Starting phenix.real_space_refine on Sun Oct 12 03:27:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iyg_35821/10_2025/8iyg_35821.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iyg_35821/10_2025/8iyg_35821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iyg_35821/10_2025/8iyg_35821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iyg_35821/10_2025/8iyg_35821.map" model { file = "/net/cci-nas-00/data/ceres_data/8iyg_35821/10_2025/8iyg_35821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iyg_35821/10_2025/8iyg_35821.cif" } resolution = 2.69 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= 0.001 sd= 0.027 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 156 5.16 5 C 14052 2.51 5 N 3036 2.21 5 O 3288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20532 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 200 Unusual residues: {'LMT': 7, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 200 Unusual residues: {'LMT': 7, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 200 Unusual residues: {'LMT': 7, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 200 Unusual residues: {'LMT': 7, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 200 Unusual residues: {'LMT': 7, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 200 Unusual residues: {'LMT': 7, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 200 Unusual residues: {'LMT': 7, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 200 Unusual residues: {'LMT': 7, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 200 Unusual residues: {'LMT': 7, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 200 Unusual residues: {'LMT': 7, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 200 Unusual residues: {'LMT': 7, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 200 Unusual residues: {'LMT': 7, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 5.19, per 1000 atoms: 0.25 Number of scatterers: 20532 At special positions: 0 Unit cell: (113.3, 108.9, 177.1, 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 156 16.00 O 3288 8.00 N 3036 7.00 C 14052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 837.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 78.1% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 19 through 46 removed outlier: 5.482A pdb=" N GLU A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.676A pdb=" N ALA A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS A 66 " --> pdb=" O CYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.507A pdb=" N TYR A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 104 Processing helix chain 'A' and resid 187 through 221 Processing helix chain 'A' and resid 246 through 285 removed outlier: 3.741A pdb=" N LYS A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TRP A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ARG A 278 " --> pdb=" O HIS A 274 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 46 removed outlier: 5.467A pdb=" N GLU B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 removed outlier: 3.668A pdb=" N ALA B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS B 66 " --> pdb=" O CYS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.507A pdb=" N TYR B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 104 Processing helix chain 'B' and resid 187 through 221 Processing helix chain 'B' and resid 246 through 285 removed outlier: 3.744A pdb=" N LYS B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TRP B 277 " --> pdb=" O ASN B 273 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ARG B 278 " --> pdb=" O HIS B 274 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 46 removed outlier: 5.483A pdb=" N GLU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N THR C 44 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 71 removed outlier: 3.676A pdb=" N ALA C 65 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS C 66 " --> pdb=" O CYS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.507A pdb=" N TYR C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 104 Processing helix chain 'C' and resid 187 through 221 Processing helix chain 'C' and resid 246 through 285 removed outlier: 3.743A pdb=" N LYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TRP C 277 " --> pdb=" O ASN C 273 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ARG C 278 " --> pdb=" O HIS C 274 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 46 removed outlier: 5.485A pdb=" N GLU D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N THR D 44 " --> pdb=" O ILE D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.678A pdb=" N ALA D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS D 66 " --> pdb=" O CYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.507A pdb=" N TYR D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 104 Processing helix chain 'D' and resid 187 through 221 Processing helix chain 'D' and resid 246 through 285 removed outlier: 3.741A pdb=" N LYS D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TRP D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ARG D 278 " --> pdb=" O HIS D 274 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 46 removed outlier: 5.471A pdb=" N GLU E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 71 removed outlier: 3.662A pdb=" N ALA E 65 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS E 66 " --> pdb=" O CYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 removed outlier: 3.507A pdb=" N TYR E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 104 Processing helix chain 'E' and resid 187 through 221 Processing helix chain 'E' and resid 246 through 285 removed outlier: 3.745A pdb=" N LYS E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TRP E 277 " --> pdb=" O ASN E 273 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ARG E 278 " --> pdb=" O HIS E 274 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 46 removed outlier: 5.481A pdb=" N GLU F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 71 removed outlier: 3.676A pdb=" N ALA F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS F 66 " --> pdb=" O CYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 removed outlier: 3.506A pdb=" N TYR F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 Processing helix chain 'F' and resid 187 through 221 Processing helix chain 'F' and resid 246 through 285 removed outlier: 3.742A pdb=" N LYS F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TRP F 277 " --> pdb=" O ASN F 273 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ARG F 278 " --> pdb=" O HIS F 274 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS F 279 " --> pdb=" O LEU F 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 46 removed outlier: 5.468A pdb=" N GLU G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR G 44 " --> pdb=" O ILE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 71 removed outlier: 3.678A pdb=" N ALA G 65 " --> pdb=" O GLY G 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS G 66 " --> pdb=" O CYS G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 removed outlier: 3.507A pdb=" N TYR G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 104 Processing helix chain 'G' and resid 187 through 221 Processing helix chain 'G' and resid 246 through 285 removed outlier: 3.743A pdb=" N LYS G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TRP G 277 " --> pdb=" O ASN G 273 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ARG G 278 " --> pdb=" O HIS G 274 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS G 279 " --> pdb=" O LEU G 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 46 removed outlier: 5.482A pdb=" N GLU H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR H 44 " --> pdb=" O ILE H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 71 removed outlier: 3.677A pdb=" N ALA H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS H 66 " --> pdb=" O CYS H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 87 removed outlier: 3.507A pdb=" N TYR H 78 " --> pdb=" O SER H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 104 Processing helix chain 'H' and resid 187 through 221 Processing helix chain 'H' and resid 246 through 285 removed outlier: 3.741A pdb=" N LYS H 250 " --> pdb=" O ARG H 246 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TRP H 277 " --> pdb=" O ASN H 273 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ARG H 278 " --> pdb=" O HIS H 274 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS H 279 " --> pdb=" O LEU H 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 46 removed outlier: 5.485A pdb=" N GLU I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N THR I 44 " --> pdb=" O ILE I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 71 removed outlier: 3.673A pdb=" N ALA I 65 " --> pdb=" O GLY I 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS I 66 " --> pdb=" O CYS I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 87 removed outlier: 3.506A pdb=" N TYR I 78 " --> pdb=" O SER I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 104 Processing helix chain 'I' and resid 187 through 221 Processing helix chain 'I' and resid 246 through 285 removed outlier: 3.744A pdb=" N LYS I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TRP I 277 " --> pdb=" O ASN I 273 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ARG I 278 " --> pdb=" O HIS I 274 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS I 279 " --> pdb=" O LEU I 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 46 removed outlier: 5.468A pdb=" N GLU J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N THR J 44 " --> pdb=" O ILE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 71 removed outlier: 3.677A pdb=" N ALA J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS J 66 " --> pdb=" O CYS J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 87 removed outlier: 3.507A pdb=" N TYR J 78 " --> pdb=" O SER J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 104 Processing helix chain 'J' and resid 187 through 221 Processing helix chain 'J' and resid 246 through 285 removed outlier: 3.742A pdb=" N LYS J 250 " --> pdb=" O ARG J 246 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TRP J 277 " --> pdb=" O ASN J 273 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ARG J 278 " --> pdb=" O HIS J 274 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS J 279 " --> pdb=" O LEU J 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 46 removed outlier: 5.489A pdb=" N GLU K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR K 44 " --> pdb=" O ILE K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 71 removed outlier: 3.675A pdb=" N ALA K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS K 66 " --> pdb=" O CYS K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 87 removed outlier: 3.507A pdb=" N TYR K 78 " --> pdb=" O SER K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 104 Processing helix chain 'K' and resid 187 through 221 Processing helix chain 'K' and resid 246 through 285 removed outlier: 3.741A pdb=" N LYS K 250 " --> pdb=" O ARG K 246 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TRP K 277 " --> pdb=" O ASN K 273 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ARG K 278 " --> pdb=" O HIS K 274 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS K 279 " --> pdb=" O LEU K 275 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 46 removed outlier: 5.467A pdb=" N GLU L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N THR L 44 " --> pdb=" O ILE L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 71 removed outlier: 3.673A pdb=" N ALA L 65 " --> pdb=" O GLY L 61 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS L 66 " --> pdb=" O CYS L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 87 removed outlier: 3.507A pdb=" N TYR L 78 " --> pdb=" O SER L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 104 Processing helix chain 'L' and resid 187 through 221 Processing helix chain 'L' and resid 246 through 285 removed outlier: 3.743A pdb=" N LYS L 250 " --> pdb=" O ARG L 246 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TRP L 277 " --> pdb=" O ASN L 273 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ARG L 278 " --> pdb=" O HIS L 274 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS L 279 " --> pdb=" O LEU L 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 4.003A pdb=" N VAL A 54 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 removed outlier: 4.010A pdb=" N VAL B 54 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55 removed outlier: 4.014A pdb=" N VAL C 54 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 removed outlier: 4.007A pdb=" N VAL D 54 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 removed outlier: 4.004A pdb=" N VAL E 54 " --> pdb=" O TYR E 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 55 removed outlier: 4.013A pdb=" N VAL F 54 " --> pdb=" O TYR F 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 55 removed outlier: 4.009A pdb=" N VAL G 54 " --> pdb=" O TYR G 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 55 removed outlier: 4.014A pdb=" N VAL H 54 " --> pdb=" O TYR H 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 54 through 55 removed outlier: 4.008A pdb=" N VAL I 54 " --> pdb=" O TYR I 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 54 through 55 removed outlier: 4.012A pdb=" N VAL J 54 " --> pdb=" O TYR J 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55 removed outlier: 4.012A pdb=" N VAL K 54 " --> pdb=" O TYR K 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 4.002A pdb=" N VAL L 54 " --> pdb=" O TYR L 243 " (cutoff:3.500A) 1416 hydrogen bonds defined for protein. 4212 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: 3.43 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3319 1.33 - 1.45: 5057 1.45 - 1.57: 12444 1.57 - 1.69: 0 1.69 - 1.82: 204 Bond restraints: 21024 Sorted by residual: bond pdb=" C3' LMT F 405 " pdb=" O3' LMT F 405 " ideal model delta sigma weight residual 1.404 1.362 0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" C3' LMT A 403 " pdb=" O3' LMT A 403 " ideal model delta sigma weight residual 1.404 1.363 0.041 2.00e-02 2.50e+03 4.24e+00 bond pdb=" C7 LMT G 405 " pdb=" C8 LMT G 405 " ideal model delta sigma weight residual 1.529 1.488 0.041 2.00e-02 2.50e+03 4.22e+00 bond pdb=" C7 LMT A 406 " pdb=" C8 LMT A 406 " ideal model delta sigma weight residual 1.529 1.488 0.041 2.00e-02 2.50e+03 4.20e+00 bond pdb=" C7 LMT B 411 " pdb=" C8 LMT B 411 " ideal model delta sigma weight residual 1.529 1.488 0.041 2.00e-02 2.50e+03 4.20e+00 ... (remaining 21019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 27631 1.95 - 3.90: 377 3.90 - 5.86: 264 5.86 - 7.81: 0 7.81 - 9.76: 204 Bond angle restraints: 28476 Sorted by residual: angle pdb=" C2 LMT H 406 " pdb=" C3 LMT H 406 " pdb=" C4 LMT H 406 " ideal model delta sigma weight residual 117.09 107.33 9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C2 LMT E 404 " pdb=" C3 LMT E 404 " pdb=" C4 LMT E 404 " ideal model delta sigma weight residual 117.09 107.34 9.75 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C2 LMT J 407 " pdb=" C3 LMT J 407 " pdb=" C4 LMT J 407 " ideal model delta sigma weight residual 117.09 107.34 9.75 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C2 LMT H 411 " pdb=" C3 LMT H 411 " pdb=" C4 LMT H 411 " ideal model delta sigma weight residual 117.09 107.35 9.74 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C2 LMT D 405 " pdb=" C3 LMT D 405 " pdb=" C4 LMT D 405 " ideal model delta sigma weight residual 117.09 107.35 9.74 3.00e+00 1.11e-01 1.05e+01 ... (remaining 28471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.63: 12851 11.63 - 23.25: 1522 23.25 - 34.88: 576 34.88 - 46.51: 184 46.51 - 58.13: 167 Dihedral angle restraints: 15300 sinusoidal: 8712 harmonic: 6588 Sorted by residual: dihedral pdb=" CB CYS D 62 " pdb=" SG CYS D 62 " pdb=" SG CYS D 236 " pdb=" CB CYS D 236 " ideal model delta sinusoidal sigma weight residual 93.00 123.36 -30.36 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CB CYS K 62 " pdb=" SG CYS K 62 " pdb=" SG CYS K 236 " pdb=" CB CYS K 236 " ideal model delta sinusoidal sigma weight residual 93.00 123.33 -30.33 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CB CYS H 62 " pdb=" SG CYS H 62 " pdb=" SG CYS H 236 " pdb=" CB CYS H 236 " ideal model delta sinusoidal sigma weight residual 93.00 123.32 -30.32 1 1.00e+01 1.00e-02 1.31e+01 ... (remaining 15297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2718 0.043 - 0.086: 552 0.086 - 0.129: 78 0.129 - 0.172: 12 0.172 - 0.215: 36 Chirality restraints: 3396 Sorted by residual: chirality pdb=" C4' LMT K 403 " pdb=" C3' LMT K 403 " pdb=" C5' LMT K 403 " pdb=" O1B LMT K 403 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C4' LMT L 405 " pdb=" C3' LMT L 405 " pdb=" C5' LMT L 405 " pdb=" O1B LMT L 405 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C4' LMT D 403 " pdb=" C3' LMT D 403 " pdb=" C5' LMT D 403 " pdb=" O1B LMT D 403 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 3393 not shown) Planarity restraints: 3144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 38 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C VAL F 38 " 0.020 2.00e-02 2.50e+03 pdb=" O VAL F 38 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA F 39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 38 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C VAL L 38 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL L 38 " 0.007 2.00e-02 2.50e+03 pdb=" N ALA L 39 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 38 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C VAL K 38 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL K 38 " 0.007 2.00e-02 2.50e+03 pdb=" N ALA K 39 " 0.007 2.00e-02 2.50e+03 ... (remaining 3141 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5953 2.84 - 3.35: 19211 3.35 - 3.87: 31954 3.87 - 4.38: 32221 4.38 - 4.90: 57963 Nonbonded interactions: 147302 Sorted by model distance: nonbonded pdb=" O TYR L 221 " pdb=" O4' LMT L 405 " model vdw 2.324 3.040 nonbonded pdb=" O TYR K 221 " pdb=" O4' LMT K 403 " model vdw 2.324 3.040 nonbonded pdb=" O TYR B 221 " pdb=" O4' LMT B 403 " model vdw 2.324 3.040 nonbonded pdb=" O TYR C 221 " pdb=" O4' LMT C 403 " model vdw 2.325 3.040 nonbonded pdb=" O TYR F 221 " pdb=" O4' LMT F 405 " model vdw 2.325 3.040 ... (remaining 147297 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 285 or (resid 401 and (name CAC or name CAD or \ name CAE or name CAI or name CAK or name CAM or name CAO or name CAP or name CAQ \ or name CAR or name CAS or name CAT or name CAU or name CAV or name CAY or name \ CAZ or name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or \ name CBH or name CBI or name OAG or name OAW)) or resid 405 through 408)) selection = (chain 'B' and (resid 18 through 285 or (resid 401 and (name CAC or name CAD or \ name CAE or name CAI or name CAK or name CAM or name CAO or name CAP or name CAQ \ or name CAR or name CAS or name CAT or name CAU or name CAV or name CAY or name \ CAZ or name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or \ name CBH or name CBI or name OAG or name OAW)) or resid 405 through 408)) selection = (chain 'C' and (resid 18 through 285 or (resid 401 and (name CAC or name CAD or \ name CAE or name CAI or name CAK or name CAM or name CAO or name CAP or name CAQ \ or name CAR or name CAS or name CAT or name CAU or name CAV or name CAY or name \ CAZ or name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or \ name CBH or name CBI or name OAG or name OAW)) or resid 405 through 408)) selection = (chain 'D' and (resid 18 through 285 or (resid 401 and (name CAC or name CAD or \ name CAE or name CAI or name CAK or name CAM or name CAO or name CAP or name CAQ \ or name CAR or name CAS or name CAT or name CAU or name CAV or name CAY or name \ CAZ or name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or \ name CBH or name CBI or name OAG or name OAW)) or resid 405 through 408)) selection = (chain 'E' and (resid 18 through 285 or (resid 401 and (name CAC or name CAD or \ name CAE or name CAI or name CAK or name CAM or name CAO or name CAP or name CAQ \ or name CAR or name CAS or name CAT or name CAU or name CAV or name CAY or name \ CAZ or name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or \ name CBH or name CBI or name OAG or name OAW)) or resid 405 through 408)) selection = (chain 'F' and (resid 18 through 401 or (resid 405 and (name C1 or name C10 or n \ ame C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ C9 )) or (resid 406 and (name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name C8 or name C9 )) or (resid 407 and (name C1 or name \ C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 408 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 )))) selection = (chain 'G' and (resid 18 through 285 or (resid 401 and (name CAC or name CAD or \ name CAE or name CAI or name CAK or name CAM or name CAO or name CAP or name CAQ \ or name CAR or name CAS or name CAT or name CAU or name CAV or name CAY or name \ CAZ or name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or \ name CBH or name CBI or name OAG or name OAW)) or resid 405 through 408)) selection = (chain 'H' and (resid 18 through 285 or (resid 401 and (name CAC or name CAD or \ name CAE or name CAI or name CAK or name CAM or name CAO or name CAP or name CAQ \ or name CAR or name CAS or name CAT or name CAU or name CAV or name CAY or name \ CAZ or name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or \ name CBH or name CBI or name OAG or name OAW)) or resid 405 through 408)) selection = (chain 'I' and (resid 18 through 285 or (resid 401 and (name CAC or name CAD or \ name CAE or name CAI or name CAK or name CAM or name CAO or name CAP or name CAQ \ or name CAR or name CAS or name CAT or name CAU or name CAV or name CAY or name \ CAZ or name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or \ name CBH or name CBI or name OAG or name OAW)) or resid 405 through 408)) selection = (chain 'J' and (resid 18 through 285 or (resid 401 and (name CAC or name CAD or \ name CAE or name CAI or name CAK or name CAM or name CAO or name CAP or name CAQ \ or name CAR or name CAS or name CAT or name CAU or name CAV or name CAY or name \ CAZ or name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or \ name CBH or name CBI or name OAG or name OAW)) or resid 405 through 408)) selection = (chain 'K' and (resid 18 through 285 or (resid 401 and (name CAC or name CAD or \ name CAE or name CAI or name CAK or name CAM or name CAO or name CAP or name CAQ \ or name CAR or name CAS or name CAT or name CAU or name CAV or name CAY or name \ CAZ or name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or \ name CBH or name CBI or name OAG or name OAW)) or resid 405 through 408)) selection = (chain 'L' and (resid 18 through 401 or (resid 405 and (name C1 or name C10 or n \ ame C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ C9 )) or (resid 406 and (name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name C8 or name C9 )) or (resid 407 and (name C1 or name \ C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 408 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.410 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 : 0.007 0.042 21060 Z= 0.331 Angle : 1.007 9.759 28548 Z= 0.370 Chirality : 0.040 0.215 3396 Planarity : 0.002 0.014 3144 Dihedral : 12.349 58.133 10944 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.37 (0.18), residues: 2196 helix: 3.96 (0.11), residues: 1680 sheet: 1.05 (0.42), residues: 120 loop : -1.87 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.003 0.000 TYR C 243 PHE 0.005 0.001 PHE E 256 TRP 0.002 0.000 TRP C 277 HIS 0.004 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00660 (21024) covalent geometry : angle 1.00765 (28476) SS BOND : bond 0.00077 ( 36) SS BOND : angle 0.53971 ( 72) hydrogen bonds : bond 0.10132 ( 1416) hydrogen bonds : angle 3.15111 ( 4212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 844 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8717 (tp40) cc_final: 0.7890 (tp40) REVERT: A 67 TYR cc_start: 0.8767 (t80) cc_final: 0.8145 (t80) REVERT: A 257 MET cc_start: 0.8855 (mmm) cc_final: 0.8509 (mmm) REVERT: B 43 GLU cc_start: 0.7976 (tt0) cc_final: 0.7603 (tm-30) REVERT: B 59 GLN cc_start: 0.8862 (tp40) cc_final: 0.8519 (tp40) REVERT: B 253 PHE cc_start: 0.7555 (t80) cc_final: 0.7207 (t80) REVERT: B 257 MET cc_start: 0.8969 (mmm) cc_final: 0.8683 (mmm) REVERT: C 43 GLU cc_start: 0.7827 (tt0) cc_final: 0.7507 (tm-30) REVERT: C 59 GLN cc_start: 0.8728 (tp40) cc_final: 0.7797 (tp40) REVERT: C 67 TYR cc_start: 0.8784 (t80) cc_final: 0.8519 (t80) REVERT: C 97 SER cc_start: 0.8550 (m) cc_final: 0.8293 (p) REVERT: C 281 LYS cc_start: 0.8969 (mttt) cc_final: 0.8656 (mmmm) REVERT: D 59 GLN cc_start: 0.8703 (tp40) cc_final: 0.7877 (tp40) REVERT: D 67 TYR cc_start: 0.8767 (t80) cc_final: 0.8148 (t80) REVERT: D 257 MET cc_start: 0.8882 (mmm) cc_final: 0.8540 (mmm) REVERT: E 43 GLU cc_start: 0.8002 (tt0) cc_final: 0.7605 (tm-30) REVERT: E 253 PHE cc_start: 0.7593 (t80) cc_final: 0.7231 (t80) REVERT: E 257 MET cc_start: 0.8969 (mmm) cc_final: 0.8677 (mmm) REVERT: F 43 GLU cc_start: 0.7816 (tt0) cc_final: 0.7476 (tm-30) REVERT: F 59 GLN cc_start: 0.8734 (tp40) cc_final: 0.7800 (tp40) REVERT: F 67 TYR cc_start: 0.8782 (t80) cc_final: 0.8508 (t80) REVERT: F 97 SER cc_start: 0.8531 (m) cc_final: 0.8283 (p) REVERT: F 281 LYS cc_start: 0.8953 (mttt) cc_final: 0.8661 (mmmm) REVERT: G 43 GLU cc_start: 0.7852 (tt0) cc_final: 0.7514 (tm-30) REVERT: G 67 TYR cc_start: 0.8786 (t80) cc_final: 0.8544 (t80) REVERT: G 97 SER cc_start: 0.8495 (m) cc_final: 0.8232 (p) REVERT: G 281 LYS cc_start: 0.8998 (mttt) cc_final: 0.8699 (mmmm) REVERT: H 59 GLN cc_start: 0.8704 (tp40) cc_final: 0.7880 (tp40) REVERT: H 63 ASN cc_start: 0.7852 (m-40) cc_final: 0.7635 (t0) REVERT: H 67 TYR cc_start: 0.8775 (t80) cc_final: 0.8147 (t80) REVERT: H 257 MET cc_start: 0.8857 (mmm) cc_final: 0.8515 (mmm) REVERT: I 43 GLU cc_start: 0.7986 (tt0) cc_final: 0.7602 (tm-30) REVERT: I 59 GLN cc_start: 0.8856 (tp40) cc_final: 0.8204 (tp40) REVERT: I 253 PHE cc_start: 0.7583 (t80) cc_final: 0.7229 (t80) REVERT: I 257 MET cc_start: 0.8980 (mmm) cc_final: 0.8691 (mmm) REVERT: J 43 GLU cc_start: 0.7814 (tt0) cc_final: 0.7476 (tm-30) REVERT: J 67 TYR cc_start: 0.8792 (t80) cc_final: 0.8526 (t80) REVERT: J 97 SER cc_start: 0.8542 (m) cc_final: 0.8290 (p) REVERT: J 281 LYS cc_start: 0.8962 (mttt) cc_final: 0.8663 (mmmm) REVERT: K 59 GLN cc_start: 0.8710 (tp40) cc_final: 0.7908 (tp40) REVERT: K 67 TYR cc_start: 0.8791 (t80) cc_final: 0.8168 (t80) REVERT: K 257 MET cc_start: 0.8875 (mmm) cc_final: 0.8547 (mmm) REVERT: L 43 GLU cc_start: 0.7993 (tt0) cc_final: 0.7593 (tm-30) REVERT: L 59 GLN cc_start: 0.8868 (tp40) cc_final: 0.8193 (tp40) REVERT: L 253 PHE cc_start: 0.7606 (t80) cc_final: 0.7247 (t80) REVERT: L 257 MET cc_start: 0.8978 (mmm) cc_final: 0.8688 (mmm) outliers start: 0 outliers final: 0 residues processed: 844 average time/residue: 0.5834 time to fit residues: 562.2760 Evaluate side-chains 424 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.0970 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 ASN H 268 ASN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 ASN ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.147218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.108906 restraints weight = 33875.022| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.04 r_work: 0.3384 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21060 Z= 0.128 Angle : 0.610 7.934 28548 Z= 0.297 Chirality : 0.037 0.151 3396 Planarity : 0.004 0.038 3144 Dihedral : 8.662 57.527 6732 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.95 % Allowed : 19.41 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.09 (0.18), residues: 2196 helix: 3.71 (0.11), residues: 1680 sheet: 1.51 (0.46), residues: 120 loop : -1.88 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 285 TYR 0.020 0.001 TYR H 96 PHE 0.010 0.001 PHE E 33 TRP 0.011 0.001 TRP A 277 HIS 0.004 0.001 HIS K 274 Details of bonding type rmsd covalent geometry : bond 0.00281 (21024) covalent geometry : angle 0.60633 (28476) SS BOND : bond 0.01134 ( 36) SS BOND : angle 1.40921 ( 72) hydrogen bonds : bond 0.03734 ( 1416) hydrogen bonds : angle 3.00434 ( 4212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 448 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8673 (tp40) cc_final: 0.7963 (tp40) REVERT: A 253 PHE cc_start: 0.7843 (t80) cc_final: 0.7547 (t80) REVERT: A 257 MET cc_start: 0.8812 (mmm) cc_final: 0.8455 (mmm) REVERT: A 278 ARG cc_start: 0.8677 (mmp-170) cc_final: 0.8367 (mmp80) REVERT: B 43 GLU cc_start: 0.8282 (tt0) cc_final: 0.7774 (tm-30) REVERT: B 230 GLU cc_start: 0.8371 (mp0) cc_final: 0.8144 (mm-30) REVERT: B 278 ARG cc_start: 0.8509 (mmp80) cc_final: 0.8300 (mmp80) REVERT: C 43 GLU cc_start: 0.8180 (tt0) cc_final: 0.7699 (tm-30) REVERT: C 59 GLN cc_start: 0.8768 (tp40) cc_final: 0.7998 (tp40) REVERT: C 78 TYR cc_start: 0.8504 (t80) cc_final: 0.8246 (t80) REVERT: C 230 GLU cc_start: 0.8198 (mp0) cc_final: 0.7981 (mp0) REVERT: D 59 GLN cc_start: 0.8678 (tp40) cc_final: 0.7967 (tp40) REVERT: D 253 PHE cc_start: 0.7841 (t80) cc_final: 0.7537 (t80) REVERT: D 257 MET cc_start: 0.8803 (mmm) cc_final: 0.8412 (mmm) REVERT: D 278 ARG cc_start: 0.8674 (mmp-170) cc_final: 0.8369 (mmp80) REVERT: E 43 GLU cc_start: 0.8285 (tt0) cc_final: 0.7714 (tm-30) REVERT: E 59 GLN cc_start: 0.8866 (tp40) cc_final: 0.8008 (tp40) REVERT: E 230 GLU cc_start: 0.8357 (mp0) cc_final: 0.8090 (mm-30) REVERT: E 253 PHE cc_start: 0.7935 (t80) cc_final: 0.7725 (t80) REVERT: E 278 ARG cc_start: 0.8708 (mmp-170) cc_final: 0.8457 (mmp80) REVERT: F 21 MET cc_start: 0.8016 (pmm) cc_final: 0.7812 (pmm) REVERT: F 43 GLU cc_start: 0.8171 (tt0) cc_final: 0.7696 (tm-30) REVERT: F 59 GLN cc_start: 0.8770 (tp40) cc_final: 0.8020 (tp40) REVERT: F 78 TYR cc_start: 0.8474 (t80) cc_final: 0.8208 (t80) REVERT: F 230 GLU cc_start: 0.8224 (mp0) cc_final: 0.8003 (mp0) REVERT: G 43 GLU cc_start: 0.8200 (tt0) cc_final: 0.7723 (tm-30) REVERT: G 78 TYR cc_start: 0.8475 (t80) cc_final: 0.8216 (t80) REVERT: G 230 GLU cc_start: 0.8178 (mp0) cc_final: 0.7966 (mp0) REVERT: H 59 GLN cc_start: 0.8664 (tp40) cc_final: 0.7975 (tp40) REVERT: H 253 PHE cc_start: 0.7814 (t80) cc_final: 0.7516 (t80) REVERT: H 257 MET cc_start: 0.8813 (mmm) cc_final: 0.8478 (mmm) REVERT: H 278 ARG cc_start: 0.8674 (mmp-170) cc_final: 0.8355 (mmp80) REVERT: I 43 GLU cc_start: 0.8231 (tt0) cc_final: 0.7679 (tm-30) REVERT: I 59 GLN cc_start: 0.8804 (tp40) cc_final: 0.8295 (tp40) REVERT: I 230 GLU cc_start: 0.8361 (mp0) cc_final: 0.8137 (mm-30) REVERT: I 253 PHE cc_start: 0.7917 (t80) cc_final: 0.7717 (t80) REVERT: I 278 ARG cc_start: 0.8546 (mmp80) cc_final: 0.8298 (mmp80) REVERT: J 59 GLN cc_start: 0.8681 (tp40) cc_final: 0.8202 (tp40) REVERT: J 78 TYR cc_start: 0.8508 (t80) cc_final: 0.8270 (t80) REVERT: J 230 GLU cc_start: 0.8239 (mp0) cc_final: 0.8007 (mp0) REVERT: J 278 ARG cc_start: 0.8680 (mmp-170) cc_final: 0.8381 (mmp80) REVERT: K 59 GLN cc_start: 0.8648 (tp40) cc_final: 0.7928 (tp40) REVERT: K 253 PHE cc_start: 0.7828 (t80) cc_final: 0.7534 (t80) REVERT: K 257 MET cc_start: 0.8824 (mmm) cc_final: 0.8446 (mmm) REVERT: K 278 ARG cc_start: 0.8688 (mmp-170) cc_final: 0.8391 (mmp80) REVERT: L 43 GLU cc_start: 0.8245 (tt0) cc_final: 0.7715 (tm-30) REVERT: L 59 GLN cc_start: 0.8799 (tp40) cc_final: 0.8290 (tp40) REVERT: L 230 GLU cc_start: 0.8365 (mp0) cc_final: 0.8138 (mm-30) outliers start: 39 outliers final: 30 residues processed: 475 average time/residue: 0.6694 time to fit residues: 356.9850 Evaluate side-chains 416 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 386 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 277 TRP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 277 TRP Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain L residue 92 CYS Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 93 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 207 ASN A 268 ASN B 75 HIS B 82 GLN B 207 ASN C 75 HIS D 75 HIS D 207 ASN D 268 ASN E 75 HIS E 82 GLN E 207 ASN F 75 HIS G 75 HIS H 75 HIS H 207 ASN H 268 ASN I 75 HIS I 82 GLN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 HIS K 75 HIS K 207 ASN K 268 ASN L 75 HIS L 82 GLN L 207 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.132815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.092447 restraints weight = 34260.285| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.90 r_work: 0.3093 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21060 Z= 0.178 Angle : 0.668 12.251 28548 Z= 0.333 Chirality : 0.041 0.263 3396 Planarity : 0.004 0.030 3144 Dihedral : 7.948 48.441 6732 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.69 % Allowed : 20.66 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.60 (0.18), residues: 2196 helix: 3.31 (0.11), residues: 1692 sheet: 0.16 (0.38), residues: 204 loop : -1.97 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 278 TYR 0.016 0.002 TYR H 234 PHE 0.010 0.001 PHE E 33 TRP 0.019 0.002 TRP G 277 HIS 0.002 0.001 HIS L 274 Details of bonding type rmsd covalent geometry : bond 0.00418 (21024) covalent geometry : angle 0.66160 (28476) SS BOND : bond 0.00211 ( 36) SS BOND : angle 1.99754 ( 72) hydrogen bonds : bond 0.05956 ( 1416) hydrogen bonds : angle 3.24414 ( 4212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 407 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8198 (ptt-90) cc_final: 0.7964 (ptp90) REVERT: A 59 GLN cc_start: 0.8928 (tp40) cc_final: 0.8121 (tp40) REVERT: A 78 TYR cc_start: 0.8900 (t80) cc_final: 0.8686 (t80) REVERT: A 217 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8413 (tt0) REVERT: A 253 PHE cc_start: 0.8598 (t80) cc_final: 0.8331 (t80) REVERT: A 257 MET cc_start: 0.8820 (mmm) cc_final: 0.8472 (mmm) REVERT: A 278 ARG cc_start: 0.8692 (mmp-170) cc_final: 0.8412 (mmp80) REVERT: B 43 GLU cc_start: 0.8330 (tt0) cc_final: 0.7862 (tm-30) REVERT: B 48 ASP cc_start: 0.9169 (p0) cc_final: 0.8830 (p0) REVERT: B 217 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8425 (tt0) REVERT: B 230 GLU cc_start: 0.8538 (mp0) cc_final: 0.8271 (mm-30) REVERT: B 281 LYS cc_start: 0.9118 (tppt) cc_final: 0.8773 (mmmm) REVERT: C 59 GLN cc_start: 0.9037 (tp40) cc_final: 0.8153 (tp40) REVERT: C 230 GLU cc_start: 0.8482 (mp0) cc_final: 0.8078 (pm20) REVERT: D 59 GLN cc_start: 0.8916 (tp40) cc_final: 0.8097 (tp40) REVERT: D 78 TYR cc_start: 0.8933 (t80) cc_final: 0.8722 (t80) REVERT: D 217 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8421 (tt0) REVERT: D 253 PHE cc_start: 0.8598 (t80) cc_final: 0.8335 (t80) REVERT: D 257 MET cc_start: 0.8820 (mmm) cc_final: 0.8428 (mmm) REVERT: D 278 ARG cc_start: 0.8707 (mmp-170) cc_final: 0.8439 (mmp80) REVERT: E 48 ASP cc_start: 0.9123 (p0) cc_final: 0.8822 (p0) REVERT: E 230 GLU cc_start: 0.8533 (mp0) cc_final: 0.8274 (mm-30) REVERT: E 239 GLU cc_start: 0.8461 (tt0) cc_final: 0.8259 (tt0) REVERT: E 281 LYS cc_start: 0.9001 (tppt) cc_final: 0.8789 (mmmm) REVERT: F 59 GLN cc_start: 0.9053 (tp40) cc_final: 0.8201 (tp40) REVERT: F 230 GLU cc_start: 0.8510 (mp0) cc_final: 0.8103 (pm20) REVERT: G 59 GLN cc_start: 0.9018 (tp40) cc_final: 0.8607 (tp40) REVERT: G 230 GLU cc_start: 0.8445 (mp0) cc_final: 0.8059 (pm20) REVERT: H 59 GLN cc_start: 0.8917 (tp40) cc_final: 0.8122 (tp40) REVERT: H 78 TYR cc_start: 0.8887 (t80) cc_final: 0.8671 (t80) REVERT: H 217 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8428 (tt0) REVERT: H 253 PHE cc_start: 0.8549 (t80) cc_final: 0.8317 (t80) REVERT: H 257 MET cc_start: 0.8806 (mmm) cc_final: 0.8449 (mmm) REVERT: H 278 ARG cc_start: 0.8723 (mmp-170) cc_final: 0.8452 (mmp80) REVERT: I 48 ASP cc_start: 0.9174 (p0) cc_final: 0.8826 (p0) REVERT: I 59 GLN cc_start: 0.9071 (tp40) cc_final: 0.8375 (tp40) REVERT: I 217 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8420 (tt0) REVERT: I 230 GLU cc_start: 0.8547 (mp0) cc_final: 0.8294 (mm-30) REVERT: I 239 GLU cc_start: 0.8463 (tt0) cc_final: 0.8262 (tt0) REVERT: I 281 LYS cc_start: 0.9095 (tppt) cc_final: 0.8757 (mmmm) REVERT: J 59 GLN cc_start: 0.9036 (tp40) cc_final: 0.8536 (tp40) REVERT: J 230 GLU cc_start: 0.8487 (mp0) cc_final: 0.8096 (pm20) REVERT: J 278 ARG cc_start: 0.8782 (mmp-170) cc_final: 0.8474 (mmp80) REVERT: K 59 GLN cc_start: 0.8905 (tp40) cc_final: 0.8098 (tp40) REVERT: K 78 TYR cc_start: 0.8911 (t80) cc_final: 0.8700 (t80) REVERT: K 217 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8419 (tt0) REVERT: K 253 PHE cc_start: 0.8587 (t80) cc_final: 0.8332 (t80) REVERT: K 257 MET cc_start: 0.8823 (mmm) cc_final: 0.8444 (mmm) REVERT: K 278 ARG cc_start: 0.8742 (mmp-170) cc_final: 0.8475 (mmp80) REVERT: L 20 THR cc_start: 0.7316 (p) cc_final: 0.6854 (p) REVERT: L 43 GLU cc_start: 0.8306 (tt0) cc_final: 0.7834 (tm-30) REVERT: L 48 ASP cc_start: 0.9110 (p0) cc_final: 0.8821 (p0) REVERT: L 59 GLN cc_start: 0.9044 (tp40) cc_final: 0.8352 (tp40) REVERT: L 217 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8419 (tt0) REVERT: L 230 GLU cc_start: 0.8526 (mp0) cc_final: 0.8271 (mm-30) REVERT: L 239 GLU cc_start: 0.8461 (tt0) cc_final: 0.8259 (tt0) REVERT: L 281 LYS cc_start: 0.9200 (tppt) cc_final: 0.8817 (mmmm) outliers start: 54 outliers final: 33 residues processed: 431 average time/residue: 0.7083 time to fit residues: 340.8991 Evaluate side-chains 402 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 369 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain L residue 92 CYS Chi-restraints excluded: chain L residue 224 SER Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 84 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN A 268 ASN B 82 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN E 82 GLN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 268 ASN I 82 GLN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 ASN L 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.133928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.094038 restraints weight = 34317.016| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.92 r_work: 0.3128 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21060 Z= 0.139 Angle : 0.637 12.298 28548 Z= 0.316 Chirality : 0.039 0.257 3396 Planarity : 0.004 0.040 3144 Dihedral : 7.460 50.145 6732 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.59 % Allowed : 21.46 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.89 (0.18), residues: 2196 helix: 3.51 (0.11), residues: 1680 sheet: -0.01 (0.37), residues: 204 loop : -1.38 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 24 TYR 0.024 0.002 TYR K 96 PHE 0.010 0.001 PHE D 33 TRP 0.017 0.001 TRP C 277 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00322 (21024) covalent geometry : angle 0.63016 (28476) SS BOND : bond 0.00723 ( 36) SS BOND : angle 1.93963 ( 72) hydrogen bonds : bond 0.04819 ( 1416) hydrogen bonds : angle 3.07032 ( 4212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 392 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8060 (ptt-90) cc_final: 0.7840 (ptp90) REVERT: A 52 MET cc_start: 0.9240 (mmt) cc_final: 0.8956 (mmm) REVERT: A 59 GLN cc_start: 0.8958 (tp40) cc_final: 0.8148 (tp40) REVERT: A 78 TYR cc_start: 0.8887 (t80) cc_final: 0.8649 (t80) REVERT: A 217 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8498 (tt0) REVERT: A 253 PHE cc_start: 0.8598 (t80) cc_final: 0.8258 (t80) REVERT: A 257 MET cc_start: 0.8827 (mmm) cc_final: 0.8439 (mmm) REVERT: A 271 GLU cc_start: 0.9240 (tp30) cc_final: 0.9029 (tp30) REVERT: A 278 ARG cc_start: 0.8760 (mmp-170) cc_final: 0.8517 (mmp80) REVERT: B 43 GLU cc_start: 0.8510 (tt0) cc_final: 0.7990 (tm-30) REVERT: B 48 ASP cc_start: 0.9118 (p0) cc_final: 0.8747 (p0) REVERT: B 230 GLU cc_start: 0.8607 (mp0) cc_final: 0.8383 (mm-30) REVERT: B 239 GLU cc_start: 0.8505 (tt0) cc_final: 0.8304 (tt0) REVERT: B 281 LYS cc_start: 0.9150 (tppt) cc_final: 0.8768 (mmmm) REVERT: C 48 ASP cc_start: 0.8934 (p0) cc_final: 0.8689 (p0) REVERT: C 59 GLN cc_start: 0.9006 (tp40) cc_final: 0.8061 (tp40) REVERT: C 230 GLU cc_start: 0.8429 (mp0) cc_final: 0.7976 (pm20) REVERT: D 52 MET cc_start: 0.9258 (mmt) cc_final: 0.8989 (mmm) REVERT: D 59 GLN cc_start: 0.8920 (tp40) cc_final: 0.8087 (tp40) REVERT: D 78 TYR cc_start: 0.8906 (t80) cc_final: 0.8660 (t80) REVERT: D 217 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8437 (tt0) REVERT: D 253 PHE cc_start: 0.8588 (t80) cc_final: 0.8250 (t80) REVERT: D 257 MET cc_start: 0.8820 (mmm) cc_final: 0.8434 (mmm) REVERT: D 278 ARG cc_start: 0.8754 (mmp-170) cc_final: 0.8508 (mmp80) REVERT: E 48 ASP cc_start: 0.9074 (p0) cc_final: 0.8715 (p0) REVERT: E 230 GLU cc_start: 0.8588 (mp0) cc_final: 0.8331 (mm-30) REVERT: E 281 LYS cc_start: 0.9170 (tppt) cc_final: 0.8790 (mmmm) REVERT: F 48 ASP cc_start: 0.8921 (p0) cc_final: 0.8653 (p0) REVERT: F 59 GLN cc_start: 0.9009 (tp40) cc_final: 0.8080 (tp40) REVERT: F 230 GLU cc_start: 0.8443 (mp0) cc_final: 0.7994 (pm20) REVERT: G 48 ASP cc_start: 0.8904 (p0) cc_final: 0.8665 (p0) REVERT: G 230 GLU cc_start: 0.8409 (mp0) cc_final: 0.7969 (pm20) REVERT: H 52 MET cc_start: 0.9250 (mmt) cc_final: 0.8898 (mmm) REVERT: H 59 GLN cc_start: 0.8916 (tp40) cc_final: 0.8114 (tp40) REVERT: H 78 TYR cc_start: 0.8852 (t80) cc_final: 0.8607 (t80) REVERT: H 217 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8407 (tt0) REVERT: H 253 PHE cc_start: 0.8569 (t80) cc_final: 0.8240 (t80) REVERT: H 257 MET cc_start: 0.8812 (mmm) cc_final: 0.8434 (mmm) REVERT: H 278 ARG cc_start: 0.8771 (mmp-170) cc_final: 0.8565 (mmp80) REVERT: I 48 ASP cc_start: 0.9127 (p0) cc_final: 0.8756 (p0) REVERT: I 59 GLN cc_start: 0.8973 (tp40) cc_final: 0.8218 (tp40) REVERT: I 230 GLU cc_start: 0.8615 (mp0) cc_final: 0.8377 (mm-30) REVERT: I 281 LYS cc_start: 0.9161 (tppt) cc_final: 0.8776 (mmmm) REVERT: J 48 ASP cc_start: 0.8918 (p0) cc_final: 0.8544 (p0) REVERT: J 59 GLN cc_start: 0.9019 (tp40) cc_final: 0.8511 (tp40) REVERT: J 230 GLU cc_start: 0.8437 (mp0) cc_final: 0.7990 (pm20) REVERT: K 26 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8921 (mt) REVERT: K 52 MET cc_start: 0.9245 (mmt) cc_final: 0.8976 (mmm) REVERT: K 59 GLN cc_start: 0.8907 (tp40) cc_final: 0.8088 (tp40) REVERT: K 78 TYR cc_start: 0.8863 (t80) cc_final: 0.8626 (t80) REVERT: K 217 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8401 (tt0) REVERT: K 253 PHE cc_start: 0.8592 (t80) cc_final: 0.8255 (t80) REVERT: K 257 MET cc_start: 0.8822 (mmm) cc_final: 0.8436 (mmm) REVERT: K 278 ARG cc_start: 0.8786 (mmp-170) cc_final: 0.8584 (mmp80) REVERT: L 43 GLU cc_start: 0.8468 (tt0) cc_final: 0.7937 (tm-30) REVERT: L 48 ASP cc_start: 0.9066 (p0) cc_final: 0.8703 (p0) REVERT: L 59 GLN cc_start: 0.8965 (tp40) cc_final: 0.8201 (tp40) REVERT: L 230 GLU cc_start: 0.8603 (mp0) cc_final: 0.8368 (mm-30) REVERT: L 281 LYS cc_start: 0.9106 (tppt) cc_final: 0.8717 (mmmm) outliers start: 52 outliers final: 17 residues processed: 418 average time/residue: 0.7155 time to fit residues: 333.5221 Evaluate side-chains 386 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 368 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 178 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN E 82 GLN E 217 GLN I 82 GLN L 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.134072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094517 restraints weight = 33698.774| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.89 r_work: 0.3134 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21060 Z= 0.133 Angle : 0.645 14.053 28548 Z= 0.321 Chirality : 0.039 0.268 3396 Planarity : 0.003 0.033 3144 Dihedral : 7.153 51.642 6732 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.50 % Allowed : 22.75 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.89 (0.18), residues: 2196 helix: 3.54 (0.11), residues: 1692 sheet: 0.48 (0.41), residues: 144 loop : -1.77 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 24 TYR 0.026 0.002 TYR D 96 PHE 0.010 0.001 PHE D 33 TRP 0.018 0.001 TRP G 277 HIS 0.003 0.001 HIS L 274 Details of bonding type rmsd covalent geometry : bond 0.00308 (21024) covalent geometry : angle 0.63758 (28476) SS BOND : bond 0.00639 ( 36) SS BOND : angle 2.07866 ( 72) hydrogen bonds : bond 0.04417 ( 1416) hydrogen bonds : angle 3.01967 ( 4212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 396 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8026 (ptt-90) cc_final: 0.7819 (ptp90) REVERT: A 48 ASP cc_start: 0.9035 (p0) cc_final: 0.8765 (p0) REVERT: A 52 MET cc_start: 0.9211 (mmt) cc_final: 0.8889 (mmm) REVERT: A 59 GLN cc_start: 0.8954 (tp40) cc_final: 0.8563 (tp40) REVERT: A 210 GLU cc_start: 0.9103 (tp30) cc_final: 0.8841 (mm-30) REVERT: A 217 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8391 (tt0) REVERT: A 230 GLU cc_start: 0.8307 (mp0) cc_final: 0.8082 (mt-10) REVERT: A 239 GLU cc_start: 0.8319 (tt0) cc_final: 0.7391 (tt0) REVERT: A 253 PHE cc_start: 0.8571 (t80) cc_final: 0.8237 (t80) REVERT: A 257 MET cc_start: 0.8793 (mmm) cc_final: 0.8411 (mmm) REVERT: A 271 GLU cc_start: 0.9229 (tp30) cc_final: 0.9003 (tp30) REVERT: B 43 GLU cc_start: 0.8560 (tt0) cc_final: 0.8067 (tm-30) REVERT: B 48 ASP cc_start: 0.9098 (p0) cc_final: 0.8838 (p0) REVERT: B 230 GLU cc_start: 0.8577 (mp0) cc_final: 0.8259 (mm-30) REVERT: B 239 GLU cc_start: 0.8468 (tt0) cc_final: 0.8232 (tt0) REVERT: B 281 LYS cc_start: 0.9144 (tppt) cc_final: 0.8767 (mmmm) REVERT: C 59 GLN cc_start: 0.9013 (tp40) cc_final: 0.8169 (tp40) REVERT: C 210 GLU cc_start: 0.9063 (tp30) cc_final: 0.8853 (tp30) REVERT: C 230 GLU cc_start: 0.8412 (mp0) cc_final: 0.8120 (mm-30) REVERT: D 48 ASP cc_start: 0.9041 (p0) cc_final: 0.8799 (p0) REVERT: D 52 MET cc_start: 0.9225 (mmt) cc_final: 0.8917 (mmm) REVERT: D 59 GLN cc_start: 0.8947 (tp40) cc_final: 0.8564 (tp40) REVERT: D 217 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8402 (tt0) REVERT: D 230 GLU cc_start: 0.8272 (mp0) cc_final: 0.8031 (mt-10) REVERT: D 239 GLU cc_start: 0.8303 (tt0) cc_final: 0.7508 (tt0) REVERT: D 253 PHE cc_start: 0.8583 (t80) cc_final: 0.8252 (t80) REVERT: D 257 MET cc_start: 0.8789 (mmm) cc_final: 0.8407 (mmm) REVERT: E 20 THR cc_start: 0.7248 (p) cc_final: 0.6464 (p) REVERT: E 48 ASP cc_start: 0.9112 (p0) cc_final: 0.8799 (p0) REVERT: E 230 GLU cc_start: 0.8608 (mp0) cc_final: 0.8324 (mm-30) REVERT: E 281 LYS cc_start: 0.9128 (tppt) cc_final: 0.8754 (mmmm) REVERT: F 48 ASP cc_start: 0.8926 (p0) cc_final: 0.8571 (p0) REVERT: F 59 GLN cc_start: 0.9008 (tp40) cc_final: 0.8139 (tp40) REVERT: F 230 GLU cc_start: 0.8419 (mp0) cc_final: 0.8121 (mm-30) REVERT: G 48 ASP cc_start: 0.8931 (p0) cc_final: 0.8586 (p0) REVERT: G 59 GLN cc_start: 0.9018 (tp40) cc_final: 0.8550 (tp40) REVERT: G 230 GLU cc_start: 0.8407 (mp0) cc_final: 0.8115 (mm-30) REVERT: H 52 MET cc_start: 0.9192 (mmt) cc_final: 0.8943 (mmm) REVERT: H 217 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8373 (tt0) REVERT: H 253 PHE cc_start: 0.8487 (t80) cc_final: 0.8154 (t80) REVERT: H 257 MET cc_start: 0.8769 (mmm) cc_final: 0.8397 (mmm) REVERT: I 20 THR cc_start: 0.7301 (p) cc_final: 0.6523 (p) REVERT: I 48 ASP cc_start: 0.9119 (p0) cc_final: 0.8866 (p0) REVERT: I 59 GLN cc_start: 0.8899 (tp40) cc_final: 0.8152 (tp40) REVERT: I 230 GLU cc_start: 0.8599 (mp0) cc_final: 0.8322 (mm-30) REVERT: I 281 LYS cc_start: 0.9125 (tppt) cc_final: 0.8748 (mmmm) REVERT: J 48 ASP cc_start: 0.8877 (p0) cc_final: 0.8534 (p0) REVERT: J 59 GLN cc_start: 0.9023 (tp40) cc_final: 0.8543 (tp40) REVERT: J 230 GLU cc_start: 0.8434 (mp0) cc_final: 0.8126 (mm-30) REVERT: K 48 ASP cc_start: 0.9035 (p0) cc_final: 0.8784 (p0) REVERT: K 52 MET cc_start: 0.9231 (mmt) cc_final: 0.8911 (mmm) REVERT: K 217 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8368 (tt0) REVERT: K 253 PHE cc_start: 0.8578 (t80) cc_final: 0.8247 (t80) REVERT: K 257 MET cc_start: 0.8782 (mmm) cc_final: 0.8403 (mmm) REVERT: L 43 GLU cc_start: 0.8553 (tt0) cc_final: 0.8064 (tm-30) REVERT: L 48 ASP cc_start: 0.9102 (p0) cc_final: 0.8794 (p0) REVERT: L 59 GLN cc_start: 0.8887 (tp40) cc_final: 0.8151 (tp40) REVERT: L 230 GLU cc_start: 0.8599 (mp0) cc_final: 0.8329 (mm-30) REVERT: L 281 LYS cc_start: 0.9137 (tppt) cc_final: 0.8769 (mmmm) outliers start: 50 outliers final: 25 residues processed: 432 average time/residue: 0.6892 time to fit residues: 332.9841 Evaluate side-chains 385 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 360 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 46 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 82 GLN E 82 GLN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN H 56 ASN I 82 GLN K 56 ASN L 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.131252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.091821 restraints weight = 33757.412| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.87 r_work: 0.3094 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21060 Z= 0.160 Angle : 0.675 10.893 28548 Z= 0.337 Chirality : 0.040 0.242 3396 Planarity : 0.004 0.047 3144 Dihedral : 7.154 54.217 6732 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.45 % Allowed : 24.75 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.87 (0.18), residues: 2196 helix: 3.50 (0.11), residues: 1692 sheet: 0.57 (0.41), residues: 144 loop : -1.65 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 285 TYR 0.027 0.002 TYR I 96 PHE 0.015 0.001 PHE H 81 TRP 0.019 0.002 TRP J 277 HIS 0.003 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00387 (21024) covalent geometry : angle 0.66764 (28476) SS BOND : bond 0.00717 ( 36) SS BOND : angle 2.06201 ( 72) hydrogen bonds : bond 0.05017 ( 1416) hydrogen bonds : angle 3.07833 ( 4212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 383 time to evaluate : 0.803 Fit side-chains REVERT: A 24 ARG cc_start: 0.7985 (ptt-90) cc_final: 0.7630 (ptp90) REVERT: A 59 GLN cc_start: 0.8984 (tp40) cc_final: 0.8094 (tp40) REVERT: A 68 ASP cc_start: 0.8511 (t70) cc_final: 0.8275 (t0) REVERT: A 210 GLU cc_start: 0.9132 (tp30) cc_final: 0.8867 (mm-30) REVERT: A 241 GLU cc_start: 0.8427 (tt0) cc_final: 0.8097 (tt0) REVERT: A 253 PHE cc_start: 0.8445 (t80) cc_final: 0.8174 (t80) REVERT: A 257 MET cc_start: 0.8819 (mmm) cc_final: 0.8416 (mmm) REVERT: A 271 GLU cc_start: 0.9244 (tp30) cc_final: 0.9012 (tp30) REVERT: B 24 ARG cc_start: 0.8151 (ptp90) cc_final: 0.7918 (ptp90) REVERT: B 43 GLU cc_start: 0.8607 (tt0) cc_final: 0.8095 (tm-30) REVERT: B 48 ASP cc_start: 0.9185 (p0) cc_final: 0.8866 (p0) REVERT: B 230 GLU cc_start: 0.8610 (mp0) cc_final: 0.8303 (mm-30) REVERT: B 239 GLU cc_start: 0.8701 (tt0) cc_final: 0.8439 (tt0) REVERT: B 281 LYS cc_start: 0.9178 (tppt) cc_final: 0.8802 (mmmm) REVERT: C 48 ASP cc_start: 0.8920 (p0) cc_final: 0.8619 (p0) REVERT: C 59 GLN cc_start: 0.9121 (tp40) cc_final: 0.8218 (tp40) REVERT: C 210 GLU cc_start: 0.9087 (tp30) cc_final: 0.8847 (tp30) REVERT: C 230 GLU cc_start: 0.8487 (mp0) cc_final: 0.8018 (pm20) REVERT: D 59 GLN cc_start: 0.8951 (tp40) cc_final: 0.8084 (tp40) REVERT: D 210 GLU cc_start: 0.9109 (tp30) cc_final: 0.8805 (mm-30) REVERT: D 241 GLU cc_start: 0.8441 (tt0) cc_final: 0.8057 (tt0) REVERT: D 253 PHE cc_start: 0.8446 (t80) cc_final: 0.8174 (t80) REVERT: D 257 MET cc_start: 0.8816 (mmm) cc_final: 0.8412 (mmm) REVERT: E 24 ARG cc_start: 0.8069 (ptt-90) cc_final: 0.7721 (pmt170) REVERT: E 48 ASP cc_start: 0.9153 (p0) cc_final: 0.8828 (p0) REVERT: E 230 GLU cc_start: 0.8627 (mp0) cc_final: 0.8309 (mm-30) REVERT: E 281 LYS cc_start: 0.9140 (tppt) cc_final: 0.8777 (mmmm) REVERT: F 48 ASP cc_start: 0.9018 (p0) cc_final: 0.8633 (p0) REVERT: F 59 GLN cc_start: 0.9124 (tp40) cc_final: 0.8161 (tp40) REVERT: F 230 GLU cc_start: 0.8517 (mp0) cc_final: 0.8054 (pm20) REVERT: G 48 ASP cc_start: 0.8999 (p0) cc_final: 0.8600 (p0) REVERT: G 230 GLU cc_start: 0.8479 (mp0) cc_final: 0.8020 (pm20) REVERT: H 48 ASP cc_start: 0.9085 (p0) cc_final: 0.8718 (p0) REVERT: H 59 GLN cc_start: 0.8979 (tp40) cc_final: 0.8097 (tp40) REVERT: H 210 GLU cc_start: 0.9114 (tp30) cc_final: 0.8816 (mm-30) REVERT: H 241 GLU cc_start: 0.8435 (tt0) cc_final: 0.8102 (tt0) REVERT: H 253 PHE cc_start: 0.8363 (t80) cc_final: 0.8132 (t80) REVERT: H 257 MET cc_start: 0.8799 (mmm) cc_final: 0.8396 (mmm) REVERT: I 24 ARG cc_start: 0.8070 (ptt-90) cc_final: 0.7725 (pmt170) REVERT: I 48 ASP cc_start: 0.9160 (p0) cc_final: 0.8842 (p0) REVERT: I 59 GLN cc_start: 0.8935 (tp40) cc_final: 0.8177 (tp40) REVERT: I 230 GLU cc_start: 0.8633 (mp0) cc_final: 0.8322 (mm-30) REVERT: I 281 LYS cc_start: 0.9135 (tppt) cc_final: 0.8775 (mmmm) REVERT: J 48 ASP cc_start: 0.9010 (p0) cc_final: 0.8608 (p0) REVERT: J 230 GLU cc_start: 0.8492 (mp0) cc_final: 0.8055 (pm20) REVERT: K 59 GLN cc_start: 0.8975 (tp40) cc_final: 0.8063 (tp40) REVERT: K 210 GLU cc_start: 0.9101 (tp30) cc_final: 0.8807 (mm-30) REVERT: K 239 GLU cc_start: 0.8401 (tt0) cc_final: 0.8147 (tt0) REVERT: K 241 GLU cc_start: 0.8431 (tt0) cc_final: 0.8115 (tt0) REVERT: K 253 PHE cc_start: 0.8445 (t80) cc_final: 0.8178 (t80) REVERT: K 257 MET cc_start: 0.8813 (mmm) cc_final: 0.8413 (mmm) REVERT: L 43 GLU cc_start: 0.8649 (tt0) cc_final: 0.8156 (tm-30) REVERT: L 48 ASP cc_start: 0.9155 (p0) cc_final: 0.8830 (p0) REVERT: L 59 GLN cc_start: 0.8922 (tp40) cc_final: 0.8197 (tp40) REVERT: L 230 GLU cc_start: 0.8622 (mp0) cc_final: 0.8305 (mm-30) REVERT: L 281 LYS cc_start: 0.9154 (tppt) cc_final: 0.8780 (mmmm) outliers start: 49 outliers final: 17 residues processed: 416 average time/residue: 0.6632 time to fit residues: 308.7899 Evaluate side-chains 388 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 371 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 177 optimal weight: 0.6980 chunk 210 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 134 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 82 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN E 82 GLN E 217 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 ASN I 82 GLN ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 ASN L 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.130552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.091101 restraints weight = 33967.529| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.88 r_work: 0.3067 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21060 Z= 0.167 Angle : 0.690 14.035 28548 Z= 0.344 Chirality : 0.040 0.205 3396 Planarity : 0.004 0.048 3144 Dihedral : 7.175 55.852 6732 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.79 % Allowed : 25.60 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.88 (0.18), residues: 2196 helix: 3.52 (0.11), residues: 1692 sheet: 0.32 (0.42), residues: 144 loop : -1.60 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 24 TYR 0.027 0.002 TYR D 96 PHE 0.013 0.001 PHE H 81 TRP 0.013 0.001 TRP J 277 HIS 0.003 0.001 HIS K 75 Details of bonding type rmsd covalent geometry : bond 0.00401 (21024) covalent geometry : angle 0.68343 (28476) SS BOND : bond 0.00640 ( 36) SS BOND : angle 1.99158 ( 72) hydrogen bonds : bond 0.05196 ( 1416) hydrogen bonds : angle 3.08805 ( 4212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 387 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7963 (ptt-90) cc_final: 0.7743 (ptt-90) REVERT: A 48 ASP cc_start: 0.9050 (p0) cc_final: 0.8743 (p0) REVERT: A 59 GLN cc_start: 0.8983 (tp40) cc_final: 0.8126 (tp40) REVERT: A 241 GLU cc_start: 0.8428 (tt0) cc_final: 0.8125 (tt0) REVERT: A 257 MET cc_start: 0.8826 (mmm) cc_final: 0.8424 (mmm) REVERT: B 43 GLU cc_start: 0.8598 (tt0) cc_final: 0.8086 (tm-30) REVERT: B 48 ASP cc_start: 0.9219 (p0) cc_final: 0.8934 (p0) REVERT: B 230 GLU cc_start: 0.8616 (mp0) cc_final: 0.8381 (mp0) REVERT: B 281 LYS cc_start: 0.9277 (tppt) cc_final: 0.8916 (mmmm) REVERT: C 48 ASP cc_start: 0.9044 (p0) cc_final: 0.8639 (p0) REVERT: C 230 GLU cc_start: 0.8520 (mp0) cc_final: 0.8064 (pm20) REVERT: D 48 ASP cc_start: 0.9116 (p0) cc_final: 0.8824 (p0) REVERT: D 59 GLN cc_start: 0.8984 (tp40) cc_final: 0.8572 (tp40) REVERT: D 241 GLU cc_start: 0.8449 (tt0) cc_final: 0.8080 (tt0) REVERT: D 257 MET cc_start: 0.8824 (mmm) cc_final: 0.8422 (mmm) REVERT: E 24 ARG cc_start: 0.8062 (ptt-90) cc_final: 0.7819 (ptt-90) REVERT: E 48 ASP cc_start: 0.9194 (p0) cc_final: 0.8886 (p0) REVERT: E 230 GLU cc_start: 0.8634 (mp0) cc_final: 0.8343 (mm-30) REVERT: E 281 LYS cc_start: 0.9179 (tppt) cc_final: 0.8810 (mmmm) REVERT: F 48 ASP cc_start: 0.9051 (p0) cc_final: 0.8623 (p0) REVERT: F 59 GLN cc_start: 0.9156 (tp40) cc_final: 0.8166 (tp40) REVERT: F 97 SER cc_start: 0.8722 (m) cc_final: 0.8353 (p) REVERT: F 210 GLU cc_start: 0.9059 (tp30) cc_final: 0.8625 (tp30) REVERT: F 230 GLU cc_start: 0.8453 (mp0) cc_final: 0.7978 (pm20) REVERT: G 48 ASP cc_start: 0.9046 (p0) cc_final: 0.8569 (p0) REVERT: G 97 SER cc_start: 0.8729 (m) cc_final: 0.8342 (p) REVERT: G 230 GLU cc_start: 0.8519 (mp0) cc_final: 0.8187 (mm-30) REVERT: G 239 GLU cc_start: 0.8490 (tt0) cc_final: 0.8108 (tt0) REVERT: H 48 ASP cc_start: 0.9148 (p0) cc_final: 0.8799 (p0) REVERT: H 52 MET cc_start: 0.9308 (mmt) cc_final: 0.8952 (mmm) REVERT: H 59 GLN cc_start: 0.8964 (tp40) cc_final: 0.8131 (tp40) REVERT: H 241 GLU cc_start: 0.8439 (tt0) cc_final: 0.8143 (tt0) REVERT: H 257 MET cc_start: 0.8804 (mmm) cc_final: 0.8410 (mmm) REVERT: I 48 ASP cc_start: 0.9183 (p0) cc_final: 0.8902 (p0) REVERT: I 59 GLN cc_start: 0.8896 (tp40) cc_final: 0.8145 (tp40) REVERT: I 230 GLU cc_start: 0.8651 (mp0) cc_final: 0.8330 (mm-30) REVERT: I 281 LYS cc_start: 0.9251 (tppt) cc_final: 0.8888 (mmmm) REVERT: J 24 ARG cc_start: 0.7935 (ptt-90) cc_final: 0.7588 (mpt180) REVERT: J 48 ASP cc_start: 0.9051 (p0) cc_final: 0.8592 (p0) REVERT: J 97 SER cc_start: 0.8720 (m) cc_final: 0.8352 (p) REVERT: J 230 GLU cc_start: 0.8454 (mp0) cc_final: 0.7981 (pm20) REVERT: K 24 ARG cc_start: 0.7862 (ptt-90) cc_final: 0.7585 (pmt170) REVERT: K 48 ASP cc_start: 0.9084 (p0) cc_final: 0.8795 (p0) REVERT: K 241 GLU cc_start: 0.8494 (tt0) cc_final: 0.8221 (tt0) REVERT: K 257 MET cc_start: 0.8818 (mmm) cc_final: 0.8421 (mmm) REVERT: L 20 THR cc_start: 0.7667 (p) cc_final: 0.7037 (p) REVERT: L 24 ARG cc_start: 0.8272 (ptp90) cc_final: 0.7986 (ptt-90) REVERT: L 43 GLU cc_start: 0.8637 (tt0) cc_final: 0.8158 (tm-30) REVERT: L 48 ASP cc_start: 0.9203 (p0) cc_final: 0.8855 (p0) REVERT: L 230 GLU cc_start: 0.8649 (mp0) cc_final: 0.8319 (mm-30) REVERT: L 281 LYS cc_start: 0.9257 (tppt) cc_final: 0.8886 (mmmm) outliers start: 56 outliers final: 18 residues processed: 422 average time/residue: 0.6592 time to fit residues: 312.4900 Evaluate side-chains 390 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 372 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain L residue 224 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 14 optimal weight: 0.2980 chunk 160 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 82 GLN D 104 GLN D 207 ASN E 82 GLN E 217 GLN H 104 GLN I 82 GLN I 104 GLN L 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.132434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.093360 restraints weight = 33960.748| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.86 r_work: 0.3117 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21060 Z= 0.140 Angle : 0.677 12.151 28548 Z= 0.336 Chirality : 0.038 0.167 3396 Planarity : 0.004 0.061 3144 Dihedral : 6.958 55.757 6732 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.95 % Allowed : 27.30 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.09 (0.18), residues: 2196 helix: 3.68 (0.11), residues: 1692 sheet: 0.27 (0.43), residues: 144 loop : -1.56 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 285 TYR 0.021 0.002 TYR K 96 PHE 0.013 0.001 PHE H 81 TRP 0.014 0.001 TRP J 277 HIS 0.003 0.001 HIS L 274 Details of bonding type rmsd covalent geometry : bond 0.00326 (21024) covalent geometry : angle 0.67274 (28476) SS BOND : bond 0.00560 ( 36) SS BOND : angle 1.62403 ( 72) hydrogen bonds : bond 0.04474 ( 1416) hydrogen bonds : angle 3.00043 ( 4212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 405 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.9145 (p0) cc_final: 0.8817 (p0) REVERT: A 59 GLN cc_start: 0.8948 (tp40) cc_final: 0.8559 (tp40) REVERT: A 241 GLU cc_start: 0.8358 (tt0) cc_final: 0.8132 (tt0) REVERT: A 257 MET cc_start: 0.8773 (mmm) cc_final: 0.8381 (mmm) REVERT: B 43 GLU cc_start: 0.8676 (tt0) cc_final: 0.8200 (tm-30) REVERT: B 48 ASP cc_start: 0.9207 (p0) cc_final: 0.8964 (p0) REVERT: B 230 GLU cc_start: 0.8545 (mp0) cc_final: 0.8319 (mp0) REVERT: B 277 TRP cc_start: 0.8288 (t-100) cc_final: 0.7967 (t-100) REVERT: B 281 LYS cc_start: 0.9296 (tppt) cc_final: 0.8762 (mmmm) REVERT: C 24 ARG cc_start: 0.7866 (ptt-90) cc_final: 0.7478 (mpt180) REVERT: C 48 ASP cc_start: 0.9074 (p0) cc_final: 0.8710 (p0) REVERT: C 97 SER cc_start: 0.8714 (m) cc_final: 0.8311 (p) REVERT: C 210 GLU cc_start: 0.9069 (tp30) cc_final: 0.8631 (tp30) REVERT: C 230 GLU cc_start: 0.8386 (mp0) cc_final: 0.7916 (pm20) REVERT: D 48 ASP cc_start: 0.9133 (p0) cc_final: 0.8857 (p0) REVERT: D 59 GLN cc_start: 0.8947 (tp40) cc_final: 0.8562 (tp40) REVERT: D 241 GLU cc_start: 0.8373 (tt0) cc_final: 0.8083 (tt0) REVERT: D 257 MET cc_start: 0.8759 (mmm) cc_final: 0.8367 (mmm) REVERT: E 48 ASP cc_start: 0.9199 (p0) cc_final: 0.8940 (p0) REVERT: E 230 GLU cc_start: 0.8533 (mp0) cc_final: 0.8326 (mm-30) REVERT: E 281 LYS cc_start: 0.9274 (tppt) cc_final: 0.8908 (mmmm) REVERT: F 24 ARG cc_start: 0.7917 (ptt-90) cc_final: 0.7452 (mpt180) REVERT: F 48 ASP cc_start: 0.9079 (p0) cc_final: 0.8656 (p0) REVERT: F 59 GLN cc_start: 0.9068 (tp40) cc_final: 0.8098 (tp40) REVERT: F 97 SER cc_start: 0.8715 (m) cc_final: 0.8316 (p) REVERT: F 210 GLU cc_start: 0.9065 (tp30) cc_final: 0.8628 (tp30) REVERT: F 230 GLU cc_start: 0.8460 (mp0) cc_final: 0.8222 (mm-30) REVERT: G 48 ASP cc_start: 0.9067 (p0) cc_final: 0.8650 (p0) REVERT: G 59 GLN cc_start: 0.9090 (tp40) cc_final: 0.8498 (tp40) REVERT: G 97 SER cc_start: 0.8715 (m) cc_final: 0.8312 (p) REVERT: G 230 GLU cc_start: 0.8486 (mp0) cc_final: 0.8186 (mm-30) REVERT: G 239 GLU cc_start: 0.8520 (tt0) cc_final: 0.8119 (tt0) REVERT: H 48 ASP cc_start: 0.9192 (p0) cc_final: 0.8846 (p0) REVERT: H 52 MET cc_start: 0.9325 (mmt) cc_final: 0.8987 (mmm) REVERT: H 241 GLU cc_start: 0.8379 (tt0) cc_final: 0.8140 (tt0) REVERT: H 257 MET cc_start: 0.8744 (mmm) cc_final: 0.8358 (mmm) REVERT: I 24 ARG cc_start: 0.8194 (ptt-90) cc_final: 0.7800 (pmt170) REVERT: I 48 ASP cc_start: 0.9195 (p0) cc_final: 0.8964 (p0) REVERT: I 59 GLN cc_start: 0.8916 (tp40) cc_final: 0.8055 (tp40) REVERT: I 230 GLU cc_start: 0.8536 (mp0) cc_final: 0.8323 (mp0) REVERT: I 281 LYS cc_start: 0.9269 (tppt) cc_final: 0.8910 (mmmm) REVERT: J 24 ARG cc_start: 0.7877 (ptt-90) cc_final: 0.7441 (mpt180) REVERT: J 48 ASP cc_start: 0.9076 (p0) cc_final: 0.8649 (p0) REVERT: J 59 GLN cc_start: 0.9103 (tp40) cc_final: 0.8514 (tp40) REVERT: J 97 SER cc_start: 0.8710 (m) cc_final: 0.8318 (p) REVERT: J 230 GLU cc_start: 0.8458 (mp0) cc_final: 0.8222 (mm-30) REVERT: K 24 ARG cc_start: 0.7795 (ptt-90) cc_final: 0.7440 (mpt180) REVERT: K 48 ASP cc_start: 0.9134 (p0) cc_final: 0.8829 (p0) REVERT: K 241 GLU cc_start: 0.8349 (tt0) cc_final: 0.8132 (tt0) REVERT: K 257 MET cc_start: 0.8756 (mmm) cc_final: 0.8368 (mmm) REVERT: L 20 THR cc_start: 0.7702 (p) cc_final: 0.7081 (p) REVERT: L 24 ARG cc_start: 0.8259 (ptp90) cc_final: 0.7980 (ptt-90) REVERT: L 43 GLU cc_start: 0.8657 (tt0) cc_final: 0.8169 (tm-30) REVERT: L 48 ASP cc_start: 0.9198 (p0) cc_final: 0.8919 (p0) REVERT: L 230 GLU cc_start: 0.8575 (mp0) cc_final: 0.8321 (mm-30) outliers start: 39 outliers final: 10 residues processed: 436 average time/residue: 0.6623 time to fit residues: 324.1607 Evaluate side-chains 389 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 379 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 88 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN B 104 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 104 GLN E 217 GLN H 207 ASN I 82 GLN K 104 GLN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 GLN L 104 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.130411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.091326 restraints weight = 34013.136| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.85 r_work: 0.3081 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21060 Z= 0.165 Angle : 0.711 15.143 28548 Z= 0.352 Chirality : 0.040 0.187 3396 Planarity : 0.005 0.085 3144 Dihedral : 7.046 57.021 6732 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.40 % Allowed : 28.19 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.98 (0.18), residues: 2196 helix: 3.58 (0.11), residues: 1692 sheet: 0.25 (0.44), residues: 144 loop : -1.50 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG I 285 TYR 0.026 0.002 TYR H 96 PHE 0.020 0.001 PHE J 81 TRP 0.019 0.002 TRP L 277 HIS 0.003 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00399 (21024) covalent geometry : angle 0.70567 (28476) SS BOND : bond 0.00631 ( 36) SS BOND : angle 1.83793 ( 72) hydrogen bonds : bond 0.05005 ( 1416) hydrogen bonds : angle 3.07553 ( 4212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 383 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.9214 (p0) cc_final: 0.8862 (p0) REVERT: A 52 MET cc_start: 0.9235 (mmt) cc_final: 0.8917 (mmm) REVERT: A 59 GLN cc_start: 0.8970 (tp40) cc_final: 0.8563 (tp40) REVERT: A 68 ASP cc_start: 0.8518 (t70) cc_final: 0.8310 (t0) REVERT: A 241 GLU cc_start: 0.8348 (tt0) cc_final: 0.8091 (tt0) REVERT: A 257 MET cc_start: 0.8803 (mmm) cc_final: 0.8427 (mmm) REVERT: B 24 ARG cc_start: 0.8212 (ptp90) cc_final: 0.7973 (ptp90) REVERT: B 43 GLU cc_start: 0.8641 (tt0) cc_final: 0.8193 (tm-30) REVERT: B 48 ASP cc_start: 0.9250 (p0) cc_final: 0.9011 (p0) REVERT: B 230 GLU cc_start: 0.8611 (mp0) cc_final: 0.8400 (mp0) REVERT: B 277 TRP cc_start: 0.8240 (t-100) cc_final: 0.7911 (t-100) REVERT: B 281 LYS cc_start: 0.9272 (tppt) cc_final: 0.8725 (mmmm) REVERT: C 48 ASP cc_start: 0.9117 (p0) cc_final: 0.8689 (p0) REVERT: C 97 SER cc_start: 0.8743 (m) cc_final: 0.8337 (p) REVERT: C 210 GLU cc_start: 0.9087 (tp30) cc_final: 0.8646 (tp30) REVERT: D 48 ASP cc_start: 0.9187 (p0) cc_final: 0.8875 (p0) REVERT: D 52 MET cc_start: 0.9247 (mmt) cc_final: 0.8932 (mmm) REVERT: D 59 GLN cc_start: 0.8957 (tp40) cc_final: 0.8545 (tp40) REVERT: D 68 ASP cc_start: 0.8563 (t70) cc_final: 0.8275 (t0) REVERT: D 241 GLU cc_start: 0.8493 (tt0) cc_final: 0.8186 (tt0) REVERT: D 257 MET cc_start: 0.8814 (mmm) cc_final: 0.8438 (mmm) REVERT: E 24 ARG cc_start: 0.8232 (ptt-90) cc_final: 0.7839 (mpt180) REVERT: E 48 ASP cc_start: 0.9228 (p0) cc_final: 0.8966 (p0) REVERT: F 48 ASP cc_start: 0.9134 (p0) cc_final: 0.8716 (p0) REVERT: F 97 SER cc_start: 0.8735 (m) cc_final: 0.8329 (p) REVERT: F 210 GLU cc_start: 0.9078 (tp30) cc_final: 0.8641 (tp30) REVERT: F 230 GLU cc_start: 0.8517 (mp0) cc_final: 0.8316 (mm-30) REVERT: G 48 ASP cc_start: 0.9129 (p0) cc_final: 0.8709 (p0) REVERT: G 97 SER cc_start: 0.8729 (m) cc_final: 0.8332 (p) REVERT: G 230 GLU cc_start: 0.8541 (mp0) cc_final: 0.8262 (mm-30) REVERT: G 239 GLU cc_start: 0.8675 (tt0) cc_final: 0.7600 (tt0) REVERT: H 48 ASP cc_start: 0.9194 (p0) cc_final: 0.8850 (p0) REVERT: H 68 ASP cc_start: 0.8546 (t70) cc_final: 0.8282 (t0) REVERT: H 230 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7852 (tp30) REVERT: H 241 GLU cc_start: 0.8405 (tt0) cc_final: 0.8090 (tt0) REVERT: H 257 MET cc_start: 0.8786 (mmm) cc_final: 0.8413 (mmm) REVERT: I 48 ASP cc_start: 0.9215 (p0) cc_final: 0.8972 (p0) REVERT: I 230 GLU cc_start: 0.8597 (mp0) cc_final: 0.8329 (mm-30) REVERT: J 48 ASP cc_start: 0.9135 (p0) cc_final: 0.8710 (p0) REVERT: J 97 SER cc_start: 0.8732 (m) cc_final: 0.8336 (p) REVERT: K 48 ASP cc_start: 0.9188 (p0) cc_final: 0.8816 (p0) REVERT: K 241 GLU cc_start: 0.8439 (tt0) cc_final: 0.8149 (tt0) REVERT: K 257 MET cc_start: 0.8785 (mmm) cc_final: 0.8413 (mmm) REVERT: L 43 GLU cc_start: 0.8621 (tt0) cc_final: 0.8230 (tm-30) REVERT: L 48 ASP cc_start: 0.9236 (p0) cc_final: 0.8967 (p0) outliers start: 28 outliers final: 17 residues processed: 408 average time/residue: 0.6630 time to fit residues: 302.3606 Evaluate side-chains 388 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 371 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain H residue 55 CYS Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain K residue 55 CYS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 116 optimal weight: 0.0870 chunk 60 optimal weight: 0.4980 chunk 154 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 201 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN C 104 GLN E 217 GLN G 104 GLN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.094930 restraints weight = 33935.515| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.87 r_work: 0.3144 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21060 Z= 0.137 Angle : 0.714 14.528 28548 Z= 0.352 Chirality : 0.038 0.164 3396 Planarity : 0.005 0.075 3144 Dihedral : 6.798 56.165 6732 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.95 % Allowed : 28.74 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.04 (0.18), residues: 2196 helix: 3.68 (0.11), residues: 1692 sheet: 0.83 (0.48), residues: 120 loop : -1.87 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG I 285 TYR 0.019 0.001 TYR K 96 PHE 0.019 0.001 PHE J 81 TRP 0.025 0.002 TRP E 277 HIS 0.004 0.000 HIS L 274 Details of bonding type rmsd covalent geometry : bond 0.00316 (21024) covalent geometry : angle 0.71082 (28476) SS BOND : bond 0.00600 ( 36) SS BOND : angle 1.46785 ( 72) hydrogen bonds : bond 0.04117 ( 1416) hydrogen bonds : angle 3.07443 ( 4212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 404 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.9192 (p0) cc_final: 0.8855 (p0) REVERT: A 59 GLN cc_start: 0.8928 (tp40) cc_final: 0.8545 (tp40) REVERT: A 230 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7863 (tp30) REVERT: A 241 GLU cc_start: 0.8252 (tt0) cc_final: 0.7723 (tt0) REVERT: A 257 MET cc_start: 0.8788 (mmm) cc_final: 0.8445 (mmm) REVERT: B 43 GLU cc_start: 0.8661 (tt0) cc_final: 0.8250 (tm-30) REVERT: B 48 ASP cc_start: 0.9243 (p0) cc_final: 0.9004 (p0) REVERT: B 59 GLN cc_start: 0.8929 (tp40) cc_final: 0.7949 (tp40) REVERT: B 277 TRP cc_start: 0.8206 (t-100) cc_final: 0.7930 (t-100) REVERT: B 281 LYS cc_start: 0.9264 (tppt) cc_final: 0.8807 (mmmm) REVERT: C 24 ARG cc_start: 0.8051 (pmt170) cc_final: 0.7829 (pmm150) REVERT: C 48 ASP cc_start: 0.9081 (p0) cc_final: 0.8696 (p0) REVERT: C 97 SER cc_start: 0.8701 (m) cc_final: 0.8292 (p) REVERT: C 210 GLU cc_start: 0.9066 (tp30) cc_final: 0.8621 (tp30) REVERT: D 48 ASP cc_start: 0.9194 (p0) cc_final: 0.8886 (p0) REVERT: D 59 GLN cc_start: 0.8923 (tp40) cc_final: 0.8543 (tp40) REVERT: D 68 ASP cc_start: 0.8477 (t70) cc_final: 0.8221 (t0) REVERT: D 230 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7890 (tp30) REVERT: D 241 GLU cc_start: 0.8206 (tt0) cc_final: 0.7738 (tt0) REVERT: D 257 MET cc_start: 0.8784 (mmm) cc_final: 0.8444 (mmm) REVERT: E 24 ARG cc_start: 0.8225 (ptt-90) cc_final: 0.7894 (pmt170) REVERT: E 48 ASP cc_start: 0.9207 (p0) cc_final: 0.8945 (p0) REVERT: F 24 ARG cc_start: 0.8059 (pmt170) cc_final: 0.7836 (pmm150) REVERT: F 48 ASP cc_start: 0.9107 (p0) cc_final: 0.8718 (p0) REVERT: F 97 SER cc_start: 0.8704 (m) cc_final: 0.8299 (p) REVERT: F 210 GLU cc_start: 0.9091 (tp30) cc_final: 0.8655 (tp30) REVERT: G 24 ARG cc_start: 0.8084 (ptt-90) cc_final: 0.7870 (pmt170) REVERT: G 48 ASP cc_start: 0.9099 (p0) cc_final: 0.8711 (p0) REVERT: G 59 GLN cc_start: 0.9023 (tp40) cc_final: 0.8223 (tp40) REVERT: G 97 SER cc_start: 0.8698 (m) cc_final: 0.8291 (p) REVERT: G 239 GLU cc_start: 0.8612 (tt0) cc_final: 0.7612 (tt0) REVERT: H 48 ASP cc_start: 0.9161 (p0) cc_final: 0.8846 (p0) REVERT: H 52 MET cc_start: 0.9303 (mmt) cc_final: 0.8973 (mmm) REVERT: H 68 ASP cc_start: 0.8456 (t70) cc_final: 0.8227 (t0) REVERT: H 230 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7873 (tp30) REVERT: H 241 GLU cc_start: 0.8237 (tt0) cc_final: 0.7737 (tt0) REVERT: H 257 MET cc_start: 0.8774 (mmm) cc_final: 0.8389 (mmm) REVERT: I 24 ARG cc_start: 0.8188 (ptt-90) cc_final: 0.7974 (pmt170) REVERT: I 48 ASP cc_start: 0.9213 (p0) cc_final: 0.8979 (p0) REVERT: I 198 PHE cc_start: 0.7548 (t80) cc_final: 0.7239 (t80) REVERT: J 24 ARG cc_start: 0.8020 (ptt-90) cc_final: 0.7783 (pmt170) REVERT: J 48 ASP cc_start: 0.9110 (p0) cc_final: 0.8746 (p0) REVERT: J 59 GLN cc_start: 0.9069 (tp40) cc_final: 0.8579 (tp40) REVERT: J 97 SER cc_start: 0.8709 (m) cc_final: 0.8313 (p) REVERT: J 230 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7702 (mm-30) REVERT: K 48 ASP cc_start: 0.9204 (p0) cc_final: 0.8822 (p0) REVERT: K 241 GLU cc_start: 0.8272 (tt0) cc_final: 0.7765 (tt0) REVERT: K 257 MET cc_start: 0.8772 (mmm) cc_final: 0.8437 (mmm) REVERT: L 43 GLU cc_start: 0.8641 (tt0) cc_final: 0.8240 (tm-30) REVERT: L 48 ASP cc_start: 0.9214 (p0) cc_final: 0.8983 (p0) REVERT: L 230 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7818 (tp30) outliers start: 19 outliers final: 14 residues processed: 422 average time/residue: 0.6451 time to fit residues: 306.8185 Evaluate side-chains 391 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 377 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain H residue 55 CYS Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain K residue 55 CYS Chi-restraints excluded: chain K residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN E 268 ASN F 104 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 268 ASN J 104 GLN ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 56 ASN L 82 GLN L 268 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.132915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094393 restraints weight = 34056.910| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.85 r_work: 0.3127 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21060 Z= 0.143 Angle : 0.710 13.637 28548 Z= 0.352 Chirality : 0.039 0.198 3396 Planarity : 0.005 0.071 3144 Dihedral : 6.769 56.724 6732 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.45 % Allowed : 29.84 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.96 (0.18), residues: 2196 helix: 3.62 (0.12), residues: 1692 sheet: 0.82 (0.48), residues: 120 loop : -1.89 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 285 TYR 0.024 0.002 TYR D 96 PHE 0.021 0.001 PHE G 81 TRP 0.025 0.002 TRP K 277 HIS 0.005 0.001 HIS L 274 Details of bonding type rmsd covalent geometry : bond 0.00337 (21024) covalent geometry : angle 0.70663 (28476) SS BOND : bond 0.00605 ( 36) SS BOND : angle 1.54891 ( 72) hydrogen bonds : bond 0.04280 ( 1416) hydrogen bonds : angle 3.04632 ( 4212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8070.78 seconds wall clock time: 137 minutes 53.02 seconds (8273.02 seconds total)