sigma weight residual 109.23 115.16 -5.93 1.55e+00 4.16e-01 1.46e+01 ... (remaining 35623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.92: 15978 25.92 - 51.83: 574 51.83 - 77.75: 80 77.75 - 103.66: 70 103.66 - 129.58: 44 Dihedral angle restraints: 16746 sinusoidal: 7704 harmonic: 9042 Sorted by residual: dihedral pdb=" CA ARG Q 54 " pdb=" C ARG Q 54 " pdb=" N PRO Q 55 " pdb=" CA PRO Q 55 " ideal model delta harmonic sigma weight residual -180.00 -50.42 -129.58 0 5.00e+00 4.00e-02 6.72e+02 dihedral pdb=" CA ARG R 54 " pdb=" C ARG R 54 " pdb=" N PRO R 55 " pdb=" CA PRO R 55 " ideal model delta harmonic sigma weight residual -180.00 -54.04 -125.96 0 5.00e+00 4.00e-02 6.35e+02 dihedral pdb=" CB CYS Q 23 " pdb=" SG CYS Q 23 " pdb=" SG CYS Q 88 " pdb=" CB CYS Q 88 " ideal model delta sinusoidal sigma weight residual -86.00 0.36 -86.36 1 1.00e+01 1.00e-02 8.99e+01 ... (remaining 16743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.943: 4176 0.943 - 1.887: 9 1.887 - 2.830: 11 2.830 - 3.773: 4 3.773 - 4.716: 1 Chirality restraints: 4201 Sorted by residual: chirality pdb=" C1 MAN n 6 " pdb=" O6 BMA n 3 " pdb=" C2 MAN n 6 " pdb=" O5 MAN n 6 " both_signs ideal model delta sigma weight residual False 2.40 -0.72 3.12 2.00e-02 2.50e+03 2.44e+04 chirality pdb=" C1 NAG o 2 " pdb=" O4 NAG o 1 " pdb=" C2 NAG o 2 " pdb=" O5 NAG o 2 " both_signs ideal model delta sigma weight residual False -2.40 0.53 -2.93 2.00e-02 2.50e+03 2.15e+04 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 0.49 -2.89 2.00e-02 2.50e+03 2.08e+04 ... (remaining 4198 not shown) Planarity restraints: 4465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " -0.346 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG p 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " -0.155 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 448 " -0.209 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN C 448 " -0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN C 448 " 0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN C 448 " -0.357 2.00e-02 2.50e+03 pdb=" C1 NAG p 1 " 0.455 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 2 " -0.175 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" C7 NAG p 2 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG p 2 " -0.128 2.00e-02 2.50e+03 pdb=" N2 NAG p 2 " 0.235 2.00e-02 2.50e+03 pdb=" O7 NAG p 2 " 0.021 2.00e-02 2.50e+03 ... (remaining 4462 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.66: 5 1.66 - 2.47: 97 2.47 - 3.28: 25424 3.28 - 4.09: 56942 4.09 - 4.90: 104982 Warning: very small nonbonded interaction distances. Nonbonded interactions: 187450 Sorted by model distance: nonbonded pdb=" CE1 TYR R 49 " pdb=" OD2 ASP R 53 " model vdw 0.844 3.340 nonbonded pdb=" CZ TYR R 49 " pdb=" OD2 ASP R 53 " model vdw 1.292 3.260 nonbonded pdb=" ND2 ASN C 448 " pdb=" C5 NAG p 1 " model vdw 1.337 2.840 nonbonded pdb=" CZ TYR Q 49 " pdb=" OD2 ASP Q 53 " model vdw 1.528 3.260 nonbonded pdb=" CE1 TYR Q 49 " pdb=" OD2 ASP Q 53 " model vdw 1.542 3.340 ... (remaining 187445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = (chain 'Q' and resid 8 through 108) selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'U' selection = chain 'c' selection = chain 'k' } ncs_group { reference = (chain 'X' and (resid 2 or resid 5 through 7)) selection = (chain 'f' and (resid 1 or resid 4 through 6)) selection = (chain 'n' and (resid 2 or resid 5 through 7)) } 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 individual isotropic 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.420 Find NCS groups from input model: 0.590 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.370 26366 Z= 0.307 Angle : 1.733 56.928 35967 Z= 0.632 Chirality : 0.185 4.716 4201 Planarity : 0.006 0.297 4428 Dihedral : 15.930 129.579 10830 Min Nonbonded Distance : 0.844 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.11 % Allowed : 4.55 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.13), residues: 3090 helix: -2.08 (0.24), residues: 357 sheet: -1.51 (0.15), residues: 1038 loop : -2.96 (0.12), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.010 0.001 TYR E 586 PHE 0.008 0.001 PHE C 383 TRP 0.010 0.001 TRP I 50 HIS 0.002 0.000 HIS P 89 Details of bonding type rmsd covalent geometry : bond 0.00362 (26238) covalent geometry : angle 0.65405 (35628) SS BOND : bond 0.00313 ( 42) SS BOND : angle 0.99747 ( 84) hydrogen bonds : bond 0.11618 ( 709) hydrogen bonds : angle 5.12952 ( 1857) Misc. bond : bond 0.27674 ( 1) link_ALPHA1-3 : bond 0.12238 ( 12) link_ALPHA1-3 : angle 31.05128 ( 36) link_ALPHA1-6 : bond 0.06484 ( 6) link_ALPHA1-6 : angle 29.83549 ( 18) link_BETA1-4 : bond 0.06399 ( 30) link_BETA1-4 : angle 19.84960 ( 90) link_NAG-ASN : bond 0.00871 ( 37) link_NAG-ASN : angle 7.66089 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 520 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7659 (tp30) cc_final: 0.7421 (tp30) REVERT: D 588 ARG cc_start: 0.7589 (tpp80) cc_final: 0.7284 (ttm-80) REVERT: D 664 ASP cc_start: 0.6167 (m-30) cc_final: 0.5592 (p0) REVERT: E 664 ASP cc_start: 0.6577 (m-30) cc_final: 0.6164 (p0) REVERT: F 588 ARG cc_start: 0.7512 (tpp80) cc_final: 0.7251 (ttm-80) REVERT: F 664 ASP cc_start: 0.6390 (m-30) cc_final: 0.6074 (p0) REVERT: I 61 GLN cc_start: 0.8028 (tp40) cc_final: 0.7610 (tm-30) REVERT: J 55 LYS cc_start: 0.7275 (mptt) cc_final: 0.7074 (mptt) REVERT: J 88 TYR cc_start: 0.7941 (m-80) cc_final: 0.7686 (m-80) REVERT: K 55 LYS cc_start: 0.7403 (mptt) cc_final: 0.7150 (mptt) REVERT: L 52 ASP cc_start: 0.7347 (m-30) cc_final: 0.6924 (m-30) REVERT: L 55 LYS cc_start: 0.7340 (mptt) cc_final: 0.6594 (mptt) REVERT: L 88 TYR cc_start: 0.8289 (m-80) cc_final: 0.8051 (m-80) REVERT: M 101 ASP cc_start: 0.7885 (p0) cc_final: 0.7573 (p0) REVERT: N 51 ILE cc_start: 0.8164 (tp) cc_final: 0.7934 (tp) REVERT: O 51 ILE cc_start: 0.8098 (tp) cc_final: 0.7700 (tp) REVERT: R 34 GLN cc_start: 0.8359 (mp-120) cc_final: 0.8005 (mp10) REVERT: R 85 ASP cc_start: 0.7032 (m-30) cc_final: 0.6356 (m-30) outliers start: 3 outliers final: 2 residues processed: 523 average time/residue: 0.1924 time to fit residues: 152.4066 Evaluate side-chains 370 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 368 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain P residue 58 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 258 GLN A 280 ASN B 103 GLN B 258 GLN C 103 GLN C 258 GLN C 280 ASN D 543 ASN D 650 GLN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 650 GLN F 543 ASN F 650 GLN H 105 GLN I 1 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN J 6 GLN J 16 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS K 6 GLN K 16 GLN L 6 GLN L 16 GLN M 64 ASN M 82AASN M 99 GLN N 99 GLN O 64 ASN O 99 GLN P 52 GLN P 66CASN Q 66CASN R 37 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.082240 restraints weight = 49868.158| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.12 r_work: 0.2889 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 26366 Z= 0.311 Angle : 0.830 18.780 35967 Z= 0.387 Chirality : 0.055 1.022 4201 Planarity : 0.005 0.081 4428 Dihedral : 13.286 111.228 5187 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.76 % Favored : 93.17 % Rotamer: Outliers : 2.44 % Allowed : 13.60 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.13), residues: 3090 helix: -1.58 (0.25), residues: 342 sheet: -1.12 (0.16), residues: 975 loop : -2.65 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 469 TYR 0.028 0.002 TYR R 49 PHE 0.030 0.003 PHE A 383 TRP 0.023 0.002 TRP A 35 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00751 (26238) covalent geometry : angle 0.78543 (35628) SS BOND : bond 0.00528 ( 42) SS BOND : angle 1.97031 ( 84) hydrogen bonds : bond 0.05556 ( 709) hydrogen bonds : angle 5.05215 ( 1857) Misc. bond : bond 0.00582 ( 1) link_ALPHA1-3 : bond 0.01066 ( 12) link_ALPHA1-3 : angle 4.44144 ( 36) link_ALPHA1-6 : bond 0.01533 ( 6) link_ALPHA1-6 : angle 2.60545 ( 18) link_BETA1-4 : bond 0.00623 ( 30) link_BETA1-4 : angle 2.49348 ( 90) link_NAG-ASN : bond 0.00919 ( 37) link_NAG-ASN : angle 3.10596 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 371 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 588 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8121 (ttm-80) REVERT: E 588 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.8161 (mtt-85) REVERT: E 658 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8320 (tm-30) REVERT: F 588 ARG cc_start: 0.8373 (tpp80) cc_final: 0.8017 (ttm-80) REVERT: F 658 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8340 (tm-30) REVERT: G 97 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8300 (pm20) REVERT: I 61 GLN cc_start: 0.8432 (tp40) cc_final: 0.7702 (tm-30) REVERT: J 52 ASP cc_start: 0.7553 (m-30) cc_final: 0.7347 (m-30) REVERT: L 49 MET cc_start: 0.8210 (mmm) cc_final: 0.7698 (mpp) REVERT: L 55 LYS cc_start: 0.7509 (mptt) cc_final: 0.7193 (mptt) REVERT: O 29 MET cc_start: 0.4987 (tmm) cc_final: 0.3523 (mmp) REVERT: O 75 LYS cc_start: 0.7880 (tppt) cc_final: 0.7603 (tptp) REVERT: O 81 LYS cc_start: 0.7225 (mmtp) cc_final: 0.6909 (mmtt) outliers start: 66 outliers final: 43 residues processed: 420 average time/residue: 0.1814 time to fit residues: 117.8592 Evaluate side-chains 385 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 342 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain Q residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 268 optimal weight: 4.9990 chunk 237 optimal weight: 7.9990 chunk 280 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 203 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 411 ASN C 105 HIS C 411 ASN D 543 ASN D 625 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN F 625 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS K 41 HIS M 64 ASN M 99 GLN N 99 GLN O 99 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.127169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.083520 restraints weight = 49505.745| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.38 r_work: 0.2888 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26366 Z= 0.193 Angle : 0.694 12.969 35967 Z= 0.329 Chirality : 0.049 0.826 4201 Planarity : 0.004 0.104 4428 Dihedral : 11.207 106.581 5185 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.10 % Allowed : 15.96 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.14), residues: 3090 helix: -1.14 (0.27), residues: 342 sheet: -0.93 (0.15), residues: 1029 loop : -2.45 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 542 TYR 0.027 0.001 TYR L 51 PHE 0.019 0.001 PHE C 383 TRP 0.016 0.001 TRP H 50 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00467 (26238) covalent geometry : angle 0.65685 (35628) SS BOND : bond 0.00576 ( 42) SS BOND : angle 1.43644 ( 84) hydrogen bonds : bond 0.04503 ( 709) hydrogen bonds : angle 4.79820 ( 1857) Misc. bond : bond 0.00094 ( 1) link_ALPHA1-3 : bond 0.00884 ( 12) link_ALPHA1-3 : angle 3.86474 ( 36) link_ALPHA1-6 : bond 0.00914 ( 6) link_ALPHA1-6 : angle 1.66432 ( 18) link_BETA1-4 : bond 0.00447 ( 30) link_BETA1-4 : angle 1.97052 ( 90) link_NAG-ASN : bond 0.00407 ( 37) link_NAG-ASN : angle 2.74984 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 367 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 411 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7829 (p0) REVERT: C 35 TRP cc_start: 0.7963 (m-10) cc_final: 0.7626 (m-10) REVERT: C 205 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7885 (m) REVERT: D 588 ARG cc_start: 0.8547 (tpp80) cc_final: 0.8147 (ttm-80) REVERT: F 588 ARG cc_start: 0.8393 (tpp80) cc_final: 0.7976 (ttm-80) REVERT: F 658 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8360 (tm-30) REVERT: G 97 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: H 48 MET cc_start: 0.8128 (mtm) cc_final: 0.7840 (mtm) REVERT: H 61 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: J 88 TYR cc_start: 0.8037 (m-80) cc_final: 0.7633 (m-80) REVERT: L 49 MET cc_start: 0.8325 (mmm) cc_final: 0.7892 (mpp) REVERT: M 75 LYS cc_start: 0.8598 (tppp) cc_final: 0.8319 (pttt) REVERT: M 91 TYR cc_start: 0.8734 (m-80) cc_final: 0.8400 (m-80) REVERT: N 51 ILE cc_start: 0.8479 (tp) cc_final: 0.8219 (tp) REVERT: N 81 LYS cc_start: 0.7578 (mttm) cc_final: 0.7320 (mmtp) REVERT: O 29 MET cc_start: 0.4944 (tmm) cc_final: 0.3593 (mmp) REVERT: O 51 ILE cc_start: 0.8523 (tp) cc_final: 0.8289 (tp) REVERT: O 75 LYS cc_start: 0.7887 (tppt) cc_final: 0.7636 (tptp) outliers start: 84 outliers final: 54 residues processed: 426 average time/residue: 0.1825 time to fit residues: 120.4131 Evaluate side-chains 399 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 341 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain Q residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 179 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 135 optimal weight: 0.0000 chunk 18 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 286 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 295 optimal weight: 9.9990 overall best weight: 2.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN B 103 GLN B 280 ASN B 411 ASN D 543 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS K 41 HIS M 64 ASN M 99 GLN N 82AASN N 99 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.127036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.083413 restraints weight = 49644.386| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.39 r_work: 0.2889 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26366 Z= 0.180 Angle : 0.671 13.119 35967 Z= 0.320 Chirality : 0.048 0.757 4201 Planarity : 0.004 0.104 4428 Dihedral : 10.217 103.287 5185 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.18 % Favored : 93.79 % Rotamer: Outliers : 4.21 % Allowed : 16.59 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.14), residues: 3090 helix: -0.95 (0.27), residues: 342 sheet: -0.82 (0.15), residues: 1029 loop : -2.33 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 542 TYR 0.028 0.001 TYR L 51 PHE 0.018 0.001 PHE C 383 TRP 0.015 0.001 TRP H 50 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00433 (26238) covalent geometry : angle 0.63627 (35628) SS BOND : bond 0.00512 ( 42) SS BOND : angle 1.50790 ( 84) hydrogen bonds : bond 0.04351 ( 709) hydrogen bonds : angle 4.73650 ( 1857) Misc. bond : bond 0.00081 ( 1) link_ALPHA1-3 : bond 0.00745 ( 12) link_ALPHA1-3 : angle 3.34520 ( 36) link_ALPHA1-6 : bond 0.00799 ( 6) link_ALPHA1-6 : angle 1.73296 ( 18) link_BETA1-4 : bond 0.00345 ( 30) link_BETA1-4 : angle 1.88187 ( 90) link_NAG-ASN : bond 0.00475 ( 37) link_NAG-ASN : angle 2.69526 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 358 time to evaluate : 1.117 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: D 588 ARG cc_start: 0.8472 (tpp80) cc_final: 0.8030 (ttm-80) REVERT: F 588 ARG cc_start: 0.8360 (tpp80) cc_final: 0.7904 (ttm-80) REVERT: F 658 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8310 (tm-30) REVERT: H 48 MET cc_start: 0.8104 (mtm) cc_final: 0.7775 (mtm) REVERT: H 61 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: I 61 GLN cc_start: 0.8449 (tm-30) cc_final: 0.7630 (tm-30) REVERT: K 49 MET cc_start: 0.8031 (mmm) cc_final: 0.7400 (mpp) REVERT: L 49 MET cc_start: 0.8376 (mmm) cc_final: 0.7901 (mpp) REVERT: M 75 LYS cc_start: 0.8586 (tppp) cc_final: 0.8360 (pttt) REVERT: M 81 LYS cc_start: 0.7829 (mttm) cc_final: 0.7610 (mmtp) REVERT: M 91 TYR cc_start: 0.8715 (m-80) cc_final: 0.8478 (m-80) REVERT: N 51 ILE cc_start: 0.8478 (tp) cc_final: 0.8227 (tp) REVERT: N 81 LYS cc_start: 0.7571 (mttm) cc_final: 0.7322 (mmtp) REVERT: O 75 LYS cc_start: 0.7871 (tppt) cc_final: 0.7643 (tptp) outliers start: 114 outliers final: 83 residues processed: 444 average time/residue: 0.1688 time to fit residues: 118.7899 Evaluate side-chains 424 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 340 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 37 ILE Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 65 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN D 543 ASN D 625 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS K 41 HIS M 64 ASN M 99 GLN N 99 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.126120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.082817 restraints weight = 49513.980| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.35 r_work: 0.2869 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26366 Z= 0.217 Angle : 0.700 13.226 35967 Z= 0.334 Chirality : 0.049 0.745 4201 Planarity : 0.005 0.100 4428 Dihedral : 10.003 101.211 5185 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.92 % Rotamer: Outliers : 4.40 % Allowed : 17.48 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.14), residues: 3090 helix: -0.97 (0.27), residues: 342 sheet: -0.74 (0.15), residues: 1026 loop : -2.31 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 103 TYR 0.027 0.001 TYR L 51 PHE 0.021 0.002 PHE C 383 TRP 0.015 0.001 TRP H 50 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00526 (26238) covalent geometry : angle 0.66630 (35628) SS BOND : bond 0.00509 ( 42) SS BOND : angle 1.49829 ( 84) hydrogen bonds : bond 0.04637 ( 709) hydrogen bonds : angle 4.78935 ( 1857) Misc. bond : bond 0.00112 ( 1) link_ALPHA1-3 : bond 0.00670 ( 12) link_ALPHA1-3 : angle 3.15448 ( 36) link_ALPHA1-6 : bond 0.00642 ( 6) link_ALPHA1-6 : angle 1.82624 ( 18) link_BETA1-4 : bond 0.00356 ( 30) link_BETA1-4 : angle 1.92375 ( 90) link_NAG-ASN : bond 0.00534 ( 37) link_NAG-ASN : angle 2.75915 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 355 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 CYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7952 (m) REVERT: D 588 ARG cc_start: 0.8496 (tpp80) cc_final: 0.8052 (ttm-80) REVERT: F 588 ARG cc_start: 0.8404 (tpp80) cc_final: 0.7940 (ttm-80) REVERT: F 658 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8322 (tm-30) REVERT: F 663 LEU cc_start: 0.8412 (mp) cc_final: 0.7959 (tt) REVERT: H 48 MET cc_start: 0.8159 (mtm) cc_final: 0.7899 (mtm) REVERT: H 61 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: I 61 GLN cc_start: 0.8471 (tm-30) cc_final: 0.7637 (tm-30) REVERT: J 88 TYR cc_start: 0.8019 (m-80) cc_final: 0.7635 (m-80) REVERT: L 49 MET cc_start: 0.8428 (mmm) cc_final: 0.7907 (mpp) REVERT: M 27 ASP cc_start: 0.4815 (m-30) cc_final: 0.4564 (m-30) REVERT: M 81 LYS cc_start: 0.7775 (mttm) cc_final: 0.7536 (mmtt) REVERT: M 91 TYR cc_start: 0.8746 (m-80) cc_final: 0.8543 (m-80) REVERT: N 51 ILE cc_start: 0.8526 (tp) cc_final: 0.8324 (tp) REVERT: O 75 LYS cc_start: 0.7864 (tppt) cc_final: 0.7631 (tptp) REVERT: Q 79 GLU cc_start: 0.6928 (pm20) cc_final: 0.6629 (pm20) REVERT: R 103 ARG cc_start: 0.6952 (mmm160) cc_final: 0.6541 (mmm160) outliers start: 119 outliers final: 97 residues processed: 451 average time/residue: 0.1758 time to fit residues: 124.9711 Evaluate side-chains 441 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 342 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 37 ILE Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 202 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 chunk 258 optimal weight: 0.0370 chunk 69 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 217 optimal weight: 8.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN C 280 ASN D 543 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS K 41 HIS M 64 ASN N 99 GLN P 26 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.124841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.080876 restraints weight = 49835.340| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.12 r_work: 0.2863 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 26366 Z= 0.272 Angle : 0.754 13.612 35967 Z= 0.360 Chirality : 0.050 0.765 4201 Planarity : 0.005 0.097 4428 Dihedral : 10.072 102.643 5185 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.61 % Favored : 92.36 % Rotamer: Outliers : 4.88 % Allowed : 18.55 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.14), residues: 3090 helix: -1.00 (0.27), residues: 342 sheet: -0.64 (0.16), residues: 1017 loop : -2.41 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 103 TYR 0.025 0.002 TYR J 51 PHE 0.025 0.002 PHE C 383 TRP 0.016 0.002 TRP H 50 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00656 (26238) covalent geometry : angle 0.71868 (35628) SS BOND : bond 0.00652 ( 42) SS BOND : angle 1.81288 ( 84) hydrogen bonds : bond 0.05117 ( 709) hydrogen bonds : angle 4.92391 ( 1857) Misc. bond : bond 0.00161 ( 1) link_ALPHA1-3 : bond 0.00688 ( 12) link_ALPHA1-3 : angle 3.08714 ( 36) link_ALPHA1-6 : bond 0.00541 ( 6) link_ALPHA1-6 : angle 1.90015 ( 18) link_BETA1-4 : bond 0.00385 ( 30) link_BETA1-4 : angle 2.07586 ( 90) link_NAG-ASN : bond 0.00637 ( 37) link_NAG-ASN : angle 2.92515 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 354 time to evaluate : 1.000 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: B 381 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7794 (mt-10) REVERT: D 588 ARG cc_start: 0.8467 (tpp80) cc_final: 0.8039 (ttm-80) REVERT: D 663 LEU cc_start: 0.8345 (mp) cc_final: 0.8087 (tt) REVERT: F 588 ARG cc_start: 0.8370 (tpp80) cc_final: 0.7903 (ttm-80) REVERT: F 663 LEU cc_start: 0.8371 (mp) cc_final: 0.7924 (tt) REVERT: G 98 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7522 (mm) REVERT: I 61 GLN cc_start: 0.8525 (tm-30) cc_final: 0.7673 (tm-30) REVERT: J 47 LYS cc_start: 0.7483 (pttp) cc_final: 0.7147 (pptt) REVERT: K 49 MET cc_start: 0.8080 (mmm) cc_final: 0.7564 (mpp) REVERT: M 27 ASP cc_start: 0.4851 (m-30) cc_final: 0.4547 (m-30) REVERT: O 43 LYS cc_start: 0.7660 (mtmm) cc_final: 0.7342 (pttm) REVERT: O 75 LYS cc_start: 0.7904 (tppt) cc_final: 0.7643 (tptp) REVERT: P 49 TYR cc_start: 0.8645 (p90) cc_final: 0.8246 (p90) REVERT: P 53 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8037 (p0) REVERT: P 58 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7912 (mp) REVERT: Q 79 GLU cc_start: 0.6928 (pm20) cc_final: 0.6652 (pm20) outliers start: 132 outliers final: 102 residues processed: 459 average time/residue: 0.1739 time to fit residues: 125.9098 Evaluate side-chains 442 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 337 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 37 ILE Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 8 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 19 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 300 optimal weight: 6.9990 chunk 268 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS K 41 HIS ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN M 99 GLN P 26 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.085593 restraints weight = 49240.657| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.32 r_work: 0.2917 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26366 Z= 0.106 Angle : 0.629 13.779 35967 Z= 0.300 Chirality : 0.046 0.642 4201 Planarity : 0.004 0.093 4428 Dihedral : 8.970 104.318 5184 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.70 % Allowed : 20.55 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.14), residues: 3090 helix: -0.91 (0.27), residues: 363 sheet: -0.55 (0.16), residues: 1053 loop : -2.10 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 103 TYR 0.029 0.001 TYR L 51 PHE 0.011 0.001 PHE A 53 TRP 0.015 0.001 TRP H 50 HIS 0.006 0.000 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00233 (26238) covalent geometry : angle 0.60048 (35628) SS BOND : bond 0.00453 ( 42) SS BOND : angle 1.00216 ( 84) hydrogen bonds : bond 0.03569 ( 709) hydrogen bonds : angle 4.51695 ( 1857) Misc. bond : bond 0.00114 ( 1) link_ALPHA1-3 : bond 0.00795 ( 12) link_ALPHA1-3 : angle 2.65657 ( 36) link_ALPHA1-6 : bond 0.00821 ( 6) link_ALPHA1-6 : angle 1.73020 ( 18) link_BETA1-4 : bond 0.00402 ( 30) link_BETA1-4 : angle 1.56299 ( 90) link_NAG-ASN : bond 0.00449 ( 37) link_NAG-ASN : angle 2.64517 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 387 time to evaluate : 1.163 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: D 588 ARG cc_start: 0.8525 (tpp80) cc_final: 0.8103 (ttm-80) REVERT: D 663 LEU cc_start: 0.8351 (mp) cc_final: 0.8083 (tt) REVERT: E 632 ASP cc_start: 0.9278 (t0) cc_final: 0.9061 (t0) REVERT: F 588 ARG cc_start: 0.8395 (tpp80) cc_final: 0.7942 (ttm-80) REVERT: F 663 LEU cc_start: 0.8336 (mp) cc_final: 0.7960 (tt) REVERT: G 98 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7075 (mm) REVERT: J 47 LYS cc_start: 0.7557 (pttp) cc_final: 0.7279 (pptt) REVERT: J 88 TYR cc_start: 0.7893 (m-80) cc_final: 0.7524 (m-80) REVERT: M 77 GLN cc_start: 0.7692 (mt0) cc_final: 0.7149 (pp30) REVERT: M 78 LEU cc_start: 0.8673 (pt) cc_final: 0.7834 (pt) REVERT: O 91 TYR cc_start: 0.8919 (m-80) cc_final: 0.8556 (m-80) REVERT: P 58 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7777 (mp) REVERT: Q 79 GLU cc_start: 0.7066 (pm20) cc_final: 0.6795 (pm20) REVERT: R 103 ARG cc_start: 0.6769 (mmm160) cc_final: 0.6333 (mmm160) outliers start: 100 outliers final: 70 residues processed: 463 average time/residue: 0.1747 time to fit residues: 126.9698 Evaluate side-chains 441 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 369 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 65 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 140 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 281 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 0.0870 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS K 41 HIS ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.084690 restraints weight = 49366.364| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.32 r_work: 0.2902 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26366 Z= 0.140 Angle : 0.653 13.479 35967 Z= 0.311 Chirality : 0.047 0.659 4201 Planarity : 0.004 0.093 4428 Dihedral : 8.855 104.613 5184 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.66 % Allowed : 20.77 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.14), residues: 3090 helix: -0.54 (0.28), residues: 345 sheet: -0.48 (0.16), residues: 1053 loop : -2.03 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 56 TYR 0.032 0.001 TYR J 51 PHE 0.013 0.001 PHE B 361 TRP 0.014 0.001 TRP H 50 HIS 0.002 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00331 (26238) covalent geometry : angle 0.62336 (35628) SS BOND : bond 0.00427 ( 42) SS BOND : angle 1.48347 ( 84) hydrogen bonds : bond 0.03878 ( 709) hydrogen bonds : angle 4.52563 ( 1857) Misc. bond : bond 0.00110 ( 1) link_ALPHA1-3 : bond 0.00679 ( 12) link_ALPHA1-3 : angle 2.65493 ( 36) link_ALPHA1-6 : bond 0.00670 ( 6) link_ALPHA1-6 : angle 1.66183 ( 18) link_BETA1-4 : bond 0.00334 ( 30) link_BETA1-4 : angle 1.69598 ( 90) link_NAG-ASN : bond 0.00434 ( 37) link_NAG-ASN : angle 2.61587 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 370 time to evaluate : 0.983 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: A 113 ASP cc_start: 0.9202 (t0) cc_final: 0.8907 (t0) REVERT: B 381 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7728 (mt-10) REVERT: D 588 ARG cc_start: 0.8507 (tpp80) cc_final: 0.8055 (ttm-80) REVERT: D 663 LEU cc_start: 0.8285 (mp) cc_final: 0.8039 (tt) REVERT: E 588 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8115 (mtt-85) REVERT: E 632 ASP cc_start: 0.9313 (t0) cc_final: 0.9101 (t0) REVERT: E 658 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8414 (tm-30) REVERT: F 588 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7910 (ttm-80) REVERT: F 663 LEU cc_start: 0.8344 (mp) cc_final: 0.7956 (tt) REVERT: G 98 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7037 (mm) REVERT: H 61 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: M 77 GLN cc_start: 0.7631 (mt0) cc_final: 0.7131 (pp30) REVERT: M 78 LEU cc_start: 0.8698 (pt) cc_final: 0.7875 (pt) REVERT: O 91 TYR cc_start: 0.8894 (m-80) cc_final: 0.8605 (m-80) REVERT: P 49 TYR cc_start: 0.8658 (p90) cc_final: 0.8260 (p90) REVERT: P 53 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8045 (p0) REVERT: P 58 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7727 (mp) REVERT: Q 79 GLU cc_start: 0.7042 (pm20) cc_final: 0.6774 (pm20) outliers start: 99 outliers final: 85 residues processed: 445 average time/residue: 0.1731 time to fit residues: 121.4869 Evaluate side-chains 451 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 362 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 305 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 chunk 262 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN C 280 ASN D 625 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS K 41 HIS ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN M 99 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.126511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.082898 restraints weight = 49440.243| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.09 r_work: 0.2898 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26366 Z= 0.158 Angle : 0.676 13.572 35967 Z= 0.322 Chirality : 0.047 0.669 4201 Planarity : 0.004 0.092 4428 Dihedral : 8.744 103.337 5184 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.62 % Allowed : 20.95 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.14), residues: 3090 helix: -0.52 (0.28), residues: 342 sheet: -0.33 (0.16), residues: 1023 loop : -2.04 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 103 TYR 0.021 0.001 TYR J 51 PHE 0.015 0.001 PHE C 383 TRP 0.013 0.001 TRP G 50 HIS 0.002 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00378 (26238) covalent geometry : angle 0.64583 (35628) SS BOND : bond 0.00455 ( 42) SS BOND : angle 1.54801 ( 84) hydrogen bonds : bond 0.04159 ( 709) hydrogen bonds : angle 4.57215 ( 1857) Misc. bond : bond 0.00138 ( 1) link_ALPHA1-3 : bond 0.00700 ( 12) link_ALPHA1-3 : angle 2.61934 ( 36) link_ALPHA1-6 : bond 0.00679 ( 6) link_ALPHA1-6 : angle 1.65118 ( 18) link_BETA1-4 : bond 0.00330 ( 30) link_BETA1-4 : angle 1.77576 ( 90) link_NAG-ASN : bond 0.00435 ( 37) link_NAG-ASN : angle 2.64784 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 363 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.9213 (t0) cc_final: 0.8934 (t0) REVERT: B 381 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7760 (mt-10) REVERT: C 205 CYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7736 (m) REVERT: D 588 ARG cc_start: 0.8452 (tpp80) cc_final: 0.8012 (ttm-80) REVERT: D 663 LEU cc_start: 0.8274 (mp) cc_final: 0.8036 (tt) REVERT: E 588 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8080 (mtt-85) REVERT: E 632 ASP cc_start: 0.9298 (t0) cc_final: 0.9092 (t0) REVERT: F 588 ARG cc_start: 0.8328 (tpp80) cc_final: 0.7878 (ttm-80) REVERT: F 663 LEU cc_start: 0.8362 (mp) cc_final: 0.7969 (tt) REVERT: G 98 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7125 (mm) REVERT: H 80 MET cc_start: 0.8694 (tmm) cc_final: 0.8424 (tmm) REVERT: M 77 GLN cc_start: 0.7626 (mt0) cc_final: 0.7162 (pp30) REVERT: M 78 LEU cc_start: 0.8785 (pt) cc_final: 0.7880 (pt) REVERT: O 91 TYR cc_start: 0.8921 (m-80) cc_final: 0.8479 (m-80) REVERT: P 49 TYR cc_start: 0.8691 (p90) cc_final: 0.8287 (p90) REVERT: P 53 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8063 (p0) REVERT: P 58 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7697 (mp) REVERT: Q 79 GLU cc_start: 0.7065 (pm20) cc_final: 0.6787 (pm20) REVERT: R 60 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7696 (tm-30) outliers start: 98 outliers final: 82 residues processed: 441 average time/residue: 0.1656 time to fit residues: 114.5661 Evaluate side-chains 441 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 355 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 37 GLN Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 65 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 41 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 271 optimal weight: 20.0000 chunk 204 optimal weight: 7.9990 chunk 99 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 283 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS K 41 HIS ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.127551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.091201 restraints weight = 49178.474| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.73 r_work: 0.2906 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26366 Z= 0.124 Angle : 0.647 13.483 35967 Z= 0.309 Chirality : 0.047 0.638 4201 Planarity : 0.004 0.092 4428 Dihedral : 8.760 105.939 5184 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.36 % Allowed : 20.92 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.14), residues: 3090 helix: -0.64 (0.28), residues: 363 sheet: -0.23 (0.16), residues: 1017 loop : -1.97 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 103 TYR 0.024 0.001 TYR J 51 PHE 0.011 0.001 PHE A 383 TRP 0.015 0.001 TRP H 50 HIS 0.002 0.000 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00288 (26238) covalent geometry : angle 0.61796 (35628) SS BOND : bond 0.00415 ( 42) SS BOND : angle 1.34551 ( 84) hydrogen bonds : bond 0.03796 ( 709) hydrogen bonds : angle 4.46214 ( 1857) Misc. bond : bond 0.00123 ( 1) link_ALPHA1-3 : bond 0.00759 ( 12) link_ALPHA1-3 : angle 2.45774 ( 36) link_ALPHA1-6 : bond 0.00746 ( 6) link_ALPHA1-6 : angle 1.53386 ( 18) link_BETA1-4 : bond 0.00357 ( 30) link_BETA1-4 : angle 1.66120 ( 90) link_NAG-ASN : bond 0.00453 ( 37) link_NAG-ASN : angle 2.66915 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 367 time to evaluate : 0.947 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: A 113 ASP cc_start: 0.9214 (t0) cc_final: 0.8947 (t0) REVERT: D 588 ARG cc_start: 0.8511 (tpp80) cc_final: 0.8091 (ttm-80) REVERT: D 663 LEU cc_start: 0.8236 (mp) cc_final: 0.8014 (tt) REVERT: E 588 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.8145 (mtt-85) REVERT: F 588 ARG cc_start: 0.8379 (tpp80) cc_final: 0.7946 (ttm-80) REVERT: F 663 LEU cc_start: 0.8313 (mp) cc_final: 0.7954 (tt) REVERT: G 98 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7130 (mm) REVERT: H 80 MET cc_start: 0.8690 (tmm) cc_final: 0.8433 (tmm) REVERT: I 80 MET cc_start: 0.8913 (tmm) cc_final: 0.8624 (tmm) REVERT: J 88 TYR cc_start: 0.7940 (m-80) cc_final: 0.7573 (m-80) REVERT: M 77 GLN cc_start: 0.7657 (mt0) cc_final: 0.7167 (pp30) REVERT: M 78 LEU cc_start: 0.8836 (pt) cc_final: 0.8025 (pt) REVERT: O 91 TYR cc_start: 0.8907 (m-80) cc_final: 0.8549 (m-80) REVERT: P 58 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7652 (mp) REVERT: Q 79 GLU cc_start: 0.7115 (pm20) cc_final: 0.6829 (pm20) REVERT: R 60 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7641 (tm-30) outliers start: 91 outliers final: 81 residues processed: 438 average time/residue: 0.1624 time to fit residues: 112.3356 Evaluate side-chains 441 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 358 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 37 ILE Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 37 GLN Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 65 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 143 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 237 optimal weight: 8.9990 chunk 249 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 282 optimal weight: 0.0370 chunk 80 optimal weight: 0.1980 overall best weight: 2.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN D 625 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS K 41 HIS M 64 ASN M 99 GLN P 26 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.082548 restraints weight = 49271.424| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.10 r_work: 0.2893 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26366 Z= 0.176 Angle : 0.688 13.509 35967 Z= 0.328 Chirality : 0.048 0.666 4201 Planarity : 0.004 0.092 4428 Dihedral : 8.990 111.039 5184 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.36 % Allowed : 21.14 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.14), residues: 3090 helix: -0.48 (0.28), residues: 342 sheet: -0.27 (0.16), residues: 1023 loop : -1.97 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 103 TYR 0.023 0.001 TYR J 51 PHE 0.017 0.001 PHE C 383 TRP 0.012 0.001 TRP H 50 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00424 (26238) covalent geometry : angle 0.65708 (35628) SS BOND : bond 0.00444 ( 42) SS BOND : angle 1.61094 ( 84) hydrogen bonds : bond 0.04271 ( 709) hydrogen bonds : angle 4.57359 ( 1857) Misc. bond : bond 0.00142 ( 1) link_ALPHA1-3 : bond 0.00649 ( 12) link_ALPHA1-3 : angle 2.52703 ( 36) link_ALPHA1-6 : bond 0.00643 ( 6) link_ALPHA1-6 : angle 1.60718 ( 18) link_BETA1-4 : bond 0.00334 ( 30) link_BETA1-4 : angle 1.83912 ( 90) link_NAG-ASN : bond 0.00570 ( 37) link_NAG-ASN : angle 2.76268 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6238.15 seconds wall clock time: 107 minutes 31.38 seconds (6451.38 seconds total)