Starting phenix.real_space_refine on Thu Mar 5 21:34:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ugo_26492/03_2026/7ugo_26492_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugo_26492/03_2026/7ugo_26492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ugo_26492/03_2026/7ugo_26492_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugo_26492/03_2026/7ugo_26492_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ugo_26492/03_2026/7ugo_26492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugo_26492/03_2026/7ugo_26492.map" } resolution = 4.1 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= 0.006 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 150 5.16 5 C 16029 2.51 5 N 4311 2.21 5 O 5100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 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: 25590 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3523 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 422} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3523 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 422} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3523 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 422} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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: "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: "G" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "H" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "K" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "L" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "h" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 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: "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: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'MAN': 1, 'NAG': 6} 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: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 106 Unusual residues: {'MAN': 2, 'NAG': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'MAN': 1, 'NAG': 6} 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: "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 Time building chain proxies: 5.95, per 1000 atoms: 0.23 Number of scatterers: 25590 At special positions: 0 Unit cell: (155.04, 164.16, 157.32, 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 150 16.00 O 5100 8.00 N 4311 7.00 C 16029 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=2.04 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=2.04 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=2.04 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 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=2.04 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 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=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " 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 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM25337 C1 MAN A 607 49.714 112.559 76.927 1.00133.36 C !!! !!! HETATM24496 C6 BMA S 3 49.574 111.401 76.960 1.00 80.71 C !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No oxygen atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Atom "HETATM25128 O5 MAN h 8 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-2 " MAN T 5 " - " MAN T 6 " " MAN X 1 " - " MAN X 2 " " MAN a 5 " - " MAN a 6 " " MAN e 1 " - " MAN e 2 " " MAN h 5 " - " MAN h 6 " " MAN h 8 " - " MAN h 9 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA a 3 " - " MAN e 1 " " MAN a 4 " - " MAN a 7 " " BMA g 3 " - " MAN g 4 " " BMA h 3 " - " MAN h 8 " " MAN h 4 " - " MAN h 7 " ALPHA1-6 " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 5 " " BMA a 3 " - " MAN a 4 " " MAN a 4 " - " MAN a 5 " " BMA g 3 " - " MAN C 606 " " BMA h 3 " - " MAN h 4 " " MAN h 4 " - " MAN h 5 " ALPHA2-6 " BMA Z 3 " - " MAN B 608 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 448 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 160 " " NAG A 606 " - " ASN A 133 " " NAG B 602 " - " ASN B 88 " " NAG B 603 " - " ASN B 234 " " NAG B 604 " - " ASN B 448 " " NAG B 605 " - " ASN B 392 " " NAG B 606 " - " ASN B 160 " " NAG B 607 " - " ASN B 133 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 448 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 133 " " NAG C 607 " - " ASN C 160 " " NAG D 701 " - " ASN D 637 " " NAG E 701 " - " ASN E 637 " " NAG F 701 " - " ASN F 637 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 363 " " NAG Y 1 " - " ASN A 156 " " NAG Z 1 " - " ASN B 262 " " NAG a 1 " - " ASN B 332 " " NAG b 1 " - " ASN B 301 " " NAG c 1 " - " ASN B 295 " " NAG d 1 " - " ASN B 363 " " NAG f 1 " - " ASN B 156 " " NAG g 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 332 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 295 " " NAG k 1 " - " ASN C 363 " " NAG l 1 " - " ASN C 156 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.0 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 52 sheets defined 14.1% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.557A pdb=" N GLN A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.815A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.560A pdb=" N GLN B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.828A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 127 " --> pdb=" O PRO B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'B' and resid 194 through 198 removed outlier: 4.129A pdb=" N ASN B 197 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.563A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.809A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 127' Processing helix chain 'C' and resid 194 through 198 removed outlier: 4.123A pdb=" N ASN C 197 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.676A pdb=" N SER C 481 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 535 through 537 No H-bonds generated for 'chain 'D' and resid 535 through 537' Processing helix chain 'D' and resid 538 through 543 removed outlier: 4.360A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 597 removed outlier: 3.514A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN D 590 " --> pdb=" O TYR D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 removed outlier: 3.572A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.574A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.576A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 535 through 537 No H-bonds generated for 'chain 'E' and resid 535 through 537' Processing helix chain 'E' and resid 538 through 543 removed outlier: 4.370A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 597 removed outlier: 3.509A pdb=" N ILE E 573 " --> pdb=" O THR E 569 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN E 575 " --> pdb=" O TRP E 571 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU E 587 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG E 588 " --> pdb=" O GLU E 584 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN E 590 " --> pdb=" O TYR E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 removed outlier: 3.624A pdb=" N ILE E 622 " --> pdb=" O ASN E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 removed outlier: 3.575A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 664 removed outlier: 3.590A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP E 664 " --> pdb=" O LEU E 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 535 through 541 removed outlier: 5.791A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 539 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 597 removed outlier: 3.521A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU F 587 " --> pdb=" O VAL F 583 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.621A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.567A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.797A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 4.153A pdb=" N THR M 87 " --> pdb=" O PRO M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 4.143A pdb=" N THR N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 100D through 100H removed outlier: 3.515A pdb=" N PHE N 100G" --> pdb=" O VAL N 100D" (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 removed outlier: 4.125A pdb=" N THR O 87 " --> pdb=" O PRO O 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'J' and resid 25 through 30 removed outlier: 3.683A pdb=" N VAL J 29 " --> pdb=" O THR J 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 30 Processing helix chain 'L' and resid 25 through 30 Processing sheet with id=AA1, first strand: chain 'A' and resid 496 through 499 removed outlier: 4.704A pdb=" N LEU A 34 " --> pdb=" O TRP D 610 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 36 " --> pdb=" O VAL D 608 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL D 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N VAL A 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR D 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.540A pdb=" N LYS A 46 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 245 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 132 removed outlier: 3.519A pdb=" N GLN A 130 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 158 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.881A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.716A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.069A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.121A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.015A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 298 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 469 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 307 Processing sheet with id=AA8, first strand: chain 'B' and resid 496 through 499 removed outlier: 4.606A pdb=" N LEU B 34 " --> pdb=" O TRP E 610 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 36 " --> pdb=" O VAL E 608 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL E 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N VAL B 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N THR E 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.560A pdb=" N LYS B 46 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 245 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 132 removed outlier: 3.514A pdb=" N GLN B 130 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 158 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AB3, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.866A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 317 through 322 removed outlier: 7.018A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE B 322 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN B 301 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 10.758A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.087A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 12.012A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 469 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 499 removed outlier: 4.701A pdb=" N LEU C 34 " --> pdb=" O TRP F 610 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.543A pdb=" N LYS C 46 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 245 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 130 through 133 removed outlier: 4.329A pdb=" N GLN C 130 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 158 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 182 through 183 Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.781A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.064A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.101A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 469 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AC2, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AC3, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.773A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.780A pdb=" N LEU M 78 " --> pdb=" O CYS M 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.020A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR M 50 " --> pdb=" O THR M 58 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR M 58 " --> pdb=" O TYR M 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.020A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'N' and resid 58 through 59 removed outlier: 4.652A pdb=" N THR N 58 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR N 50 " --> pdb=" O THR N 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE N 48 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 58 through 59 removed outlier: 4.652A pdb=" N THR N 58 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR N 50 " --> pdb=" O THR N 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE N 48 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 67 through 72 Processing sheet with id=AD2, first strand: chain 'O' and resid 3 through 7 removed outlier: 4.161A pdb=" N LEU O 78 " --> pdb=" O CYS O 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 11 through 12 removed outlier: 4.005A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE O 48 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR O 50 " --> pdb=" O THR O 58 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR O 58 " --> pdb=" O TYR O 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 11 through 12 removed outlier: 4.005A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.415A pdb=" N LEU P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 20 through 22 Processing sheet with id=AD7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.332A pdb=" N LEU Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 19 through 22 removed outlier: 3.534A pdb=" N ALA Q 19 " --> pdb=" O ILE Q 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.189A pdb=" N LEU R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 19 through 22 removed outlier: 3.574A pdb=" N ALA R 19 " --> pdb=" O ILE R 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 3 through 5 removed outlier: 4.406A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS G 22 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 3 through 5 removed outlier: 4.406A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS G 22 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.366A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 5 removed outlier: 4.453A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS H 22 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 3 through 5 removed outlier: 4.453A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS H 22 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.385A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 3 through 5 removed outlier: 4.421A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS I 22 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 5 removed outlier: 4.421A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS I 22 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.369A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 9 through 10 removed outlier: 6.222A pdb=" N GLN J 39 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 18 through 21 Processing sheet with id=AF4, first strand: chain 'K' and resid 9 through 10 removed outlier: 6.973A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 18 through 22 removed outlier: 3.528A pdb=" N CYS K 22 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA K 73 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.239A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 18 through 22 removed outlier: 3.527A pdb=" N CYS L 22 " --> pdb=" O ALA L 73 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA L 73 " --> pdb=" O CYS L 22 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 3.02 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: 8095 1.34 - 1.47: 6687 1.47 - 1.59: 11138 1.59 - 1.71: 0 1.71 - 1.83: 210 Bond restraints: 26130 Sorted by residual: bond pdb=" N SER C 158 " pdb=" CA SER C 158 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" N VAL A 172 " pdb=" CA VAL A 172 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.15e+01 bond pdb=" N GLN A 170 " pdb=" CA GLN A 170 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.21e-02 6.83e+03 7.66e+00 bond pdb=" N LYS A 171 " pdb=" CA LYS A 171 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.22e-02 6.72e+03 7.19e+00 bond pdb=" N PHE C 159 " pdb=" CA PHE C 159 " ideal model delta sigma weight residual 1.455 1.479 -0.025 1.29e-02 6.01e+03 3.72e+00 ... (remaining 26125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 34639 1.98 - 3.95: 753 3.95 - 5.93: 71 5.93 - 7.91: 13 7.91 - 9.88: 2 Bond angle restraints: 35478 Sorted by residual: angle pdb=" N ASN C 160 " pdb=" CA ASN C 160 " pdb=" C ASN C 160 " ideal model delta sigma weight residual 111.28 120.15 -8.87 1.09e+00 8.42e-01 6.63e+01 angle pdb=" N PHE C 159 " pdb=" CA PHE C 159 " pdb=" C PHE C 159 " ideal model delta sigma weight residual 109.24 119.12 -9.88 1.51e+00 4.39e-01 4.28e+01 angle pdb=" N ASP C 167 " pdb=" CA ASP C 167 " pdb=" C ASP C 167 " ideal model delta sigma weight residual 111.36 116.75 -5.39 1.09e+00 8.42e-01 2.44e+01 angle pdb=" CA SER C 158 " pdb=" C SER C 158 " pdb=" N PHE C 159 " ideal model delta sigma weight residual 116.29 122.70 -6.41 1.30e+00 5.92e-01 2.43e+01 angle pdb=" N LEU C 165 " pdb=" CA LEU C 165 " pdb=" C LEU C 165 " ideal model delta sigma weight residual 109.96 103.46 6.50 1.50e+00 4.44e-01 1.88e+01 ... (remaining 35473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 15701 24.08 - 48.16: 712 48.16 - 72.24: 148 72.24 - 96.32: 68 96.32 - 120.40: 48 Dihedral angle restraints: 16677 sinusoidal: 7677 harmonic: 9000 Sorted by residual: dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -158.09 72.09 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -157.36 71.36 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -157.16 71.16 1 1.00e+01 1.00e-02 6.50e+01 ... (remaining 16674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.944: 4164 0.944 - 1.887: 6 1.887 - 2.831: 4 2.831 - 3.774: 6 3.774 - 4.718: 7 Chirality restraints: 4187 Sorted by residual: chirality pdb=" C1 MAN e 2 " pdb=" O2 MAN e 1 " pdb=" C2 MAN e 2 " pdb=" O5 MAN e 2 " both_signs ideal model delta sigma weight residual False 2.40 -2.32 4.72 2.00e-02 2.50e+03 5.56e+04 chirality pdb=" C1 MAN h 9 " pdb=" O2 MAN h 8 " pdb=" C2 MAN h 9 " pdb=" O5 MAN h 9 " both_signs ideal model delta sigma weight residual False 2.40 -2.31 4.71 2.00e-02 2.50e+03 5.56e+04 chirality pdb=" C1 MAN g 4 " pdb=" O3 BMA g 3 " pdb=" C2 MAN g 4 " pdb=" O5 MAN g 4 " both_signs ideal model delta sigma weight residual False 2.40 -2.31 4.71 2.00e-02 2.50e+03 5.56e+04 ... (remaining 4184 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 607 " 0.248 2.00e-02 2.50e+03 2.07e-01 5.38e+02 pdb=" C7 NAG C 607 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG C 607 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG C 607 " -0.346 2.00e-02 2.50e+03 pdb=" O7 NAG C 607 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 160 " 0.150 2.00e-02 2.50e+03 1.59e-01 3.16e+02 pdb=" CG ASN C 160 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN C 160 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN C 160 " -0.249 2.00e-02 2.50e+03 pdb=" C1 NAG C 607 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 157 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C CYS C 157 " -0.038 2.00e-02 2.50e+03 pdb=" O CYS C 157 " 0.014 2.00e-02 2.50e+03 pdb=" N SER C 158 " 0.013 2.00e-02 2.50e+03 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.75: 7 1.75 - 2.54: 189 2.54 - 3.33: 28547 3.33 - 4.11: 54529 4.11 - 4.90: 96666 Warning: very small nonbonded interaction distances. Nonbonded interactions: 179938 Sorted by model distance: nonbonded pdb=" O2 MAN T 4 " pdb=" O5 MAN T 7 " model vdw 0.965 3.040 nonbonded pdb=" C6 BMA S 3 " pdb=" C1 MAN A 607 " model vdw 1.167 3.870 nonbonded pdb=" O2 MAN T 4 " pdb=" C1 MAN T 7 " model vdw 1.399 3.470 nonbonded pdb=" O3 MAN T 4 " pdb=" C2 MAN T 7 " model vdw 1.408 3.470 nonbonded pdb=" O3 MAN T 4 " pdb=" C1 MAN T 7 " model vdw 1.659 3.470 ... (remaining 179933 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 506 or resid 602 through 605)) selection = (chain 'B' and (resid 32 through 506 or resid 602 through 605)) selection = (chain 'C' and (resid 32 through 506 or resid 602 through 605)) } 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' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'g' } ncs_group { reference = chain 'T' selection = chain 'a' } ncs_group { reference = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'X' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.130 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.006 0.527 26257 Z= 0.427 Angle : 1.291 53.746 35811 Z= 0.506 Chirality : 0.250 4.718 4187 Planarity : 0.004 0.207 4401 Dihedral : 16.021 120.404 10785 Min Nonbonded Distance : 0.965 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % 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: -3.57 (0.13), residues: 3072 helix: -1.18 (0.27), residues: 342 sheet: -1.70 (0.15), residues: 984 loop : -3.15 (0.12), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 327 TYR 0.013 0.001 TYR K 51 PHE 0.007 0.001 PHE L 64 TRP 0.011 0.001 TRP A 45 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00374 (26130) covalent geometry : angle 0.63840 (35478) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.55145 ( 84) hydrogen bonds : bond 0.14995 ( 672) hydrogen bonds : angle 6.08125 ( 1845) Misc. bond : bond 0.37270 ( 2) link_ALPHA1-2 : bond 0.02648 ( 6) link_ALPHA1-2 : angle 4.33815 ( 18) link_ALPHA1-3 : bond 0.18932 ( 6) link_ALPHA1-3 : angle 24.91908 ( 18) link_ALPHA1-6 : bond 0.06129 ( 7) link_ALPHA1-6 : angle 15.23587 ( 21) link_ALPHA2-6 : bond 0.25234 ( 1) link_ALPHA2-6 : angle 21.20524 ( 3) link_BETA1-4 : bond 0.06213 ( 24) link_BETA1-4 : angle 19.21223 ( 72) link_NAG-ASN : bond 0.01384 ( 39) link_NAG-ASN : angle 2.48052 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 722 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 161 MET cc_start: 0.8721 (tpp) cc_final: 0.8065 (tpt) REVERT: A 195 ASN cc_start: 0.7842 (p0) cc_final: 0.7319 (p0) REVERT: B 125 LEU cc_start: 0.9289 (tp) cc_final: 0.9044 (tp) REVERT: B 161 MET cc_start: 0.8806 (tpp) cc_final: 0.8471 (tpp) REVERT: B 474 ASP cc_start: 0.7695 (p0) cc_final: 0.7402 (p0) REVERT: C 125 LEU cc_start: 0.9289 (tp) cc_final: 0.9004 (tp) REVERT: C 475 MET cc_start: 0.8292 (ptt) cc_final: 0.8078 (ptt) REVERT: D 630 GLN cc_start: 0.7875 (pt0) cc_final: 0.7596 (pt0) REVERT: E 540 GLN cc_start: 0.8428 (mp10) cc_final: 0.8214 (mp10) REVERT: F 540 GLN cc_start: 0.8531 (mp10) cc_final: 0.8079 (mp10) REVERT: F 542 ARG cc_start: 0.8464 (ptt-90) cc_final: 0.8256 (ptt90) REVERT: F 653 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7640 (mt0) REVERT: M 29 MET cc_start: 0.4488 (pmm) cc_final: 0.4264 (pmm) REVERT: M 91 TYR cc_start: 0.7262 (m-80) cc_final: 0.6958 (m-10) REVERT: M 100 MET cc_start: 0.7749 (mpp) cc_final: 0.7520 (mtm) REVERT: M 103 TRP cc_start: 0.8169 (m100) cc_final: 0.7878 (m-10) REVERT: N 21 THR cc_start: 0.8763 (m) cc_final: 0.8472 (t) REVERT: N 29 MET cc_start: 0.4731 (pmm) cc_final: 0.4360 (pmm) REVERT: N 91 TYR cc_start: 0.7416 (m-80) cc_final: 0.7059 (m-10) REVERT: N 96 ARG cc_start: 0.9050 (ttp-110) cc_final: 0.8749 (ttp-110) REVERT: N 103 TRP cc_start: 0.8207 (m100) cc_final: 0.7956 (m-10) REVERT: O 29 MET cc_start: 0.4748 (pmm) cc_final: 0.4402 (pmm) REVERT: O 100 TYR cc_start: 0.8588 (p90) cc_final: 0.8344 (p90) REVERT: P 31 ARG cc_start: 0.6787 (ttp-110) cc_final: 0.6426 (ttp-110) REVERT: P 83 GLU cc_start: 0.7986 (tt0) cc_final: 0.7319 (tt0) REVERT: Q 38 HIS cc_start: 0.7197 (t70) cc_final: 0.6970 (t70) REVERT: G 34 MET cc_start: 0.8496 (ttp) cc_final: 0.8163 (ttp) REVERT: G 82 LEU cc_start: 0.8658 (tp) cc_final: 0.8427 (tp) REVERT: H 34 MET cc_start: 0.8368 (ttp) cc_final: 0.8109 (ttm) REVERT: I 34 MET cc_start: 0.8372 (ttp) cc_final: 0.8065 (ttp) REVERT: I 86 ASP cc_start: 0.6459 (t0) cc_final: 0.5884 (t0) REVERT: J 47 LYS cc_start: 0.8953 (ttpp) cc_final: 0.8625 (ttpt) REVERT: J 102 LEU cc_start: 0.7894 (tt) cc_final: 0.7550 (tt) REVERT: K 47 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8785 (ttpt) REVERT: L 38 TYR cc_start: 0.8009 (m-80) cc_final: 0.7690 (m-80) REVERT: L 41 HIS cc_start: 0.7729 (m90) cc_final: 0.7227 (m90) REVERT: L 47 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8299 (ttpt) REVERT: L 102 LEU cc_start: 0.8125 (tt) cc_final: 0.7465 (tt) outliers start: 4 outliers final: 1 residues processed: 723 average time/residue: 0.1878 time to fit residues: 203.6178 Evaluate side-chains 523 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 522 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.7980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN A 258 GLN A 283 ASN A 293 GLN A 302 ASN B 186AASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN B 293 GLN B 302 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186AASN C 283 ASN C 293 GLN C 302 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN D 630 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN M 60 ASN N 60 ASN O 1 GLN O 60 ASN Q 26 GLN R 26 GLN I 58 ASN J 39 GLN J 41 HIS J 81 GLN K 39 GLN K 81 GLN L 39 GLN L 81 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111983 restraints weight = 45374.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111664 restraints weight = 30427.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112730 restraints weight = 29964.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113128 restraints weight = 22334.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.114182 restraints weight = 19703.477| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26257 Z= 0.214 Angle : 0.743 20.825 35811 Z= 0.347 Chirality : 0.049 0.427 4187 Planarity : 0.004 0.060 4401 Dihedral : 14.964 117.823 5154 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.07 % Allowed : 6.34 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % 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: -2.87 (0.14), residues: 3072 helix: -0.44 (0.29), residues: 336 sheet: -1.17 (0.15), residues: 999 loop : -2.78 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 83 TYR 0.018 0.002 TYR L 38 PHE 0.030 0.002 PHE C 159 TRP 0.031 0.002 TRP M 36 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00492 (26130) covalent geometry : angle 0.69088 (35478) SS BOND : bond 0.00487 ( 42) SS BOND : angle 1.91535 ( 84) hydrogen bonds : bond 0.04670 ( 672) hydrogen bonds : angle 5.22851 ( 1845) Misc. bond : bond 0.00263 ( 2) link_ALPHA1-2 : bond 0.01944 ( 6) link_ALPHA1-2 : angle 3.68779 ( 18) link_ALPHA1-3 : bond 0.01418 ( 6) link_ALPHA1-3 : angle 4.84516 ( 18) link_ALPHA1-6 : bond 0.01928 ( 7) link_ALPHA1-6 : angle 4.65945 ( 21) link_ALPHA2-6 : bond 0.03888 ( 1) link_ALPHA2-6 : angle 5.41946 ( 3) link_BETA1-4 : bond 0.01086 ( 24) link_BETA1-4 : angle 3.29213 ( 72) link_NAG-ASN : bond 0.00536 ( 39) link_NAG-ASN : angle 2.18247 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 602 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 161 MET cc_start: 0.8776 (tpp) cc_final: 0.8516 (tpp) REVERT: A 195 ASN cc_start: 0.8013 (p0) cc_final: 0.7571 (p0) REVERT: A 307 ILE cc_start: 0.8972 (pt) cc_final: 0.8770 (pt) REVERT: B 125 LEU cc_start: 0.9324 (tp) cc_final: 0.8796 (tt) REVERT: B 161 MET cc_start: 0.8871 (tpp) cc_final: 0.8543 (tpp) REVERT: C 125 LEU cc_start: 0.9379 (tp) cc_final: 0.8972 (tp) REVERT: C 434 MET cc_start: 0.8872 (ttm) cc_final: 0.8466 (ttm) REVERT: C 475 MET cc_start: 0.8455 (ptt) cc_final: 0.8243 (ptt) REVERT: D 540 GLN cc_start: 0.8257 (mp10) cc_final: 0.7981 (mp10) REVERT: E 630 GLN cc_start: 0.7910 (pt0) cc_final: 0.7344 (pt0) REVERT: F 540 GLN cc_start: 0.8586 (mp10) cc_final: 0.8127 (mp10) REVERT: F 542 ARG cc_start: 0.8560 (ptt-90) cc_final: 0.8248 (ptt90) REVERT: F 626 MET cc_start: 0.7275 (tpp) cc_final: 0.6703 (tpp) REVERT: M 29 MET cc_start: 0.4535 (pmm) cc_final: 0.4261 (pmm) REVERT: M 91 TYR cc_start: 0.7248 (m-80) cc_final: 0.6869 (m-10) REVERT: M 100 GLU cc_start: 0.8257 (mp0) cc_final: 0.7735 (mp0) REVERT: M 103 TRP cc_start: 0.8371 (m100) cc_final: 0.8050 (m-10) REVERT: N 51 ILE cc_start: 0.8436 (tp) cc_final: 0.8222 (tp) REVERT: N 86 ASP cc_start: 0.8001 (m-30) cc_final: 0.7757 (m-30) REVERT: N 91 TYR cc_start: 0.7606 (m-80) cc_final: 0.7233 (m-10) REVERT: N 96 ARG cc_start: 0.9049 (ttp-110) cc_final: 0.8746 (ttp-110) REVERT: N 100 GLU cc_start: 0.7798 (mm-30) cc_final: 0.6891 (mm-30) REVERT: N 103 TRP cc_start: 0.8326 (m100) cc_final: 0.7902 (m-10) REVERT: O 29 MET cc_start: 0.4604 (pmm) cc_final: 0.4139 (pmm) REVERT: O 69 ILE cc_start: 0.7634 (tp) cc_final: 0.7263 (tp) REVERT: O 100 GLU cc_start: 0.8320 (mp0) cc_final: 0.8071 (mp0) REVERT: P 66 ASP cc_start: 0.7657 (t0) cc_final: 0.7434 (t0) REVERT: H 34 MET cc_start: 0.8385 (ttp) cc_final: 0.8145 (ttm) REVERT: H 86 ASP cc_start: 0.7185 (t0) cc_final: 0.6554 (t0) REVERT: I 34 MET cc_start: 0.8409 (ttp) cc_final: 0.8118 (ttp) REVERT: I 83 ARG cc_start: 0.7227 (ttm110) cc_final: 0.6496 (mpt-90) REVERT: I 86 ASP cc_start: 0.6886 (t0) cc_final: 0.6302 (t0) REVERT: J 38 TYR cc_start: 0.8791 (m-80) cc_final: 0.7969 (m-80) REVERT: J 47 LYS cc_start: 0.9015 (ttpp) cc_final: 0.8742 (ttpt) REVERT: K 47 LYS cc_start: 0.9046 (ttpp) cc_final: 0.8606 (ttpt) REVERT: L 38 TYR cc_start: 0.8351 (m-80) cc_final: 0.7873 (m-80) REVERT: L 47 LYS cc_start: 0.9047 (ttpp) cc_final: 0.8710 (ttpt) outliers start: 2 outliers final: 0 residues processed: 604 average time/residue: 0.1647 time to fit residues: 155.2564 Evaluate side-chains 497 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 295 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 291 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 293 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 374 HIS B 478 ASN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN D 591 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 ASN N 60 ASN O 60 ASN Q 26 GLN R 26 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.108288 restraints weight = 45664.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.107240 restraints weight = 35585.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107767 restraints weight = 34560.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.108411 restraints weight = 26793.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.110685 restraints weight = 22384.311| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 26257 Z= 0.293 Angle : 0.818 18.937 35811 Z= 0.395 Chirality : 0.051 0.399 4187 Planarity : 0.005 0.051 4401 Dihedral : 13.043 115.149 5154 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.11 % Allowed : 7.08 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.14), residues: 3072 helix: -0.54 (0.28), residues: 333 sheet: -1.01 (0.16), residues: 1008 loop : -2.73 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG O 100 TYR 0.023 0.002 TYR C 435 PHE 0.021 0.002 PHE C 53 TRP 0.038 0.002 TRP M 36 HIS 0.007 0.002 HIS P 89 Details of bonding type rmsd covalent geometry : bond 0.00681 (26130) covalent geometry : angle 0.77500 (35478) SS BOND : bond 0.01083 ( 42) SS BOND : angle 2.68694 ( 84) hydrogen bonds : bond 0.05366 ( 672) hydrogen bonds : angle 5.52462 ( 1845) Misc. bond : bond 0.00205 ( 2) link_ALPHA1-2 : bond 0.01639 ( 6) link_ALPHA1-2 : angle 2.67980 ( 18) link_ALPHA1-3 : bond 0.01107 ( 6) link_ALPHA1-3 : angle 3.87974 ( 18) link_ALPHA1-6 : bond 0.00970 ( 7) link_ALPHA1-6 : angle 2.59511 ( 21) link_ALPHA2-6 : bond 0.01420 ( 1) link_ALPHA2-6 : angle 3.57377 ( 3) link_BETA1-4 : bond 0.01010 ( 24) link_BETA1-4 : angle 3.07361 ( 72) link_NAG-ASN : bond 0.00680 ( 39) link_NAG-ASN : angle 2.62487 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 574 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9233 (tpp) cc_final: 0.8448 (tpp) REVERT: A 161 MET cc_start: 0.8754 (tpp) cc_final: 0.8443 (tpp) REVERT: B 35 TRP cc_start: 0.7407 (m-90) cc_final: 0.7197 (m-90) REVERT: B 161 MET cc_start: 0.8835 (tpp) cc_final: 0.8463 (tpp) REVERT: C 104 MET cc_start: 0.9244 (tpp) cc_final: 0.8719 (tpt) REVERT: C 434 MET cc_start: 0.8845 (ttm) cc_final: 0.8464 (ttm) REVERT: D 540 GLN cc_start: 0.8434 (mp10) cc_final: 0.8169 (mp10) REVERT: E 653 GLN cc_start: 0.8292 (mt0) cc_final: 0.8027 (mt0) REVERT: F 540 GLN cc_start: 0.8754 (mp10) cc_final: 0.8246 (mp10) REVERT: F 542 ARG cc_start: 0.8565 (ptt-90) cc_final: 0.8294 (ptt90) REVERT: M 29 MET cc_start: 0.4286 (pmm) cc_final: 0.4002 (pmm) REVERT: M 36 TRP cc_start: 0.7671 (m100) cc_final: 0.7470 (m100) REVERT: M 91 TYR cc_start: 0.7184 (m-80) cc_final: 0.6845 (m-10) REVERT: M 100 GLU cc_start: 0.8229 (mp0) cc_final: 0.7808 (mp0) REVERT: M 103 TRP cc_start: 0.8519 (m100) cc_final: 0.8199 (m-10) REVERT: N 51 ILE cc_start: 0.8522 (tp) cc_final: 0.8314 (tp) REVERT: N 86 ASP cc_start: 0.7992 (m-30) cc_final: 0.7732 (m-30) REVERT: N 96 ARG cc_start: 0.8994 (ttp-110) cc_final: 0.8578 (ttp-110) REVERT: N 103 TRP cc_start: 0.8522 (m100) cc_final: 0.7959 (m-10) REVERT: O 29 MET cc_start: 0.4651 (pmm) cc_final: 0.4115 (pmm) REVERT: H 34 MET cc_start: 0.8471 (ttp) cc_final: 0.8209 (ttm) REVERT: H 48 MET cc_start: 0.8109 (mtm) cc_final: 0.7867 (mtm) REVERT: H 86 ASP cc_start: 0.7422 (t0) cc_final: 0.6932 (t0) REVERT: I 86 ASP cc_start: 0.7217 (t0) cc_final: 0.6658 (t0) REVERT: J 47 LYS cc_start: 0.9008 (ttpp) cc_final: 0.8676 (ttpt) REVERT: K 47 LYS cc_start: 0.9153 (ttpp) cc_final: 0.8588 (ttpt) REVERT: K 102 LEU cc_start: 0.7662 (tt) cc_final: 0.7197 (tt) REVERT: L 38 TYR cc_start: 0.8446 (m-80) cc_final: 0.8035 (m-10) REVERT: L 47 LYS cc_start: 0.9156 (ttpp) cc_final: 0.8875 (ttpt) REVERT: L 102 LEU cc_start: 0.7683 (tt) cc_final: 0.7425 (tt) outliers start: 3 outliers final: 0 residues processed: 577 average time/residue: 0.1718 time to fit residues: 153.0204 Evaluate side-chains 473 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 285 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 275 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 300 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN B 99 ASN B 293 GLN C 374 HIS C 478 ASN D 577 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN F 630 GLN F 650 GLN M 60 ASN N 60 ASN O 60 ASN Q 89 HIS R 26 GLN R 38 HIS H 64 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN K 6 GLN K 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114294 restraints weight = 45022.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113861 restraints weight = 30410.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114823 restraints weight = 31956.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115448 restraints weight = 22587.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117143 restraints weight = 19602.480| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26257 Z= 0.120 Angle : 0.653 18.608 35811 Z= 0.319 Chirality : 0.046 0.374 4187 Planarity : 0.004 0.047 4401 Dihedral : 11.522 124.562 5154 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.11 % Allowed : 2.60 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % 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: -2.51 (0.14), residues: 3072 helix: -0.06 (0.30), residues: 327 sheet: -0.87 (0.16), residues: 960 loop : -2.55 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 100 TYR 0.029 0.001 TYR F 638 PHE 0.012 0.001 PHE L 93 TRP 0.022 0.001 TRP A 45 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00258 (26130) covalent geometry : angle 0.61580 (35478) SS BOND : bond 0.00490 ( 42) SS BOND : angle 2.04397 ( 84) hydrogen bonds : bond 0.04028 ( 672) hydrogen bonds : angle 5.06133 ( 1845) Misc. bond : bond 0.00628 ( 2) link_ALPHA1-2 : bond 0.01685 ( 6) link_ALPHA1-2 : angle 2.46365 ( 18) link_ALPHA1-3 : bond 0.01235 ( 6) link_ALPHA1-3 : angle 3.08410 ( 18) link_ALPHA1-6 : bond 0.00868 ( 7) link_ALPHA1-6 : angle 2.01575 ( 21) link_ALPHA2-6 : bond 0.01454 ( 1) link_ALPHA2-6 : angle 3.15791 ( 3) link_BETA1-4 : bond 0.00902 ( 24) link_BETA1-4 : angle 2.74245 ( 72) link_NAG-ASN : bond 0.00260 ( 39) link_NAG-ASN : angle 2.14846 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 626 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9322 (tp) cc_final: 0.9116 (tp) REVERT: A 161 MET cc_start: 0.8671 (tpp) cc_final: 0.8350 (tpp) REVERT: A 258 GLN cc_start: 0.9049 (tt0) cc_final: 0.8819 (pt0) REVERT: A 307 ILE cc_start: 0.8870 (pt) cc_final: 0.8644 (pt) REVERT: B 125 LEU cc_start: 0.9288 (tp) cc_final: 0.9031 (tp) REVERT: B 161 MET cc_start: 0.8816 (tpp) cc_final: 0.8326 (tpp) REVERT: B 178 LYS cc_start: 0.8692 (tptp) cc_final: 0.8479 (ttmt) REVERT: B 307 ILE cc_start: 0.8976 (pt) cc_final: 0.8644 (pt) REVERT: C 125 LEU cc_start: 0.9370 (tp) cc_final: 0.8918 (tp) REVERT: C 434 MET cc_start: 0.8727 (ttm) cc_final: 0.8371 (ttm) REVERT: D 540 GLN cc_start: 0.8387 (mp10) cc_final: 0.8127 (mp10) REVERT: D 542 ARG cc_start: 0.8383 (ptt90) cc_final: 0.8166 (ptm-80) REVERT: E 540 GLN cc_start: 0.8554 (mp10) cc_final: 0.8264 (mp10) REVERT: E 653 GLN cc_start: 0.8241 (mt0) cc_final: 0.7881 (mm-40) REVERT: F 540 GLN cc_start: 0.8650 (mp10) cc_final: 0.8145 (mp10) REVERT: F 542 ARG cc_start: 0.8537 (ptt-90) cc_final: 0.8269 (ptt90) REVERT: M 29 MET cc_start: 0.4170 (pmm) cc_final: 0.3849 (pmm) REVERT: M 91 TYR cc_start: 0.7119 (m-80) cc_final: 0.6772 (m-10) REVERT: M 100 GLU cc_start: 0.8295 (mp0) cc_final: 0.8028 (mp0) REVERT: M 103 TRP cc_start: 0.8446 (m100) cc_final: 0.8163 (m-10) REVERT: N 96 ARG cc_start: 0.8947 (ttp-110) cc_final: 0.8639 (ttp-110) REVERT: N 103 TRP cc_start: 0.8382 (m100) cc_final: 0.7827 (m-10) REVERT: O 69 ILE cc_start: 0.8208 (mm) cc_final: 0.7977 (tp) REVERT: O 100 GLU cc_start: 0.8326 (mp0) cc_final: 0.8092 (mp0) REVERT: G 34 MET cc_start: 0.8082 (ttp) cc_final: 0.7820 (ttm) REVERT: G 83 ARG cc_start: 0.7024 (mmt90) cc_final: 0.6765 (mpt-90) REVERT: H 34 MET cc_start: 0.8261 (ttp) cc_final: 0.7964 (ttm) REVERT: H 86 ASP cc_start: 0.7306 (t0) cc_final: 0.6798 (t0) REVERT: H 103 TRP cc_start: 0.8095 (m100) cc_final: 0.7752 (m100) REVERT: I 83 ARG cc_start: 0.7494 (ttm110) cc_final: 0.6589 (mpt-90) REVERT: I 86 ASP cc_start: 0.7296 (t0) cc_final: 0.6620 (t0) REVERT: J 47 LYS cc_start: 0.8948 (ttpp) cc_final: 0.8702 (ttpt) REVERT: J 71 ASN cc_start: 0.5913 (t0) cc_final: 0.5659 (t0) REVERT: K 47 LYS cc_start: 0.9093 (ttpp) cc_final: 0.8740 (ttpt) REVERT: L 38 TYR cc_start: 0.8265 (m-80) cc_final: 0.7894 (m-10) REVERT: L 47 LYS cc_start: 0.9046 (ttpp) cc_final: 0.8734 (ttpt) REVERT: L 102 LEU cc_start: 0.7826 (tt) cc_final: 0.7562 (tt) outliers start: 3 outliers final: 1 residues processed: 629 average time/residue: 0.1691 time to fit residues: 165.3408 Evaluate side-chains 508 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 507 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 136 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 257 optimal weight: 0.0050 chunk 254 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 478 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 GLN N 60 ASN O 60 ASN P 38 HIS Q 26 GLN R 26 GLN R 38 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 6 GLN L 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112925 restraints weight = 44573.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.112251 restraints weight = 29065.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113556 restraints weight = 28920.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113954 restraints weight = 21318.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115002 restraints weight = 19003.943| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26257 Z= 0.138 Angle : 0.639 18.338 35811 Z= 0.311 Chirality : 0.045 0.364 4187 Planarity : 0.005 0.203 4401 Dihedral : 10.724 120.662 5154 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % 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: -2.36 (0.14), residues: 3072 helix: 0.00 (0.30), residues: 327 sheet: -0.68 (0.16), residues: 981 loop : -2.52 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG O 100 TYR 0.027 0.001 TYR F 638 PHE 0.011 0.001 PHE O 100G TRP 0.028 0.001 TRP M 36 HIS 0.006 0.001 HIS Q 89 Details of bonding type rmsd covalent geometry : bond 0.00311 (26130) covalent geometry : angle 0.60160 (35478) SS BOND : bond 0.00433 ( 42) SS BOND : angle 1.99661 ( 84) hydrogen bonds : bond 0.04020 ( 672) hydrogen bonds : angle 5.02383 ( 1845) Misc. bond : bond 0.00993 ( 2) link_ALPHA1-2 : bond 0.01734 ( 6) link_ALPHA1-2 : angle 3.02297 ( 18) link_ALPHA1-3 : bond 0.01234 ( 6) link_ALPHA1-3 : angle 2.79308 ( 18) link_ALPHA1-6 : bond 0.00805 ( 7) link_ALPHA1-6 : angle 1.97592 ( 21) link_ALPHA2-6 : bond 0.01574 ( 1) link_ALPHA2-6 : angle 3.19169 ( 3) link_BETA1-4 : bond 0.00901 ( 24) link_BETA1-4 : angle 2.77345 ( 72) link_NAG-ASN : bond 0.00265 ( 39) link_NAG-ASN : angle 2.01378 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 607 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 161 MET cc_start: 0.8705 (tpp) cc_final: 0.8357 (tpp) REVERT: A 307 ILE cc_start: 0.8918 (pt) cc_final: 0.8701 (pt) REVERT: B 125 LEU cc_start: 0.9340 (tp) cc_final: 0.9086 (tp) REVERT: B 161 MET cc_start: 0.8830 (tpp) cc_final: 0.8332 (tpp) REVERT: B 307 ILE cc_start: 0.8973 (pt) cc_final: 0.8675 (pt) REVERT: C 104 MET cc_start: 0.8884 (tpp) cc_final: 0.8142 (tpp) REVERT: C 125 LEU cc_start: 0.9368 (tp) cc_final: 0.8976 (tp) REVERT: C 434 MET cc_start: 0.8800 (ttm) cc_final: 0.8394 (ttm) REVERT: D 540 GLN cc_start: 0.8484 (mp10) cc_final: 0.8177 (mp10) REVERT: E 540 GLN cc_start: 0.8552 (mp10) cc_final: 0.8270 (mp10) REVERT: F 540 GLN cc_start: 0.8673 (mp10) cc_final: 0.8137 (mp10) REVERT: F 542 ARG cc_start: 0.8516 (ptt-90) cc_final: 0.8247 (ptt90) REVERT: M 29 MET cc_start: 0.4173 (pmm) cc_final: 0.3824 (pmm) REVERT: M 100 GLU cc_start: 0.8307 (mp0) cc_final: 0.7789 (mp0) REVERT: M 103 TRP cc_start: 0.8430 (m100) cc_final: 0.8192 (m-10) REVERT: N 51 ILE cc_start: 0.8530 (tp) cc_final: 0.8322 (tp) REVERT: N 96 ARG cc_start: 0.8986 (ttp-110) cc_final: 0.8657 (ttp-110) REVERT: N 103 TRP cc_start: 0.8403 (m100) cc_final: 0.8009 (m-10) REVERT: O 100 GLU cc_start: 0.8258 (mp0) cc_final: 0.7738 (mp0) REVERT: R 36 TYR cc_start: 0.8547 (m-80) cc_final: 0.8096 (m-80) REVERT: G 34 MET cc_start: 0.8167 (ttp) cc_final: 0.7853 (ttm) REVERT: G 83 ARG cc_start: 0.7052 (mmt90) cc_final: 0.6785 (mpt-90) REVERT: H 34 MET cc_start: 0.8292 (ttp) cc_final: 0.7968 (ttm) REVERT: H 86 ASP cc_start: 0.7323 (t0) cc_final: 0.6816 (t0) REVERT: I 86 ASP cc_start: 0.7405 (t0) cc_final: 0.6742 (t0) REVERT: J 47 LYS cc_start: 0.9009 (ttpp) cc_final: 0.8746 (ttpt) REVERT: J 56 ARG cc_start: 0.6800 (ttp-110) cc_final: 0.6599 (ttp80) REVERT: K 47 LYS cc_start: 0.9137 (ttpp) cc_final: 0.8721 (ttpt) REVERT: K 55 LYS cc_start: 0.6981 (mtpp) cc_final: 0.6593 (ttpp) REVERT: L 38 TYR cc_start: 0.8267 (m-80) cc_final: 0.7884 (m-10) REVERT: L 47 LYS cc_start: 0.9099 (ttpp) cc_final: 0.8652 (ttpt) outliers start: 0 outliers final: 0 residues processed: 607 average time/residue: 0.1670 time to fit residues: 159.3272 Evaluate side-chains 492 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 128 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 214 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 265 optimal weight: 0.0980 chunk 302 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 478 ASN C 478 ASN D 591 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN O 60 ASN ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 GLN R 26 GLN R 38 HIS H 58 ASN H 64 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN K 6 GLN K 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110236 restraints weight = 45088.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110220 restraints weight = 32173.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.110267 restraints weight = 37545.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.111151 restraints weight = 24439.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112496 restraints weight = 20973.925| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26257 Z= 0.221 Angle : 0.715 18.199 35811 Z= 0.349 Chirality : 0.048 0.362 4187 Planarity : 0.004 0.076 4401 Dihedral : 10.692 178.447 5154 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.04 % Allowed : 2.15 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % 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: -2.36 (0.14), residues: 3072 helix: -0.05 (0.30), residues: 330 sheet: -0.65 (0.16), residues: 1014 loop : -2.57 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 83 TYR 0.035 0.002 TYR C 217 PHE 0.024 0.002 PHE J 64 TRP 0.027 0.002 TRP A 45 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00514 (26130) covalent geometry : angle 0.67388 (35478) SS BOND : bond 0.00720 ( 42) SS BOND : angle 2.50487 ( 84) hydrogen bonds : bond 0.04577 ( 672) hydrogen bonds : angle 5.18874 ( 1845) Misc. bond : bond 0.00371 ( 2) link_ALPHA1-2 : bond 0.01833 ( 6) link_ALPHA1-2 : angle 2.85683 ( 18) link_ALPHA1-3 : bond 0.01066 ( 6) link_ALPHA1-3 : angle 3.19979 ( 18) link_ALPHA1-6 : bond 0.00772 ( 7) link_ALPHA1-6 : angle 2.15395 ( 21) link_ALPHA2-6 : bond 0.01636 ( 1) link_ALPHA2-6 : angle 2.98180 ( 3) link_BETA1-4 : bond 0.01016 ( 24) link_BETA1-4 : angle 2.84739 ( 72) link_NAG-ASN : bond 0.00469 ( 39) link_NAG-ASN : angle 2.29575 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 592 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 104 MET cc_start: 0.8897 (tpp) cc_final: 0.8688 (tpt) REVERT: A 161 MET cc_start: 0.8809 (tpp) cc_final: 0.8451 (tpp) REVERT: A 307 ILE cc_start: 0.8885 (pt) cc_final: 0.8656 (pt) REVERT: B 100 MET cc_start: 0.8714 (mtp) cc_final: 0.8396 (mtm) REVERT: B 161 MET cc_start: 0.8824 (tpp) cc_final: 0.8466 (tpp) REVERT: C 434 MET cc_start: 0.8838 (ttm) cc_final: 0.8300 (ttm) REVERT: D 540 GLN cc_start: 0.8547 (mp10) cc_final: 0.8276 (mp10) REVERT: E 630 GLN cc_start: 0.8106 (pt0) cc_final: 0.7902 (pt0) REVERT: E 647 GLU cc_start: 0.8462 (pt0) cc_final: 0.8236 (pt0) REVERT: F 540 GLN cc_start: 0.8754 (mp10) cc_final: 0.8177 (mp10) REVERT: F 542 ARG cc_start: 0.8519 (ptt-90) cc_final: 0.8221 (ptt90) REVERT: M 29 MET cc_start: 0.3739 (pmm) cc_final: 0.3296 (pmm) REVERT: M 100 GLU cc_start: 0.8279 (mp0) cc_final: 0.7768 (mp0) REVERT: N 96 ARG cc_start: 0.8942 (ttp-110) cc_final: 0.8587 (ttp-110) REVERT: N 103 TRP cc_start: 0.8372 (m100) cc_final: 0.7984 (m-10) REVERT: O 48 ILE cc_start: 0.8413 (pt) cc_final: 0.8198 (pt) REVERT: O 100 GLU cc_start: 0.8266 (mp0) cc_final: 0.7700 (mp0) REVERT: G 83 ARG cc_start: 0.7082 (mmt90) cc_final: 0.6807 (mpt-90) REVERT: H 34 MET cc_start: 0.8441 (ttp) cc_final: 0.8086 (ttm) REVERT: H 86 ASP cc_start: 0.7404 (t0) cc_final: 0.6915 (t0) REVERT: I 83 ARG cc_start: 0.7466 (ttm110) cc_final: 0.6470 (mtt-85) REVERT: I 86 ASP cc_start: 0.7570 (t0) cc_final: 0.6927 (t0) REVERT: J 47 LYS cc_start: 0.8943 (ttpp) cc_final: 0.8548 (ttpt) REVERT: J 48 LEU cc_start: 0.8403 (tp) cc_final: 0.8113 (tp) REVERT: J 71 ASN cc_start: 0.6070 (t0) cc_final: 0.5771 (t0) REVERT: K 47 LYS cc_start: 0.9170 (ttpp) cc_final: 0.8728 (ttpt) REVERT: L 38 TYR cc_start: 0.8367 (m-80) cc_final: 0.8042 (m-10) REVERT: L 47 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8842 (ttpt) outliers start: 1 outliers final: 0 residues processed: 593 average time/residue: 0.1700 time to fit residues: 156.6040 Evaluate side-chains 479 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 233 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 301 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 293 GLN B 478 ASN C 478 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 GLN R 38 HIS J 6 GLN J 39 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 6 GLN L 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112292 restraints weight = 44660.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111647 restraints weight = 30717.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112374 restraints weight = 33569.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.113248 restraints weight = 23424.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114644 restraints weight = 20341.848| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26257 Z= 0.143 Angle : 0.651 18.019 35811 Z= 0.320 Chirality : 0.045 0.352 4187 Planarity : 0.004 0.074 4401 Dihedral : 10.205 177.602 5154 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % 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: -2.23 (0.14), residues: 3072 helix: 0.10 (0.30), residues: 330 sheet: -0.51 (0.16), residues: 978 loop : -2.49 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 83 TYR 0.031 0.001 TYR C 217 PHE 0.022 0.001 PHE J 64 TRP 0.031 0.002 TRP R 96 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00328 (26130) covalent geometry : angle 0.61562 (35478) SS BOND : bond 0.00476 ( 42) SS BOND : angle 1.97207 ( 84) hydrogen bonds : bond 0.04086 ( 672) hydrogen bonds : angle 5.00880 ( 1845) Misc. bond : bond 0.00225 ( 2) link_ALPHA1-2 : bond 0.01501 ( 6) link_ALPHA1-2 : angle 2.62722 ( 18) link_ALPHA1-3 : bond 0.01074 ( 6) link_ALPHA1-3 : angle 2.67711 ( 18) link_ALPHA1-6 : bond 0.00736 ( 7) link_ALPHA1-6 : angle 1.95949 ( 21) link_ALPHA2-6 : bond 0.01634 ( 1) link_ALPHA2-6 : angle 3.12972 ( 3) link_BETA1-4 : bond 0.00864 ( 24) link_BETA1-4 : angle 2.72090 ( 72) link_NAG-ASN : bond 0.00237 ( 39) link_NAG-ASN : angle 2.05622 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 607 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8881 (tpp) cc_final: 0.8608 (tpt) REVERT: A 161 MET cc_start: 0.8746 (tpp) cc_final: 0.8402 (tpp) REVERT: A 307 ILE cc_start: 0.8910 (pt) cc_final: 0.8695 (pt) REVERT: A 474 ASP cc_start: 0.7587 (p0) cc_final: 0.7360 (p0) REVERT: A 475 MET cc_start: 0.8293 (ptt) cc_final: 0.7950 (ttp) REVERT: B 100 MET cc_start: 0.8699 (mtp) cc_final: 0.8395 (mtm) REVERT: B 125 LEU cc_start: 0.9331 (tp) cc_final: 0.9088 (tp) REVERT: B 161 MET cc_start: 0.8819 (tpp) cc_final: 0.8373 (tpp) REVERT: B 307 ILE cc_start: 0.8910 (pt) cc_final: 0.8668 (pt) REVERT: B 474 ASP cc_start: 0.7506 (p0) cc_final: 0.7241 (p0) REVERT: B 475 MET cc_start: 0.8453 (ptt) cc_final: 0.8017 (ttp) REVERT: C 125 LEU cc_start: 0.9362 (tp) cc_final: 0.8939 (tp) REVERT: C 434 MET cc_start: 0.8829 (ttm) cc_final: 0.8275 (ttm) REVERT: C 475 MET cc_start: 0.8308 (ptt) cc_final: 0.7908 (ttp) REVERT: D 540 GLN cc_start: 0.8510 (mp10) cc_final: 0.8234 (mp10) REVERT: E 650 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7578 (mm-40) REVERT: F 540 GLN cc_start: 0.8699 (mp10) cc_final: 0.8126 (mp10) REVERT: F 542 ARG cc_start: 0.8477 (ptt-90) cc_final: 0.8183 (ptt90) REVERT: F 617 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7212 (mtt180) REVERT: M 29 MET cc_start: 0.3785 (pmm) cc_final: 0.3347 (pmm) REVERT: M 100 GLU cc_start: 0.8312 (mp0) cc_final: 0.7754 (mp0) REVERT: N 47 TRP cc_start: 0.8671 (t60) cc_final: 0.8433 (t60) REVERT: N 51 ILE cc_start: 0.8515 (tp) cc_final: 0.8301 (tp) REVERT: N 96 ARG cc_start: 0.8963 (ttp-110) cc_final: 0.8642 (ttp-110) REVERT: N 103 TRP cc_start: 0.8342 (m100) cc_final: 0.7845 (m-10) REVERT: O 48 ILE cc_start: 0.8366 (pt) cc_final: 0.8078 (pt) REVERT: O 69 ILE cc_start: 0.8070 (mm) cc_final: 0.7822 (tp) REVERT: O 100 GLU cc_start: 0.8393 (mp0) cc_final: 0.7820 (mp0) REVERT: P 31 ARG cc_start: 0.7981 (mtp-110) cc_final: 0.7615 (mtm-85) REVERT: P 36 TYR cc_start: 0.8578 (m-80) cc_final: 0.8266 (m-10) REVERT: P 83 GLU cc_start: 0.8049 (tt0) cc_final: 0.7761 (tt0) REVERT: G 34 MET cc_start: 0.8065 (ttp) cc_final: 0.7789 (ttm) REVERT: G 83 ARG cc_start: 0.6969 (mmt90) cc_final: 0.6731 (mpt-90) REVERT: H 34 MET cc_start: 0.8302 (ttp) cc_final: 0.7928 (ttm) REVERT: H 81 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7768 (mm-30) REVERT: H 86 ASP cc_start: 0.7320 (t0) cc_final: 0.6787 (t0) REVERT: I 34 MET cc_start: 0.8169 (ttm) cc_final: 0.7963 (ttm) REVERT: I 83 ARG cc_start: 0.7481 (ttm110) cc_final: 0.6485 (mtt-85) REVERT: I 86 ASP cc_start: 0.7671 (t0) cc_final: 0.6995 (t0) REVERT: J 47 LYS cc_start: 0.8975 (ttpp) cc_final: 0.8678 (ttpt) REVERT: J 48 LEU cc_start: 0.8362 (tp) cc_final: 0.8093 (tp) REVERT: K 47 LYS cc_start: 0.9147 (ttpp) cc_final: 0.8679 (ttpt) REVERT: K 55 LYS cc_start: 0.7234 (mtpp) cc_final: 0.6745 (ttpp) REVERT: L 38 TYR cc_start: 0.8289 (m-80) cc_final: 0.7945 (m-10) REVERT: L 47 LYS cc_start: 0.9095 (ttpp) cc_final: 0.8691 (ttpt) outliers start: 0 outliers final: 0 residues processed: 607 average time/residue: 0.1635 time to fit residues: 156.1219 Evaluate side-chains 498 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 109 optimal weight: 0.8980 chunk 283 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 287 optimal weight: 20.0000 chunk 263 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN C 478 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 ASN P 26 GLN P 38 HIS Q 26 GLN R 38 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 71 ASN K 6 GLN K 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.148563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111269 restraints weight = 44924.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.111188 restraints weight = 31457.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.112168 restraints weight = 29822.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112503 restraints weight = 23084.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113035 restraints weight = 20087.841| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26257 Z= 0.168 Angle : 0.674 18.248 35811 Z= 0.333 Chirality : 0.046 0.346 4187 Planarity : 0.004 0.078 4401 Dihedral : 10.008 175.497 5154 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.07 % Allowed : 1.15 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % 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: -2.21 (0.14), residues: 3072 helix: 0.36 (0.31), residues: 303 sheet: -0.52 (0.16), residues: 966 loop : -2.46 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 83 TYR 0.036 0.001 TYR C 217 PHE 0.061 0.002 PHE R 95B TRP 0.037 0.002 TRP C 45 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00392 (26130) covalent geometry : angle 0.63333 (35478) SS BOND : bond 0.00495 ( 42) SS BOND : angle 2.66387 ( 84) hydrogen bonds : bond 0.04169 ( 672) hydrogen bonds : angle 5.03326 ( 1845) Misc. bond : bond 0.00076 ( 2) link_ALPHA1-2 : bond 0.01439 ( 6) link_ALPHA1-2 : angle 2.60169 ( 18) link_ALPHA1-3 : bond 0.00965 ( 6) link_ALPHA1-3 : angle 2.74084 ( 18) link_ALPHA1-6 : bond 0.00781 ( 7) link_ALPHA1-6 : angle 2.00573 ( 21) link_ALPHA2-6 : bond 0.01749 ( 1) link_ALPHA2-6 : angle 3.08681 ( 3) link_BETA1-4 : bond 0.00838 ( 24) link_BETA1-4 : angle 2.78760 ( 72) link_NAG-ASN : bond 0.00323 ( 39) link_NAG-ASN : angle 2.13472 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 591 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7394 (p-80) cc_final: 0.6578 (t70) REVERT: A 104 MET cc_start: 0.8927 (tpp) cc_final: 0.8621 (tpt) REVERT: A 161 MET cc_start: 0.8758 (tpp) cc_final: 0.8435 (tpp) REVERT: A 307 ILE cc_start: 0.8914 (pt) cc_final: 0.8691 (pt) REVERT: B 100 MET cc_start: 0.8711 (mtp) cc_final: 0.8416 (mtm) REVERT: B 125 LEU cc_start: 0.9368 (tp) cc_final: 0.9125 (tp) REVERT: B 161 MET cc_start: 0.8840 (tpp) cc_final: 0.8372 (tpp) REVERT: B 307 ILE cc_start: 0.8959 (pt) cc_final: 0.8718 (pt) REVERT: B 434 MET cc_start: 0.8406 (ptp) cc_final: 0.8173 (ptp) REVERT: C 66 HIS cc_start: 0.7335 (p-80) cc_final: 0.6674 (t70) REVERT: C 125 LEU cc_start: 0.9266 (tp) cc_final: 0.8834 (tp) REVERT: C 434 MET cc_start: 0.8860 (ttm) cc_final: 0.8500 (ttm) REVERT: D 540 GLN cc_start: 0.8533 (mp10) cc_final: 0.8248 (mp10) REVERT: E 650 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7699 (mm-40) REVERT: F 540 GLN cc_start: 0.8718 (mp10) cc_final: 0.8488 (mp10) REVERT: F 542 ARG cc_start: 0.8472 (ptt-90) cc_final: 0.8191 (ptt90) REVERT: F 634 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7606 (mt-10) REVERT: M 29 MET cc_start: 0.3777 (pmm) cc_final: 0.3330 (pmm) REVERT: M 60 ASN cc_start: 0.7593 (m-40) cc_final: 0.7338 (m110) REVERT: M 100 GLU cc_start: 0.8270 (mp0) cc_final: 0.7705 (mp0) REVERT: N 47 TRP cc_start: 0.8731 (t60) cc_final: 0.8030 (t60) REVERT: N 51 ILE cc_start: 0.8529 (tp) cc_final: 0.8316 (tp) REVERT: N 96 ARG cc_start: 0.8925 (ttp-110) cc_final: 0.8616 (ttp-110) REVERT: N 103 TRP cc_start: 0.8480 (m100) cc_final: 0.7778 (m-10) REVERT: O 100 GLU cc_start: 0.8348 (mp0) cc_final: 0.7868 (mp0) REVERT: P 36 TYR cc_start: 0.8538 (m-80) cc_final: 0.8219 (m-10) REVERT: P 83 GLU cc_start: 0.8062 (tt0) cc_final: 0.7739 (tt0) REVERT: Q 30 SER cc_start: 0.8530 (m) cc_final: 0.8322 (m) REVERT: G 34 MET cc_start: 0.8133 (ttp) cc_final: 0.7854 (ttm) REVERT: G 83 ARG cc_start: 0.7000 (mmt90) cc_final: 0.6750 (mpt-90) REVERT: H 34 MET cc_start: 0.8351 (ttp) cc_final: 0.8003 (ttm) REVERT: H 86 ASP cc_start: 0.7448 (t0) cc_final: 0.6941 (t0) REVERT: I 83 ARG cc_start: 0.7521 (ttm110) cc_final: 0.6545 (mtt-85) REVERT: I 86 ASP cc_start: 0.7746 (t0) cc_final: 0.7059 (t0) REVERT: J 47 LYS cc_start: 0.8997 (ttpp) cc_final: 0.8615 (ttpt) REVERT: J 48 LEU cc_start: 0.8409 (tp) cc_final: 0.8103 (tp) REVERT: K 47 LYS cc_start: 0.9174 (ttpp) cc_final: 0.8754 (ttpt) REVERT: L 38 TYR cc_start: 0.8291 (m-80) cc_final: 0.7993 (m-10) REVERT: L 47 LYS cc_start: 0.9073 (ttpp) cc_final: 0.8658 (ttpt) outliers start: 2 outliers final: 0 residues processed: 592 average time/residue: 0.1635 time to fit residues: 152.3920 Evaluate side-chains 494 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 267 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 165 optimal weight: 0.4980 chunk 132 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 99 ASN B 478 ASN C 478 ASN D 650 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN P 26 GLN Q 26 GLN G 58 ASN J 6 GLN J 39 GLN J 71 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 6 GLN L 39 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.150450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113648 restraints weight = 44728.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113889 restraints weight = 29543.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115418 restraints weight = 24455.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115687 restraints weight = 19276.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115950 restraints weight = 17987.675| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26257 Z= 0.114 Angle : 0.631 18.391 35811 Z= 0.311 Chirality : 0.045 0.349 4187 Planarity : 0.004 0.072 4401 Dihedral : 9.575 174.472 5154 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.07 % Allowed : 1.00 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % 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: -2.06 (0.14), residues: 3072 helix: 0.34 (0.31), residues: 312 sheet: -0.51 (0.16), residues: 1008 loop : -2.32 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 83 TYR 0.024 0.001 TYR C 217 PHE 0.029 0.001 PHE R 95B TRP 0.029 0.001 TRP B 45 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00249 (26130) covalent geometry : angle 0.59538 (35478) SS BOND : bond 0.00476 ( 42) SS BOND : angle 2.06847 ( 84) hydrogen bonds : bond 0.03733 ( 672) hydrogen bonds : angle 4.89318 ( 1845) Misc. bond : bond 0.00070 ( 2) link_ALPHA1-2 : bond 0.01395 ( 6) link_ALPHA1-2 : angle 2.56903 ( 18) link_ALPHA1-3 : bond 0.01039 ( 6) link_ALPHA1-3 : angle 2.55349 ( 18) link_ALPHA1-6 : bond 0.00847 ( 7) link_ALPHA1-6 : angle 1.93582 ( 21) link_ALPHA2-6 : bond 0.01669 ( 1) link_ALPHA2-6 : angle 3.31087 ( 3) link_BETA1-4 : bond 0.00933 ( 24) link_BETA1-4 : angle 2.72714 ( 72) link_NAG-ASN : bond 0.00235 ( 39) link_NAG-ASN : angle 1.92888 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 606 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7293 (p-80) cc_final: 0.6487 (t70) REVERT: A 161 MET cc_start: 0.8699 (tpp) cc_final: 0.8407 (tpp) REVERT: A 307 ILE cc_start: 0.8897 (pt) cc_final: 0.8684 (pt) REVERT: A 474 ASP cc_start: 0.7555 (p0) cc_final: 0.7347 (p0) REVERT: A 475 MET cc_start: 0.8269 (ptt) cc_final: 0.7953 (ttp) REVERT: B 125 LEU cc_start: 0.9334 (tp) cc_final: 0.9102 (tp) REVERT: B 161 MET cc_start: 0.8823 (tpp) cc_final: 0.8350 (tpp) REVERT: B 307 ILE cc_start: 0.8902 (pt) cc_final: 0.8626 (pt) REVERT: B 475 MET cc_start: 0.8463 (ptt) cc_final: 0.8021 (ttp) REVERT: C 66 HIS cc_start: 0.7269 (p-80) cc_final: 0.6647 (t70) REVERT: C 104 MET cc_start: 0.8976 (tpp) cc_final: 0.8453 (tpt) REVERT: C 125 LEU cc_start: 0.9360 (tp) cc_final: 0.8973 (tp) REVERT: C 434 MET cc_start: 0.8744 (ttm) cc_final: 0.8192 (ttm) REVERT: C 475 MET cc_start: 0.8188 (ptt) cc_final: 0.7768 (ttp) REVERT: D 540 GLN cc_start: 0.8470 (mp10) cc_final: 0.8194 (mp10) REVERT: D 653 GLN cc_start: 0.7933 (mt0) cc_final: 0.7623 (mm-40) REVERT: E 540 GLN cc_start: 0.8530 (mp10) cc_final: 0.8251 (mp10) REVERT: E 650 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7687 (mm-40) REVERT: F 540 GLN cc_start: 0.8686 (mp10) cc_final: 0.8064 (mp10) REVERT: F 542 ARG cc_start: 0.8450 (ptt-90) cc_final: 0.8214 (ptt90) REVERT: F 634 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6911 (mt-10) REVERT: M 29 MET cc_start: 0.3841 (pmm) cc_final: 0.3409 (pmm) REVERT: M 100 GLU cc_start: 0.8287 (mp0) cc_final: 0.7788 (mp0) REVERT: N 51 ILE cc_start: 0.8481 (tp) cc_final: 0.8272 (tp) REVERT: N 96 ARG cc_start: 0.8966 (ttp-110) cc_final: 0.8652 (ttp-110) REVERT: N 103 TRP cc_start: 0.8293 (m100) cc_final: 0.7773 (m-10) REVERT: O 100 GLU cc_start: 0.8412 (mp0) cc_final: 0.7837 (mp0) REVERT: P 36 TYR cc_start: 0.8437 (m-80) cc_final: 0.8076 (m-10) REVERT: P 83 GLU cc_start: 0.8067 (tt0) cc_final: 0.7772 (tt0) REVERT: Q 30 SER cc_start: 0.8425 (m) cc_final: 0.8188 (m) REVERT: G 83 ARG cc_start: 0.6932 (mmt90) cc_final: 0.6692 (mpt-90) REVERT: H 34 MET cc_start: 0.8364 (ttp) cc_final: 0.8014 (ttm) REVERT: H 86 ASP cc_start: 0.7274 (t0) cc_final: 0.6769 (t0) REVERT: I 83 ARG cc_start: 0.7424 (ttm110) cc_final: 0.6488 (mtt-85) REVERT: I 86 ASP cc_start: 0.7622 (t0) cc_final: 0.6877 (t0) REVERT: J 47 LYS cc_start: 0.8849 (ttpp) cc_final: 0.8511 (ttpt) REVERT: J 60 VAL cc_start: 0.8130 (p) cc_final: 0.7892 (p) REVERT: K 47 LYS cc_start: 0.9148 (ttpp) cc_final: 0.8716 (ttpt) REVERT: K 55 LYS cc_start: 0.7229 (mtpp) cc_final: 0.6710 (ttpp) REVERT: L 38 TYR cc_start: 0.8197 (m-80) cc_final: 0.7789 (m-10) REVERT: L 47 LYS cc_start: 0.9056 (ttpp) cc_final: 0.8651 (ttpt) outliers start: 2 outliers final: 1 residues processed: 607 average time/residue: 0.1661 time to fit residues: 158.2805 Evaluate side-chains 506 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 505 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 50 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 269 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 156 optimal weight: 0.0040 chunk 190 optimal weight: 8.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 99 ASN B 293 GLN B 478 ASN C 478 ASN D 650 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 ASN J 39 GLN K 6 GLN K 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112689 restraints weight = 44719.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112490 restraints weight = 30812.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113621 restraints weight = 28697.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113892 restraints weight = 22717.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114668 restraints weight = 19813.262| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26257 Z= 0.137 Angle : 0.649 18.323 35811 Z= 0.321 Chirality : 0.045 0.347 4187 Planarity : 0.004 0.072 4401 Dihedral : 9.398 175.245 5154 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.04 % Allowed : 0.48 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % 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: -2.05 (0.14), residues: 3072 helix: 0.41 (0.31), residues: 306 sheet: -0.50 (0.16), residues: 1059 loop : -2.37 (0.13), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 31 TYR 0.027 0.001 TYR M 59 PHE 0.039 0.001 PHE R 95B TRP 0.044 0.002 TRP P 96 HIS 0.005 0.001 HIS Q 89 Details of bonding type rmsd covalent geometry : bond 0.00313 (26130) covalent geometry : angle 0.61170 (35478) SS BOND : bond 0.00432 ( 42) SS BOND : angle 2.26013 ( 84) hydrogen bonds : bond 0.03852 ( 672) hydrogen bonds : angle 4.90360 ( 1845) Misc. bond : bond 0.00078 ( 2) link_ALPHA1-2 : bond 0.01438 ( 6) link_ALPHA1-2 : angle 2.61636 ( 18) link_ALPHA1-3 : bond 0.00975 ( 6) link_ALPHA1-3 : angle 2.62099 ( 18) link_ALPHA1-6 : bond 0.00910 ( 7) link_ALPHA1-6 : angle 2.00975 ( 21) link_ALPHA2-6 : bond 0.01575 ( 1) link_ALPHA2-6 : angle 3.19250 ( 3) link_BETA1-4 : bond 0.00919 ( 24) link_BETA1-4 : angle 2.75480 ( 72) link_NAG-ASN : bond 0.00245 ( 39) link_NAG-ASN : angle 1.96323 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 589 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 66 HIS cc_start: 0.7284 (p-80) cc_final: 0.6533 (t70) REVERT: A 104 MET cc_start: 0.8965 (tpp) cc_final: 0.8735 (tpt) REVERT: A 161 MET cc_start: 0.8764 (tpp) cc_final: 0.8425 (tpp) REVERT: A 307 ILE cc_start: 0.8900 (pt) cc_final: 0.8682 (pt) REVERT: A 474 ASP cc_start: 0.7566 (p0) cc_final: 0.7345 (p0) REVERT: A 475 MET cc_start: 0.8292 (ptt) cc_final: 0.7940 (ttp) REVERT: B 125 LEU cc_start: 0.9356 (tp) cc_final: 0.9107 (tp) REVERT: B 161 MET cc_start: 0.8851 (tpp) cc_final: 0.8562 (tpp) REVERT: B 307 ILE cc_start: 0.8914 (pt) cc_final: 0.8644 (pt) REVERT: C 66 HIS cc_start: 0.7284 (p-80) cc_final: 0.6685 (t70) REVERT: C 104 MET cc_start: 0.9001 (tpp) cc_final: 0.8533 (tpt) REVERT: C 125 LEU cc_start: 0.9346 (tp) cc_final: 0.8925 (tp) REVERT: D 540 GLN cc_start: 0.8435 (mp10) cc_final: 0.8181 (mp10) REVERT: D 653 GLN cc_start: 0.7899 (mt0) cc_final: 0.7604 (mm-40) REVERT: E 540 GLN cc_start: 0.8539 (mp10) cc_final: 0.8295 (mp10) REVERT: E 650 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7704 (mm-40) REVERT: F 540 GLN cc_start: 0.8675 (mp10) cc_final: 0.8458 (mp10) REVERT: F 542 ARG cc_start: 0.8447 (ptt-90) cc_final: 0.8191 (ptt90) REVERT: F 634 GLU cc_start: 0.7551 (mt-10) cc_final: 0.6905 (mt-10) REVERT: M 36 TRP cc_start: 0.7592 (m100) cc_final: 0.7179 (m100) REVERT: M 100 GLU cc_start: 0.8274 (mp0) cc_final: 0.7801 (mp0) REVERT: N 47 TRP cc_start: 0.8621 (t60) cc_final: 0.8398 (t60) REVERT: N 51 ILE cc_start: 0.8484 (tp) cc_final: 0.8267 (tp) REVERT: N 96 ARG cc_start: 0.8975 (ttp-110) cc_final: 0.8620 (ttp-110) REVERT: N 103 TRP cc_start: 0.8419 (m100) cc_final: 0.7832 (m-10) REVERT: O 100 GLU cc_start: 0.8415 (mp0) cc_final: 0.7844 (mp0) REVERT: P 36 TYR cc_start: 0.8585 (m-80) cc_final: 0.8238 (m-10) REVERT: P 83 GLU cc_start: 0.8076 (tt0) cc_final: 0.7764 (tt0) REVERT: Q 30 SER cc_start: 0.8522 (m) cc_final: 0.8296 (m) REVERT: G 83 ARG cc_start: 0.6933 (mmt90) cc_final: 0.6657 (mpt-90) REVERT: H 34 MET cc_start: 0.8378 (ttp) cc_final: 0.8046 (ttm) REVERT: H 86 ASP cc_start: 0.7391 (t0) cc_final: 0.6897 (t0) REVERT: I 34 MET cc_start: 0.8280 (ttm) cc_final: 0.8077 (ttm) REVERT: I 83 ARG cc_start: 0.7493 (ttm110) cc_final: 0.6554 (mtt-85) REVERT: I 86 ASP cc_start: 0.7692 (t0) cc_final: 0.6980 (t0) REVERT: J 47 LYS cc_start: 0.8929 (ttpp) cc_final: 0.8501 (ttpt) REVERT: K 47 LYS cc_start: 0.9162 (ttpp) cc_final: 0.8738 (ttpt) REVERT: K 55 LYS cc_start: 0.7280 (mtpp) cc_final: 0.6681 (ttpp) REVERT: L 38 TYR cc_start: 0.8121 (m-80) cc_final: 0.7858 (m-10) REVERT: L 47 LYS cc_start: 0.9040 (ttpp) cc_final: 0.8616 (ttpt) outliers start: 1 outliers final: 0 residues processed: 590 average time/residue: 0.1653 time to fit residues: 153.4782 Evaluate side-chains 486 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 129 optimal weight: 0.0030 chunk 268 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 224 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 478 ASN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 ASN O 60 ASN Q 26 GLN J 39 GLN J 71 ASN K 39 GLN L 6 GLN L 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.150249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113226 restraints weight = 44338.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113618 restraints weight = 28424.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114071 restraints weight = 29432.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114820 restraints weight = 20685.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115816 restraints weight = 17952.444| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26257 Z= 0.119 Angle : 0.631 18.336 35811 Z= 0.313 Chirality : 0.045 0.348 4187 Planarity : 0.004 0.068 4401 Dihedral : 9.161 175.070 5154 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.04 % Allowed : 0.41 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.10 % Twisted Proline : 0.00 % 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: -2.01 (0.14), residues: 3072 helix: 0.46 (0.31), residues: 300 sheet: -0.44 (0.17), residues: 930 loop : -2.25 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 56 TYR 0.023 0.001 TYR D 638 PHE 0.089 0.001 PHE P 95B TRP 0.058 0.002 TRP P 96 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00263 (26130) covalent geometry : angle 0.59680 (35478) SS BOND : bond 0.00431 ( 42) SS BOND : angle 1.98239 ( 84) hydrogen bonds : bond 0.03697 ( 672) hydrogen bonds : angle 4.81962 ( 1845) Misc. bond : bond 0.00079 ( 2) link_ALPHA1-2 : bond 0.01512 ( 6) link_ALPHA1-2 : angle 2.58669 ( 18) link_ALPHA1-3 : bond 0.01018 ( 6) link_ALPHA1-3 : angle 2.52585 ( 18) link_ALPHA1-6 : bond 0.01012 ( 7) link_ALPHA1-6 : angle 2.06948 ( 21) link_ALPHA2-6 : bond 0.01679 ( 1) link_ALPHA2-6 : angle 3.24151 ( 3) link_BETA1-4 : bond 0.00939 ( 24) link_BETA1-4 : angle 2.71229 ( 72) link_NAG-ASN : bond 0.00213 ( 39) link_NAG-ASN : angle 1.87931 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4174.13 seconds wall clock time: 73 minutes 0.01 seconds (4380.01 seconds total)