Starting phenix.real_space_refine on Tue May 20 22:53:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iyg_35821/05_2025/8iyg_35821.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iyg_35821/05_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_35821/05_2025/8iyg_35821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iyg_35821/05_2025/8iyg_35821.map" model { file = "/net/cci-nas-00/data/ceres_data/8iyg_35821/05_2025/8iyg_35821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iyg_35821/05_2025/8iyg_35821.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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-2': 1, 'Y01:plan-1': 3} 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-2': 1, 'Y01:plan-1': 3} 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-2': 1, 'Y01:plan-1': 3} 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-2': 1, 'Y01:plan-1': 3} 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-2': 1, 'Y01:plan-1': 3} 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-2': 1, 'Y01:plan-1': 3} 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-2': 1, 'Y01:plan-1': 3} 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-2': 1, 'Y01:plan-1': 3} 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-2': 1, 'Y01:plan-1': 3} 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-2': 1, 'Y01:plan-1': 3} 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-2': 1, 'Y01:plan-1': 3} 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-2': 1, 'Y01:plan-1': 3} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 13.03, per 1000 atoms: 0.63 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: 5.17 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.58 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: 5.70 Time building geometry restraints manager: 6.07 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: 0.09 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 285 or resid 401 or (resid 405 and (name C1 or \ name C10 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or na \ me 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 (nam \ e C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or (re \ sid 408 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or n \ ame C7 or name 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 285 or resid 401 or (resid 405 and (name C1 or \ name C10 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or na \ me 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 (nam \ e C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or (re \ sid 408 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or n \ ame C7 or name 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 45.140 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.002 0.000 TRP C 277 HIS 0.004 0.001 HIS C 274 PHE 0.005 0.001 PHE E 256 TYR 0.003 0.000 TYR C 243 ARG 0.001 0.000 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.10132 ( 1416) hydrogen bonds : angle 3.15111 ( 4212) SS BOND : bond 0.00077 ( 36) SS BOND : angle 0.53971 ( 72) covalent geometry : bond 0.00660 (21024) covalent geometry : angle 1.00765 (28476) *********************** 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 : 2.082 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: 1.1037 time to fit residues: 1070.7953 Evaluate side-chains 429 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN D 268 ASN 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 = 0.4074 r_free = 0.4074 target = 0.144203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104838 restraints weight = 33831.323| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.01 r_work: 0.3315 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21060 Z= 0.134 Angle : 0.625 8.160 28548 Z= 0.304 Chirality : 0.038 0.152 3396 Planarity : 0.004 0.033 3144 Dihedral : 8.542 57.355 6732 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.90 % Allowed : 19.11 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.18), residues: 2196 helix: 3.69 (0.11), residues: 1680 sheet: 1.43 (0.47), residues: 120 loop : -1.98 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 277 HIS 0.004 0.001 HIS J 274 PHE 0.010 0.001 PHE E 33 TYR 0.018 0.002 TYR H 96 ARG 0.010 0.001 ARG G 285 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 1416) hydrogen bonds : angle 3.05236 ( 4212) SS BOND : bond 0.00574 ( 36) SS BOND : angle 1.40434 ( 72) covalent geometry : bond 0.00306 (21024) covalent geometry : angle 0.62173 (28476) *********************** 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 480 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 442 time to evaluate : 2.496 Fit side-chains REVERT: A 59 GLN cc_start: 0.8742 (tp40) cc_final: 0.8011 (tp40) REVERT: A 253 PHE cc_start: 0.8007 (t80) cc_final: 0.7734 (t80) REVERT: A 257 MET cc_start: 0.8841 (mmm) cc_final: 0.8453 (mmm) REVERT: A 278 ARG cc_start: 0.8691 (mmp-170) cc_final: 0.8377 (mmp80) REVERT: B 43 GLU cc_start: 0.8327 (tt0) cc_final: 0.7746 (tm-30) REVERT: B 59 GLN cc_start: 0.8887 (tp40) cc_final: 0.8283 (tp40) REVERT: B 230 GLU cc_start: 0.8400 (mp0) cc_final: 0.8170 (mm-30) REVERT: B 278 ARG cc_start: 0.8653 (mmp80) cc_final: 0.8429 (mmp80) REVERT: C 43 GLU cc_start: 0.8221 (tt0) cc_final: 0.7993 (tt0) REVERT: C 59 GLN cc_start: 0.8816 (tp40) cc_final: 0.8043 (tp40) REVERT: C 78 TYR cc_start: 0.8624 (t80) cc_final: 0.8424 (t80) REVERT: C 230 GLU cc_start: 0.8250 (mp0) cc_final: 0.7991 (mp0) REVERT: D 59 GLN cc_start: 0.8728 (tp40) cc_final: 0.7997 (tp40) REVERT: D 253 PHE cc_start: 0.7994 (t80) cc_final: 0.7721 (t80) REVERT: D 257 MET cc_start: 0.8827 (mmm) cc_final: 0.8445 (mmm) REVERT: D 278 ARG cc_start: 0.8685 (mmp-170) cc_final: 0.8373 (mmp80) REVERT: E 43 GLU cc_start: 0.8304 (tt0) cc_final: 0.7731 (tm-30) REVERT: E 230 GLU cc_start: 0.8356 (mp0) cc_final: 0.8116 (mm-30) REVERT: E 253 PHE cc_start: 0.8178 (t80) cc_final: 0.7967 (t80) REVERT: E 278 ARG cc_start: 0.8723 (mmp-170) cc_final: 0.8476 (mmp80) REVERT: F 21 MET cc_start: 0.8014 (pmm) cc_final: 0.7813 (pmm) REVERT: F 43 GLU cc_start: 0.8209 (tt0) cc_final: 0.7981 (tt0) REVERT: F 59 GLN cc_start: 0.8824 (tp40) cc_final: 0.8052 (tp40) REVERT: F 230 GLU cc_start: 0.8273 (mp0) cc_final: 0.8012 (mp0) REVERT: G 43 GLU cc_start: 0.8228 (tt0) cc_final: 0.7997 (tt0) REVERT: G 59 GLN cc_start: 0.8801 (tp40) cc_final: 0.8024 (tp40) REVERT: G 78 TYR cc_start: 0.8600 (t80) cc_final: 0.8395 (t80) REVERT: G 230 GLU cc_start: 0.8228 (mp0) cc_final: 0.7974 (mp0) REVERT: H 59 GLN cc_start: 0.8728 (tp40) cc_final: 0.8011 (tp40) REVERT: H 253 PHE cc_start: 0.7971 (t80) cc_final: 0.7714 (t80) REVERT: H 257 MET cc_start: 0.8832 (mmm) cc_final: 0.8449 (mmm) REVERT: H 278 ARG cc_start: 0.8699 (mmp-170) cc_final: 0.8385 (mmp80) REVERT: I 43 GLU cc_start: 0.8305 (tt0) cc_final: 0.7732 (tm-30) REVERT: I 59 GLN cc_start: 0.8869 (tp40) cc_final: 0.8267 (tp40) REVERT: I 230 GLU cc_start: 0.8383 (mp0) cc_final: 0.8155 (mm-30) REVERT: I 253 PHE cc_start: 0.8149 (t80) cc_final: 0.7945 (t80) REVERT: I 278 ARG cc_start: 0.8664 (mmp80) cc_final: 0.8441 (mmp80) REVERT: J 21 MET cc_start: 0.7986 (pmm) cc_final: 0.7784 (pmm) REVERT: J 59 GLN cc_start: 0.8755 (tp40) cc_final: 0.8418 (tp40) REVERT: J 278 ARG cc_start: 0.8705 (mmp-170) cc_final: 0.8401 (mmp80) REVERT: K 59 GLN cc_start: 0.8712 (tp40) cc_final: 0.7986 (tp40) REVERT: K 253 PHE cc_start: 0.7963 (t80) cc_final: 0.7703 (t80) REVERT: K 257 MET cc_start: 0.8839 (mmm) cc_final: 0.8440 (mmm) REVERT: K 278 ARG cc_start: 0.8678 (mmp-170) cc_final: 0.8375 (mmp80) REVERT: K 285 ARG cc_start: 0.7506 (mmm160) cc_final: 0.7236 (mmp-170) REVERT: L 43 GLU cc_start: 0.8323 (tt0) cc_final: 0.7738 (tm-30) REVERT: L 59 GLN cc_start: 0.8879 (tp40) cc_final: 0.8287 (tp40) REVERT: L 230 GLU cc_start: 0.8382 (mp0) cc_final: 0.8156 (mm-30) REVERT: L 253 PHE cc_start: 0.8210 (t80) cc_final: 0.8001 (t80) outliers start: 38 outliers final: 28 residues processed: 469 average time/residue: 1.2827 time to fit residues: 679.7764 Evaluate side-chains 407 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 379 time to evaluate : 2.205 ------------------------------------------------------------------------------- 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 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 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 161 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS D 75 HIS D 207 ASN D 268 ASN E 75 HIS E 82 GLN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.134060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.094061 restraints weight = 34000.368| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.91 r_work: 0.3129 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 21060 Z= 0.162 Angle : 0.630 6.732 28548 Z= 0.315 Chirality : 0.040 0.156 3396 Planarity : 0.004 0.032 3144 Dihedral : 7.913 48.745 6732 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.45 % Allowed : 20.56 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.18), residues: 2196 helix: 3.52 (0.11), residues: 1680 sheet: 0.26 (0.38), residues: 204 loop : -1.52 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 277 HIS 0.003 0.001 HIS D 75 PHE 0.010 0.001 PHE D 33 TYR 0.020 0.002 TYR E 96 ARG 0.010 0.001 ARG D 285 Details of bonding type rmsd hydrogen bonds : bond 0.05323 ( 1416) hydrogen bonds : angle 3.11908 ( 4212) SS BOND : bond 0.00151 ( 36) SS BOND : angle 1.78463 ( 72) covalent geometry : bond 0.00384 (21024) covalent geometry : angle 0.62443 (28476) *********************** 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 464 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 415 time to evaluate : 2.169 Fit side-chains REVERT: A 59 GLN cc_start: 0.8903 (tp40) cc_final: 0.8094 (tp40) REVERT: A 78 TYR cc_start: 0.8878 (t80) cc_final: 0.8672 (t80) REVERT: A 217 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8430 (tt0) REVERT: A 253 PHE cc_start: 0.8542 (t80) cc_final: 0.8214 (t80) REVERT: A 257 MET cc_start: 0.8847 (mmm) cc_final: 0.8437 (mmm) REVERT: A 278 ARG cc_start: 0.8701 (mmp-170) cc_final: 0.8418 (mmp80) REVERT: B 43 GLU cc_start: 0.8349 (tt0) cc_final: 0.7889 (tm-30) REVERT: B 48 ASP cc_start: 0.9156 (p0) cc_final: 0.8850 (p0) REVERT: B 59 GLN cc_start: 0.9064 (tp40) cc_final: 0.8372 (tp40) REVERT: B 230 GLU cc_start: 0.8529 (mp0) cc_final: 0.8281 (mm-30) REVERT: B 281 LYS cc_start: 0.9103 (tppt) cc_final: 0.8766 (mmmm) REVERT: C 21 MET cc_start: 0.7847 (pmm) cc_final: 0.7619 (pmm) REVERT: C 59 GLN cc_start: 0.9009 (tp40) cc_final: 0.8164 (tp40) REVERT: C 78 TYR cc_start: 0.8861 (t80) cc_final: 0.8383 (t80) REVERT: C 230 GLU cc_start: 0.8457 (mp0) cc_final: 0.8040 (pm20) REVERT: D 24 ARG cc_start: 0.8033 (ptt-90) cc_final: 0.7815 (ptt-90) REVERT: D 59 GLN cc_start: 0.8894 (tp40) cc_final: 0.8076 (tp40) REVERT: D 217 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8442 (tt0) REVERT: D 253 PHE cc_start: 0.8534 (t80) cc_final: 0.8207 (t80) REVERT: D 257 MET cc_start: 0.8848 (mmm) cc_final: 0.8440 (mmm) REVERT: D 278 ARG cc_start: 0.8734 (mmp-170) cc_final: 0.8473 (mmp80) REVERT: E 48 ASP cc_start: 0.9083 (p0) cc_final: 0.8805 (p0) REVERT: E 230 GLU cc_start: 0.8518 (mp0) cc_final: 0.8290 (mm-30) REVERT: E 281 LYS cc_start: 0.8992 (tppt) cc_final: 0.8783 (mmmm) REVERT: F 21 MET cc_start: 0.7949 (pmm) cc_final: 0.7723 (pmm) REVERT: F 48 ASP cc_start: 0.9009 (p0) cc_final: 0.8806 (p0) REVERT: F 59 GLN cc_start: 0.9025 (tp40) cc_final: 0.8157 (tp40) REVERT: F 230 GLU cc_start: 0.8478 (mp0) cc_final: 0.8056 (pm20) REVERT: G 21 MET cc_start: 0.7818 (pmm) cc_final: 0.7579 (pmm) REVERT: G 59 GLN cc_start: 0.8996 (tp40) cc_final: 0.8105 (tp40) REVERT: G 230 GLU cc_start: 0.8409 (mp0) cc_final: 0.8005 (pm20) REVERT: H 59 GLN cc_start: 0.8903 (tp40) cc_final: 0.8113 (tp40) REVERT: H 78 TYR cc_start: 0.8840 (t80) cc_final: 0.8631 (t80) REVERT: H 217 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8415 (tt0) REVERT: H 253 PHE cc_start: 0.8503 (t80) cc_final: 0.8189 (t80) REVERT: H 257 MET cc_start: 0.8836 (mmm) cc_final: 0.8467 (mmm) REVERT: H 278 ARG cc_start: 0.8728 (mmp-170) cc_final: 0.8458 (mmp80) REVERT: I 24 ARG cc_start: 0.8061 (ptt-90) cc_final: 0.7852 (ptt-90) REVERT: I 48 ASP cc_start: 0.9069 (p0) cc_final: 0.8799 (p0) REVERT: I 59 GLN cc_start: 0.9051 (tp40) cc_final: 0.8361 (tp40) REVERT: I 230 GLU cc_start: 0.8512 (mp0) cc_final: 0.8293 (mm-30) REVERT: I 281 LYS cc_start: 0.9081 (tppt) cc_final: 0.8750 (mmmm) REVERT: J 21 MET cc_start: 0.7934 (pmm) cc_final: 0.7731 (pmm) REVERT: J 59 GLN cc_start: 0.8989 (tp40) cc_final: 0.8521 (tp40) REVERT: J 230 GLU cc_start: 0.8439 (mp0) cc_final: 0.8070 (pm20) REVERT: J 278 ARG cc_start: 0.8768 (mmp-170) cc_final: 0.8509 (mmp80) REVERT: K 24 ARG cc_start: 0.7988 (ptt-90) cc_final: 0.7785 (ptt-90) REVERT: K 59 GLN cc_start: 0.8895 (tp40) cc_final: 0.8076 (tp40) REVERT: K 78 TYR cc_start: 0.8874 (t80) cc_final: 0.8662 (t80) REVERT: K 217 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8411 (tt0) REVERT: K 253 PHE cc_start: 0.8510 (t80) cc_final: 0.8186 (t80) REVERT: K 257 MET cc_start: 0.8856 (mmm) cc_final: 0.8442 (mmm) REVERT: K 278 ARG cc_start: 0.8762 (mmp-170) cc_final: 0.8490 (mmp80) REVERT: L 43 GLU cc_start: 0.8336 (tt0) cc_final: 0.7874 (tm-30) REVERT: L 48 ASP cc_start: 0.9045 (p0) cc_final: 0.8765 (p0) REVERT: L 59 GLN cc_start: 0.9039 (tp40) cc_final: 0.8357 (tp40) REVERT: L 230 GLU cc_start: 0.8502 (mp0) cc_final: 0.8255 (mm-30) REVERT: L 281 LYS cc_start: 0.9155 (tppt) cc_final: 0.8793 (mmmm) outliers start: 49 outliers final: 26 residues processed: 437 average time/residue: 1.3539 time to fit residues: 664.1672 Evaluate side-chains 402 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 376 time to evaluate : 2.106 ------------------------------------------------------------------------------- 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 92 CYS 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 92 CYS 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 92 CYS Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 92 CYS 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 282 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 142 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 82 GLN D 268 ASN E 82 GLN H 268 ASN I 82 GLN K 268 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 = 0.3968 r_free = 0.3968 target = 0.135905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.096389 restraints weight = 34218.229| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.91 r_work: 0.3163 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21060 Z= 0.134 Angle : 0.633 13.226 28548 Z= 0.315 Chirality : 0.039 0.257 3396 Planarity : 0.004 0.037 3144 Dihedral : 7.403 49.303 6732 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.95 % Allowed : 21.76 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.18), residues: 2196 helix: 3.57 (0.11), residues: 1680 sheet: -0.26 (0.37), residues: 204 loop : -1.37 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 277 HIS 0.002 0.001 HIS H 75 PHE 0.009 0.001 PHE E 33 TYR 0.023 0.002 TYR I 96 ARG 0.011 0.001 ARG L 285 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 1416) hydrogen bonds : angle 3.03738 ( 4212) SS BOND : bond 0.00749 ( 36) SS BOND : angle 2.10822 ( 72) covalent geometry : bond 0.00312 (21024) covalent geometry : angle 0.62526 (28476) *********************** 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 437 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 398 time to evaluate : 2.067 Fit side-chains REVERT: A 24 ARG cc_start: 0.8005 (ptt-90) cc_final: 0.7740 (ptp90) REVERT: A 48 ASP cc_start: 0.9050 (p0) cc_final: 0.8808 (p0) REVERT: A 59 GLN cc_start: 0.8885 (tp40) cc_final: 0.8066 (tp40) REVERT: A 217 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8452 (tt0) REVERT: A 253 PHE cc_start: 0.8443 (t80) cc_final: 0.8099 (t80) REVERT: A 257 MET cc_start: 0.8814 (mmm) cc_final: 0.8373 (mmm) REVERT: A 278 ARG cc_start: 0.8757 (mmp-170) cc_final: 0.8501 (mmp80) REVERT: B 24 ARG cc_start: 0.7974 (ptt-90) cc_final: 0.7718 (ptt-90) REVERT: B 43 GLU cc_start: 0.8539 (tt0) cc_final: 0.8056 (tm-30) REVERT: B 48 ASP cc_start: 0.9104 (p0) cc_final: 0.8791 (p0) REVERT: B 59 GLN cc_start: 0.8968 (tp40) cc_final: 0.8240 (tp40) REVERT: B 230 GLU cc_start: 0.8560 (mp0) cc_final: 0.8341 (mm-30) REVERT: B 239 GLU cc_start: 0.8435 (tt0) cc_final: 0.8229 (tt0) REVERT: B 281 LYS cc_start: 0.9147 (tppt) cc_final: 0.8729 (mmmm) REVERT: C 48 ASP cc_start: 0.8951 (p0) cc_final: 0.8530 (p0) REVERT: C 59 GLN cc_start: 0.9009 (tp40) cc_final: 0.8176 (tp40) REVERT: C 210 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8797 (tp30) REVERT: C 230 GLU cc_start: 0.8400 (mp0) cc_final: 0.8194 (mm-30) REVERT: C 239 GLU cc_start: 0.8286 (tt0) cc_final: 0.7920 (tt0) REVERT: D 48 ASP cc_start: 0.9039 (p0) cc_final: 0.8807 (p0) REVERT: D 59 GLN cc_start: 0.8851 (tp40) cc_final: 0.7999 (tp40) REVERT: D 217 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8521 (tt0) REVERT: D 253 PHE cc_start: 0.8440 (t80) cc_final: 0.8086 (t80) REVERT: D 257 MET cc_start: 0.8809 (mmm) cc_final: 0.8370 (mmm) REVERT: D 278 ARG cc_start: 0.8760 (mmp-170) cc_final: 0.8556 (mmp80) REVERT: E 24 ARG cc_start: 0.7979 (ptt-90) cc_final: 0.7722 (ptt-90) REVERT: E 43 GLU cc_start: 0.8471 (tt0) cc_final: 0.7858 (tm-30) REVERT: E 48 ASP cc_start: 0.9065 (p0) cc_final: 0.8741 (p0) REVERT: E 230 GLU cc_start: 0.8551 (mp0) cc_final: 0.8330 (mm-30) REVERT: E 281 LYS cc_start: 0.9209 (tppt) cc_final: 0.8800 (mmmm) REVERT: F 48 ASP cc_start: 0.9028 (p0) cc_final: 0.8705 (p0) REVERT: F 59 GLN cc_start: 0.8995 (tp40) cc_final: 0.8111 (tp40) REVERT: F 230 GLU cc_start: 0.8459 (mp0) cc_final: 0.8067 (pm20) REVERT: G 48 ASP cc_start: 0.8924 (p0) cc_final: 0.8609 (p0) REVERT: G 59 GLN cc_start: 0.8981 (tp40) cc_final: 0.8073 (tp40) REVERT: G 230 GLU cc_start: 0.8418 (mp0) cc_final: 0.8048 (pm20) REVERT: H 48 ASP cc_start: 0.9032 (p0) cc_final: 0.8794 (p0) REVERT: H 59 GLN cc_start: 0.8873 (tp40) cc_final: 0.8075 (tp40) REVERT: H 217 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8462 (tt0) REVERT: H 253 PHE cc_start: 0.8416 (t80) cc_final: 0.8073 (t80) REVERT: H 257 MET cc_start: 0.8799 (mmm) cc_final: 0.8363 (mmm) REVERT: H 278 ARG cc_start: 0.8750 (mmp-170) cc_final: 0.8544 (mmp80) REVERT: I 24 ARG cc_start: 0.8045 (ptt-90) cc_final: 0.7804 (ptt-90) REVERT: I 43 GLU cc_start: 0.8468 (tt0) cc_final: 0.7861 (tm-30) REVERT: I 48 ASP cc_start: 0.9046 (p0) cc_final: 0.8731 (p0) REVERT: I 59 GLN cc_start: 0.8970 (tp40) cc_final: 0.8247 (tp40) REVERT: I 230 GLU cc_start: 0.8553 (mp0) cc_final: 0.8339 (mm-30) REVERT: I 281 LYS cc_start: 0.9199 (tppt) cc_final: 0.8841 (mmmm) REVERT: J 48 ASP cc_start: 0.8925 (p0) cc_final: 0.8577 (p0) REVERT: J 59 GLN cc_start: 0.8982 (tp40) cc_final: 0.8554 (tp40) REVERT: J 239 GLU cc_start: 0.8276 (tt0) cc_final: 0.7533 (tt0) REVERT: J 278 ARG cc_start: 0.8756 (mmp-170) cc_final: 0.8535 (mmp80) REVERT: K 48 ASP cc_start: 0.9039 (p0) cc_final: 0.8798 (p0) REVERT: K 59 GLN cc_start: 0.8846 (tp40) cc_final: 0.8001 (tp40) REVERT: K 217 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8425 (tt0) REVERT: K 253 PHE cc_start: 0.8420 (t80) cc_final: 0.8026 (t80) REVERT: K 257 MET cc_start: 0.8811 (mmm) cc_final: 0.8377 (mmm) REVERT: K 278 ARG cc_start: 0.8798 (mmp-170) cc_final: 0.8597 (mmp80) REVERT: L 24 ARG cc_start: 0.7955 (ptt-90) cc_final: 0.7695 (ptt-90) REVERT: L 43 GLU cc_start: 0.8459 (tt0) cc_final: 0.7968 (tm-30) REVERT: L 48 ASP cc_start: 0.9043 (p0) cc_final: 0.8712 (p0) REVERT: L 59 GLN cc_start: 0.8959 (tp40) cc_final: 0.8224 (tp40) REVERT: L 230 GLU cc_start: 0.8549 (mp0) cc_final: 0.8334 (mm-30) REVERT: L 281 LYS cc_start: 0.9214 (tppt) cc_final: 0.8804 (mmmm) outliers start: 39 outliers final: 17 residues processed: 426 average time/residue: 1.3728 time to fit residues: 658.5451 Evaluate side-chains 385 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 368 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 92 CYS Chi-restraints excluded: chain C residue 272 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 92 CYS Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 92 CYS 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 19 optimal weight: 1.9990 chunk 159 optimal weight: 0.0670 chunk 76 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 138 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN B 217 GLN E 82 GLN E 217 GLN I 82 GLN ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.137247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098086 restraints weight = 33993.286| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.96 r_work: 0.3200 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21060 Z= 0.121 Angle : 0.604 13.051 28548 Z= 0.297 Chirality : 0.037 0.183 3396 Planarity : 0.004 0.035 3144 Dihedral : 6.959 50.385 6732 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 2.40 % Allowed : 23.85 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.18), residues: 2196 helix: 3.66 (0.11), residues: 1680 sheet: -0.33 (0.37), residues: 204 loop : -1.30 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 277 HIS 0.002 0.000 HIS A 274 PHE 0.010 0.001 PHE E 253 TYR 0.025 0.001 TYR D 96 ARG 0.008 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 1416) hydrogen bonds : angle 2.94115 ( 4212) SS BOND : bond 0.00541 ( 36) SS BOND : angle 1.62600 ( 72) covalent geometry : bond 0.00266 (21024) covalent geometry : angle 0.59971 (28476) *********************** 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 469 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 421 time to evaluate : 2.348 Fit side-chains revert: symmetry clash REVERT: A 48 ASP cc_start: 0.9048 (p0) cc_final: 0.8805 (p0) REVERT: A 59 GLN cc_start: 0.8848 (tp40) cc_final: 0.8057 (tp40) REVERT: A 210 GLU cc_start: 0.9078 (tp30) cc_final: 0.8827 (mm-30) REVERT: A 217 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8417 (tt0) REVERT: A 253 PHE cc_start: 0.8315 (t80) cc_final: 0.7865 (t80) REVERT: A 257 MET cc_start: 0.8742 (mmm) cc_final: 0.8285 (mmm) REVERT: B 43 GLU cc_start: 0.8596 (tt0) cc_final: 0.8091 (tm-30) REVERT: B 48 ASP cc_start: 0.9078 (p0) cc_final: 0.8807 (p0) REVERT: B 59 GLN cc_start: 0.8850 (tp40) cc_final: 0.8131 (tp40) REVERT: B 230 GLU cc_start: 0.8521 (mp0) cc_final: 0.8236 (mm-30) REVERT: B 239 GLU cc_start: 0.8411 (tt0) cc_final: 0.8174 (tt0) REVERT: B 281 LYS cc_start: 0.9108 (tppt) cc_final: 0.8711 (mmmm) REVERT: C 48 ASP cc_start: 0.8901 (p0) cc_final: 0.8553 (p0) REVERT: C 59 GLN cc_start: 0.8989 (tp40) cc_final: 0.8142 (tp40) REVERT: C 210 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8787 (tp30) REVERT: C 239 GLU cc_start: 0.8206 (tt0) cc_final: 0.7687 (tt0) REVERT: D 24 ARG cc_start: 0.7962 (ptt-90) cc_final: 0.7760 (ptt-90) REVERT: D 48 ASP cc_start: 0.9042 (p0) cc_final: 0.8798 (p0) REVERT: D 59 GLN cc_start: 0.8898 (tp40) cc_final: 0.8062 (tp40) REVERT: D 217 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8374 (tt0) REVERT: D 253 PHE cc_start: 0.8336 (t80) cc_final: 0.7872 (t80) REVERT: D 257 MET cc_start: 0.8745 (mmm) cc_final: 0.8290 (mmm) REVERT: E 43 GLU cc_start: 0.8521 (tt0) cc_final: 0.7867 (tm-30) REVERT: E 48 ASP cc_start: 0.9062 (p0) cc_final: 0.8792 (p0) REVERT: E 230 GLU cc_start: 0.8504 (mp0) cc_final: 0.8215 (mm-30) REVERT: E 239 GLU cc_start: 0.8472 (tt0) cc_final: 0.8232 (tt0) REVERT: E 281 LYS cc_start: 0.9185 (tppt) cc_final: 0.8778 (mmmm) REVERT: F 48 ASP cc_start: 0.8970 (p0) cc_final: 0.8733 (p0) REVERT: F 59 GLN cc_start: 0.8977 (tp40) cc_final: 0.8125 (tp40) REVERT: F 230 GLU cc_start: 0.8411 (mp0) cc_final: 0.7961 (pm20) REVERT: G 48 ASP cc_start: 0.8846 (p0) cc_final: 0.8521 (p0) REVERT: G 59 GLN cc_start: 0.8946 (tp40) cc_final: 0.8062 (tp40) REVERT: G 210 GLU cc_start: 0.9007 (tp30) cc_final: 0.8572 (tp30) REVERT: G 230 GLU cc_start: 0.8369 (mp0) cc_final: 0.7936 (pm20) REVERT: H 48 ASP cc_start: 0.9012 (p0) cc_final: 0.8762 (p0) REVERT: H 59 GLN cc_start: 0.8843 (tp40) cc_final: 0.8068 (tp40) REVERT: H 68 ASP cc_start: 0.8320 (t70) cc_final: 0.8084 (t0) REVERT: H 210 GLU cc_start: 0.9072 (tp30) cc_final: 0.8827 (mm-30) REVERT: H 217 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8344 (tt0) REVERT: H 253 PHE cc_start: 0.8321 (t80) cc_final: 0.7873 (t80) REVERT: H 257 MET cc_start: 0.8728 (mmm) cc_final: 0.8278 (mmm) REVERT: I 24 ARG cc_start: 0.8046 (ptt-90) cc_final: 0.7789 (ptt-90) REVERT: I 48 ASP cc_start: 0.9030 (p0) cc_final: 0.8788 (p0) REVERT: I 59 GLN cc_start: 0.8851 (tp40) cc_final: 0.8144 (tp40) REVERT: I 230 GLU cc_start: 0.8523 (mp0) cc_final: 0.8242 (mm-30) REVERT: I 239 GLU cc_start: 0.8490 (tt0) cc_final: 0.8250 (tt0) REVERT: I 281 LYS cc_start: 0.9105 (tppt) cc_final: 0.8714 (mmmm) REVERT: J 48 ASP cc_start: 0.8883 (p0) cc_final: 0.8539 (p0) REVERT: J 59 GLN cc_start: 0.8943 (tp40) cc_final: 0.8586 (tp40) REVERT: J 230 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7777 (mt-10) REVERT: J 239 GLU cc_start: 0.8211 (tt0) cc_final: 0.7523 (tt0) REVERT: K 24 ARG cc_start: 0.7897 (ptt-90) cc_final: 0.7626 (ptt-90) REVERT: K 48 ASP cc_start: 0.9013 (p0) cc_final: 0.8775 (p0) REVERT: K 59 GLN cc_start: 0.8749 (tp40) cc_final: 0.8058 (tp40) REVERT: K 210 GLU cc_start: 0.9077 (tp30) cc_final: 0.8833 (mm-30) REVERT: K 217 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8344 (tt0) REVERT: K 253 PHE cc_start: 0.8321 (t80) cc_final: 0.7860 (t80) REVERT: K 257 MET cc_start: 0.8742 (mmm) cc_final: 0.8293 (mmm) REVERT: L 43 GLU cc_start: 0.8558 (tt0) cc_final: 0.8072 (tm-30) REVERT: L 48 ASP cc_start: 0.9037 (p0) cc_final: 0.8750 (p0) REVERT: L 59 GLN cc_start: 0.8840 (tp40) cc_final: 0.8129 (tp40) REVERT: L 230 GLU cc_start: 0.8521 (mp0) cc_final: 0.8235 (mm-30) REVERT: L 239 GLU cc_start: 0.8505 (tt0) cc_final: 0.8280 (tt0) REVERT: L 281 LYS cc_start: 0.9142 (tppt) cc_final: 0.8748 (mmmm) outliers start: 48 outliers final: 23 residues processed: 457 average time/residue: 1.2599 time to fit residues: 650.9465 Evaluate side-chains 404 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 381 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 272 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 F residue 91 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 282 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 28 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 217 GLN B 268 ASN E 82 GLN E 217 GLN E 268 ASN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN L 82 GLN L 217 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.132754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.093300 restraints weight = 34169.638| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.89 r_work: 0.3122 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21060 Z= 0.158 Angle : 0.699 15.165 28548 Z= 0.345 Chirality : 0.041 0.278 3396 Planarity : 0.004 0.045 3144 Dihedral : 7.024 53.292 6732 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.84 % Allowed : 23.55 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.18), residues: 2196 helix: 3.54 (0.11), residues: 1680 sheet: 1.17 (0.43), residues: 120 loop : -1.64 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 277 HIS 0.003 0.001 HIS A 75 PHE 0.015 0.001 PHE A 81 TYR 0.026 0.002 TYR I 96 ARG 0.011 0.001 ARG K 285 Details of bonding type rmsd hydrogen bonds : bond 0.04889 ( 1416) hydrogen bonds : angle 3.06873 ( 4212) SS BOND : bond 0.00770 ( 36) SS BOND : angle 2.39631 ( 72) covalent geometry : bond 0.00383 (21024) covalent geometry : angle 0.68911 (28476) *********************** 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 446 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 389 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.9128 (p0) cc_final: 0.8876 (p0) REVERT: A 52 MET cc_start: 0.9284 (mmt) cc_final: 0.8938 (mmm) REVERT: A 59 GLN cc_start: 0.8961 (tp40) cc_final: 0.8579 (tp40) REVERT: A 210 GLU cc_start: 0.9107 (tp30) cc_final: 0.8800 (mm-30) REVERT: A 217 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8507 (tt0) REVERT: A 253 PHE cc_start: 0.8605 (t80) cc_final: 0.8271 (t80) REVERT: A 257 MET cc_start: 0.8835 (mmm) cc_final: 0.8409 (mmm) REVERT: B 43 GLU cc_start: 0.8554 (tt0) cc_final: 0.8032 (tm-30) REVERT: B 48 ASP cc_start: 0.9134 (p0) cc_final: 0.8855 (p0) REVERT: B 59 GLN cc_start: 0.8952 (tp40) cc_final: 0.8216 (tp40) REVERT: B 230 GLU cc_start: 0.8602 (mp0) cc_final: 0.8279 (mm-30) REVERT: B 239 GLU cc_start: 0.8619 (tt0) cc_final: 0.8369 (tt0) REVERT: B 281 LYS cc_start: 0.9154 (tppt) cc_final: 0.8794 (mmmm) REVERT: C 48 ASP cc_start: 0.9052 (p0) cc_final: 0.8649 (p0) REVERT: C 59 GLN cc_start: 0.9003 (tp40) cc_final: 0.8138 (tp40) REVERT: C 230 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7842 (mm-30) REVERT: C 239 GLU cc_start: 0.8227 (tt0) cc_final: 0.7729 (tt0) REVERT: D 21 MET cc_start: 0.7963 (pmm) cc_final: 0.7746 (pmm) REVERT: D 48 ASP cc_start: 0.9154 (p0) cc_final: 0.8911 (p0) REVERT: D 52 MET cc_start: 0.9310 (mmt) cc_final: 0.8974 (mmm) REVERT: D 59 GLN cc_start: 0.9002 (tp40) cc_final: 0.8554 (tp40) REVERT: D 210 GLU cc_start: 0.9105 (tp30) cc_final: 0.8815 (mm-30) REVERT: D 217 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8499 (tt0) REVERT: D 239 GLU cc_start: 0.8370 (tt0) cc_final: 0.8162 (tt0) REVERT: D 253 PHE cc_start: 0.8575 (t80) cc_final: 0.8258 (t80) REVERT: D 257 MET cc_start: 0.8831 (mmm) cc_final: 0.8409 (mmm) REVERT: E 48 ASP cc_start: 0.9072 (p0) cc_final: 0.8737 (p0) REVERT: E 230 GLU cc_start: 0.8599 (mp0) cc_final: 0.8299 (mm-30) REVERT: E 239 GLU cc_start: 0.8692 (tt0) cc_final: 0.8446 (tt0) REVERT: E 281 LYS cc_start: 0.9140 (tppt) cc_final: 0.8767 (mmmm) REVERT: F 48 ASP cc_start: 0.8961 (p0) cc_final: 0.8631 (p0) REVERT: F 59 GLN cc_start: 0.9026 (tp40) cc_final: 0.8188 (tp40) REVERT: F 230 GLU cc_start: 0.8529 (mp0) cc_final: 0.8050 (pm20) REVERT: G 48 ASP cc_start: 0.9005 (p0) cc_final: 0.8638 (p0) REVERT: G 59 GLN cc_start: 0.9035 (tp40) cc_final: 0.8173 (tp40) REVERT: G 210 GLU cc_start: 0.9079 (tp30) cc_final: 0.8627 (tp30) REVERT: G 230 GLU cc_start: 0.8489 (mp0) cc_final: 0.8036 (pm20) REVERT: H 48 ASP cc_start: 0.9126 (p0) cc_final: 0.8789 (p0) REVERT: H 210 GLU cc_start: 0.9112 (tp30) cc_final: 0.8811 (mm-30) REVERT: H 217 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8477 (tt0) REVERT: H 253 PHE cc_start: 0.8545 (t80) cc_final: 0.8223 (t80) REVERT: H 257 MET cc_start: 0.8826 (mmm) cc_final: 0.8415 (mmm) REVERT: I 48 ASP cc_start: 0.9049 (p0) cc_final: 0.8751 (p0) REVERT: I 59 GLN cc_start: 0.8939 (tp40) cc_final: 0.8217 (tp40) REVERT: I 230 GLU cc_start: 0.8598 (mp0) cc_final: 0.8300 (mm-30) REVERT: I 239 GLU cc_start: 0.8686 (tt0) cc_final: 0.8442 (tt0) REVERT: I 281 LYS cc_start: 0.9141 (tppt) cc_final: 0.8749 (mmmm) REVERT: J 48 ASP cc_start: 0.9053 (p0) cc_final: 0.8642 (p0) REVERT: J 59 GLN cc_start: 0.8998 (tp40) cc_final: 0.8560 (tp40) REVERT: J 230 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7763 (mt-10) REVERT: K 48 ASP cc_start: 0.9136 (p0) cc_final: 0.8904 (p0) REVERT: K 52 MET cc_start: 0.9292 (mmt) cc_final: 0.8950 (mmm) REVERT: K 210 GLU cc_start: 0.9117 (tp30) cc_final: 0.8822 (mm-30) REVERT: K 217 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8437 (tt0) REVERT: K 253 PHE cc_start: 0.8565 (t80) cc_final: 0.8251 (t80) REVERT: K 257 MET cc_start: 0.8834 (mmm) cc_final: 0.8426 (mmm) REVERT: L 24 ARG cc_start: 0.8085 (ptt-90) cc_final: 0.7875 (ptt-90) REVERT: L 43 GLU cc_start: 0.8522 (tt0) cc_final: 0.8008 (tm-30) REVERT: L 48 ASP cc_start: 0.9062 (p0) cc_final: 0.8695 (p0) REVERT: L 59 GLN cc_start: 0.8935 (tp40) cc_final: 0.8214 (tp40) REVERT: L 230 GLU cc_start: 0.8605 (mp0) cc_final: 0.8308 (mm-30) REVERT: L 239 GLU cc_start: 0.8699 (tt0) cc_final: 0.8457 (tt0) REVERT: L 281 LYS cc_start: 0.9167 (tppt) cc_final: 0.8784 (mmmm) outliers start: 57 outliers final: 25 residues processed: 427 average time/residue: 1.2856 time to fit residues: 618.2705 Evaluate side-chains 398 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 373 time to evaluate : 2.074 ------------------------------------------------------------------------------- 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 224 SER Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain L residue 224 SER 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 52 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 217 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 217 GLN H 56 ASN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 GLN L 217 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.134610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.095809 restraints weight = 33791.375| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.89 r_work: 0.3160 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21060 Z= 0.138 Angle : 0.693 13.920 28548 Z= 0.337 Chirality : 0.039 0.225 3396 Planarity : 0.004 0.054 3144 Dihedral : 6.834 53.419 6732 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.54 % Allowed : 26.15 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.18), residues: 2196 helix: 3.63 (0.11), residues: 1680 sheet: 1.01 (0.43), residues: 120 loop : -1.55 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 277 HIS 0.002 0.000 HIS I 274 PHE 0.014 0.001 PHE A 81 TYR 0.026 0.002 TYR A 96 ARG 0.012 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 1416) hydrogen bonds : angle 3.05155 ( 4212) SS BOND : bond 0.00715 ( 36) SS BOND : angle 1.98364 ( 72) covalent geometry : bond 0.00321 (21024) covalent geometry : angle 0.68622 (28476) *********************** 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 451 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 400 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: A 59 GLN cc_start: 0.8927 (tp40) cc_final: 0.8537 (tp40) REVERT: A 210 GLU cc_start: 0.9086 (tp30) cc_final: 0.8768 (mm-30) REVERT: A 241 GLU cc_start: 0.8308 (tt0) cc_final: 0.8037 (tt0) REVERT: A 253 PHE cc_start: 0.8488 (t80) cc_final: 0.8133 (t80) REVERT: A 257 MET cc_start: 0.8788 (mmm) cc_final: 0.8372 (mmm) REVERT: B 24 ARG cc_start: 0.8060 (ptt-90) cc_final: 0.7817 (ptt-90) REVERT: B 43 GLU cc_start: 0.8586 (tt0) cc_final: 0.8101 (tm-30) REVERT: B 48 ASP cc_start: 0.9148 (p0) cc_final: 0.8865 (p0) REVERT: B 59 GLN cc_start: 0.8912 (tp40) cc_final: 0.8214 (tp40) REVERT: B 239 GLU cc_start: 0.8680 (tt0) cc_final: 0.8472 (tt0) REVERT: B 281 LYS cc_start: 0.9157 (tppt) cc_final: 0.8780 (mmmm) REVERT: C 48 ASP cc_start: 0.9059 (p0) cc_final: 0.8679 (p0) REVERT: C 59 GLN cc_start: 0.9009 (tp40) cc_final: 0.8131 (tp40) REVERT: C 230 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7823 (mm-30) REVERT: D 59 GLN cc_start: 0.9013 (tp40) cc_final: 0.8527 (tp40) REVERT: D 241 GLU cc_start: 0.8370 (tt0) cc_final: 0.7874 (tt0) REVERT: D 253 PHE cc_start: 0.8483 (t80) cc_final: 0.8087 (t80) REVERT: D 257 MET cc_start: 0.8792 (mmm) cc_final: 0.8381 (mmm) REVERT: E 48 ASP cc_start: 0.9100 (p0) cc_final: 0.8806 (p0) REVERT: E 54 VAL cc_start: 0.9032 (t) cc_final: 0.8817 (m) REVERT: E 281 LYS cc_start: 0.9152 (tppt) cc_final: 0.8779 (mmmm) REVERT: F 48 ASP cc_start: 0.9036 (p0) cc_final: 0.8678 (p0) REVERT: F 59 GLN cc_start: 0.9044 (tp40) cc_final: 0.8159 (tp40) REVERT: F 230 GLU cc_start: 0.8487 (mp0) cc_final: 0.8028 (pm20) REVERT: G 48 ASP cc_start: 0.9009 (p0) cc_final: 0.8589 (p0) REVERT: G 59 GLN cc_start: 0.9032 (tp40) cc_final: 0.8144 (tp40) REVERT: G 210 GLU cc_start: 0.9060 (tp30) cc_final: 0.8655 (tp30) REVERT: G 230 GLU cc_start: 0.8446 (mp0) cc_final: 0.7990 (pm20) REVERT: H 43 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: H 210 GLU cc_start: 0.9095 (tp30) cc_final: 0.8785 (mm-30) REVERT: H 241 GLU cc_start: 0.8362 (tt0) cc_final: 0.8053 (tt0) REVERT: H 253 PHE cc_start: 0.8449 (t80) cc_final: 0.8060 (t80) REVERT: H 257 MET cc_start: 0.8783 (mmm) cc_final: 0.8379 (mmm) REVERT: I 43 GLU cc_start: 0.8274 (tt0) cc_final: 0.7688 (tm-30) REVERT: I 48 ASP cc_start: 0.9043 (p0) cc_final: 0.8778 (p0) REVERT: I 54 VAL cc_start: 0.9037 (t) cc_final: 0.8825 (m) REVERT: I 59 GLN cc_start: 0.8894 (tp40) cc_final: 0.8215 (tp40) REVERT: I 281 LYS cc_start: 0.9133 (tppt) cc_final: 0.8758 (mmmm) REVERT: J 48 ASP cc_start: 0.9056 (p0) cc_final: 0.8681 (p0) REVERT: J 59 GLN cc_start: 0.8978 (tp40) cc_final: 0.8587 (tp40) REVERT: J 230 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7752 (mt-10) REVERT: K 210 GLU cc_start: 0.9100 (tp30) cc_final: 0.8796 (mm-30) REVERT: K 217 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8420 (tt0) REVERT: K 239 GLU cc_start: 0.8304 (tt0) cc_final: 0.8088 (tt0) REVERT: K 241 GLU cc_start: 0.8380 (tt0) cc_final: 0.8074 (tt0) REVERT: K 253 PHE cc_start: 0.8463 (t80) cc_final: 0.8070 (t80) REVERT: K 257 MET cc_start: 0.8789 (mmm) cc_final: 0.8386 (mmm) REVERT: L 24 ARG cc_start: 0.8082 (ptt-90) cc_final: 0.7876 (ptt-90) REVERT: L 43 GLU cc_start: 0.8614 (tt0) cc_final: 0.8127 (tm-30) REVERT: L 48 ASP cc_start: 0.9101 (p0) cc_final: 0.8784 (p0) REVERT: L 59 GLN cc_start: 0.8882 (tp40) cc_final: 0.8179 (tp40) REVERT: L 281 LYS cc_start: 0.9137 (tppt) cc_final: 0.8761 (mmmm) outliers start: 51 outliers final: 26 residues processed: 437 average time/residue: 1.2959 time to fit residues: 640.6467 Evaluate side-chains 407 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 379 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU 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 C residue 55 CYS Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 55 CYS Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain L residue 224 SER Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 117 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN C 56 ASN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 217 GLN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN I 268 ASN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 GLN L 217 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 = 0.3952 r_free = 0.3952 target = 0.134405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.095620 restraints weight = 33994.826| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.89 r_work: 0.3167 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21060 Z= 0.137 Angle : 0.688 13.266 28548 Z= 0.336 Chirality : 0.039 0.193 3396 Planarity : 0.004 0.056 3144 Dihedral : 6.749 54.082 6732 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.25 % Allowed : 27.40 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.18), residues: 2196 helix: 3.59 (0.12), residues: 1692 sheet: 0.90 (0.42), residues: 120 loop : -1.88 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 277 HIS 0.002 0.001 HIS I 274 PHE 0.019 0.001 PHE J 81 TYR 0.026 0.001 TYR I 96 ARG 0.014 0.001 ARG J 24 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 1416) hydrogen bonds : angle 3.04471 ( 4212) SS BOND : bond 0.00661 ( 36) SS BOND : angle 1.83875 ( 72) covalent geometry : bond 0.00323 (21024) covalent geometry : angle 0.68241 (28476) *********************** 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 450 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 405 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: A 48 ASP cc_start: 0.9054 (p0) cc_final: 0.8728 (p0) REVERT: A 59 GLN cc_start: 0.8929 (tp40) cc_final: 0.8536 (tp40) REVERT: A 68 ASP cc_start: 0.8424 (t70) cc_final: 0.8192 (t0) REVERT: A 241 GLU cc_start: 0.8291 (tt0) cc_final: 0.7899 (tt0) REVERT: A 253 PHE cc_start: 0.8470 (t80) cc_final: 0.8076 (t80) REVERT: A 257 MET cc_start: 0.8828 (mmm) cc_final: 0.8401 (mmm) REVERT: B 43 GLU cc_start: 0.8669 (tt0) cc_final: 0.8179 (tm-30) REVERT: B 48 ASP cc_start: 0.9191 (p0) cc_final: 0.8909 (p0) REVERT: B 59 GLN cc_start: 0.8978 (tp40) cc_final: 0.8767 (tp40) REVERT: B 198 PHE cc_start: 0.7467 (t80) cc_final: 0.7155 (t80) REVERT: B 239 GLU cc_start: 0.8725 (tt0) cc_final: 0.8513 (tt0) REVERT: B 281 LYS cc_start: 0.9174 (tppt) cc_final: 0.8804 (mmmm) REVERT: C 48 ASP cc_start: 0.9086 (p0) cc_final: 0.8702 (p0) REVERT: C 59 GLN cc_start: 0.9069 (tp40) cc_final: 0.8086 (tp40) REVERT: C 97 SER cc_start: 0.8725 (m) cc_final: 0.8308 (p) REVERT: C 230 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7931 (mm-30) REVERT: D 48 ASP cc_start: 0.9074 (p0) cc_final: 0.8701 (p0) REVERT: D 52 MET cc_start: 0.9209 (mmt) cc_final: 0.8866 (mmm) REVERT: D 59 GLN cc_start: 0.8997 (tp40) cc_final: 0.8503 (tp40) REVERT: D 68 ASP cc_start: 0.8449 (t70) cc_final: 0.8220 (t0) REVERT: D 241 GLU cc_start: 0.8355 (tt0) cc_final: 0.7900 (tt0) REVERT: D 253 PHE cc_start: 0.8486 (t80) cc_final: 0.8081 (t80) REVERT: D 257 MET cc_start: 0.8842 (mmm) cc_final: 0.8407 (mmm) REVERT: E 24 ARG cc_start: 0.8083 (ptt-90) cc_final: 0.7676 (pmt170) REVERT: E 48 ASP cc_start: 0.9140 (p0) cc_final: 0.8855 (p0) REVERT: E 281 LYS cc_start: 0.9156 (tppt) cc_final: 0.8784 (mmmm) REVERT: F 24 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7890 (pmt170) REVERT: F 48 ASP cc_start: 0.9080 (p0) cc_final: 0.8728 (p0) REVERT: F 59 GLN cc_start: 0.9095 (tp40) cc_final: 0.8118 (tp40) REVERT: F 97 SER cc_start: 0.8710 (m) cc_final: 0.8298 (p) REVERT: F 230 GLU cc_start: 0.8426 (mp0) cc_final: 0.7949 (pm20) REVERT: G 48 ASP cc_start: 0.9031 (p0) cc_final: 0.8637 (p0) REVERT: G 210 GLU cc_start: 0.9074 (tp30) cc_final: 0.8666 (tp30) REVERT: G 230 GLU cc_start: 0.8446 (mp0) cc_final: 0.8005 (pm20) REVERT: H 43 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7972 (tm-30) REVERT: H 48 ASP cc_start: 0.9042 (p0) cc_final: 0.8684 (p0) REVERT: H 52 MET cc_start: 0.9185 (mmt) cc_final: 0.8838 (mmm) REVERT: H 68 ASP cc_start: 0.8416 (t70) cc_final: 0.8205 (t0) REVERT: H 241 GLU cc_start: 0.8330 (tt0) cc_final: 0.7904 (tt0) REVERT: H 253 PHE cc_start: 0.8460 (t80) cc_final: 0.8056 (t80) REVERT: H 257 MET cc_start: 0.8826 (mmm) cc_final: 0.8399 (mmm) REVERT: I 48 ASP cc_start: 0.9076 (p0) cc_final: 0.8821 (p0) REVERT: I 59 GLN cc_start: 0.8980 (tp40) cc_final: 0.8147 (tp40) REVERT: I 198 PHE cc_start: 0.7425 (t80) cc_final: 0.7149 (t80) REVERT: I 281 LYS cc_start: 0.9138 (tppt) cc_final: 0.8785 (mmmm) REVERT: J 48 ASP cc_start: 0.9078 (p0) cc_final: 0.8684 (p0) REVERT: J 59 GLN cc_start: 0.9022 (tp40) cc_final: 0.8535 (tp40) REVERT: J 230 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7709 (mt-10) REVERT: J 239 GLU cc_start: 0.8296 (tt0) cc_final: 0.7648 (tt0) REVERT: K 48 ASP cc_start: 0.9056 (p0) cc_final: 0.8747 (p0) REVERT: K 68 ASP cc_start: 0.8417 (t70) cc_final: 0.8195 (t0) REVERT: K 210 GLU cc_start: 0.9103 (tp30) cc_final: 0.8777 (mm-30) REVERT: K 217 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8480 (tt0) REVERT: K 241 GLU cc_start: 0.8367 (tt0) cc_final: 0.7930 (tt0) REVERT: K 253 PHE cc_start: 0.8489 (t80) cc_final: 0.8101 (t80) REVERT: K 257 MET cc_start: 0.8817 (mmm) cc_final: 0.8419 (mmm) REVERT: L 24 ARG cc_start: 0.8053 (ptt-90) cc_final: 0.7770 (ptt-90) REVERT: L 43 GLU cc_start: 0.8646 (tt0) cc_final: 0.8164 (tm-30) REVERT: L 48 ASP cc_start: 0.9138 (p0) cc_final: 0.8828 (p0) REVERT: L 59 GLN cc_start: 0.8968 (tp40) cc_final: 0.8141 (tp40) REVERT: L 281 LYS cc_start: 0.9156 (tppt) cc_final: 0.8792 (mmmm) outliers start: 45 outliers final: 25 residues processed: 435 average time/residue: 1.2688 time to fit residues: 622.8373 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 : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU 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 224 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 91 LEU 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 F residue 24 ARG Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 272 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 40 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN B 217 GLN C 56 ASN D 104 GLN E 217 GLN H 104 GLN I 82 GLN I 104 GLN I 268 ASN J 56 ASN L 217 GLN L 268 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.134223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095488 restraints weight = 34009.099| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.89 r_work: 0.3149 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21060 Z= 0.140 Angle : 0.708 15.708 28548 Z= 0.346 Chirality : 0.039 0.177 3396 Planarity : 0.005 0.063 3144 Dihedral : 6.698 54.589 6732 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.20 % Allowed : 28.39 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.18), residues: 2196 helix: 3.55 (0.12), residues: 1692 sheet: 0.68 (0.43), residues: 120 loop : -1.87 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 277 HIS 0.002 0.001 HIS K 75 PHE 0.019 0.001 PHE C 81 TYR 0.025 0.002 TYR A 96 ARG 0.013 0.001 ARG C 278 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 1416) hydrogen bonds : angle 3.10120 ( 4212) SS BOND : bond 0.00640 ( 36) SS BOND : angle 1.77336 ( 72) covalent geometry : bond 0.00330 (21024) covalent geometry : angle 0.70350 (28476) *********************** 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 445 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 401 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: A 48 ASP cc_start: 0.9133 (p0) cc_final: 0.8807 (p0) REVERT: A 59 GLN cc_start: 0.8913 (tp40) cc_final: 0.8532 (tp40) REVERT: A 68 ASP cc_start: 0.8510 (t70) cc_final: 0.8300 (t0) REVERT: A 241 GLU cc_start: 0.8356 (tt0) cc_final: 0.8072 (tt0) REVERT: A 253 PHE cc_start: 0.8499 (t80) cc_final: 0.8108 (t80) REVERT: A 257 MET cc_start: 0.8843 (mmm) cc_final: 0.8408 (mmm) REVERT: B 24 ARG cc_start: 0.8093 (ptt-90) cc_final: 0.7781 (pmt170) REVERT: B 43 GLU cc_start: 0.8616 (tt0) cc_final: 0.8168 (tm-30) REVERT: B 48 ASP cc_start: 0.9245 (p0) cc_final: 0.8980 (p0) REVERT: B 59 GLN cc_start: 0.8969 (tp40) cc_final: 0.8020 (tp40) REVERT: B 198 PHE cc_start: 0.7460 (t80) cc_final: 0.7159 (t80) REVERT: B 239 GLU cc_start: 0.8775 (tt0) cc_final: 0.8514 (tt0) REVERT: B 277 TRP cc_start: 0.8270 (t-100) cc_final: 0.8059 (t-100) REVERT: B 281 LYS cc_start: 0.9265 (tppt) cc_final: 0.8892 (mmmm) REVERT: C 48 ASP cc_start: 0.9135 (p0) cc_final: 0.8735 (p0) REVERT: C 59 GLN cc_start: 0.8987 (tp40) cc_final: 0.8074 (tp40) REVERT: C 97 SER cc_start: 0.8717 (m) cc_final: 0.8310 (p) REVERT: D 48 ASP cc_start: 0.9100 (p0) cc_final: 0.8775 (p0) REVERT: D 59 GLN cc_start: 0.8996 (tp40) cc_final: 0.8521 (tp40) REVERT: D 68 ASP cc_start: 0.8519 (t70) cc_final: 0.8308 (t0) REVERT: D 241 GLU cc_start: 0.8360 (tt0) cc_final: 0.7990 (tt0) REVERT: D 253 PHE cc_start: 0.8510 (t80) cc_final: 0.8133 (t80) REVERT: D 257 MET cc_start: 0.8851 (mmm) cc_final: 0.8423 (mmm) REVERT: E 48 ASP cc_start: 0.9175 (p0) cc_final: 0.8891 (p0) REVERT: E 230 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7719 (tp30) REVERT: F 48 ASP cc_start: 0.9138 (p0) cc_final: 0.8786 (p0) REVERT: F 59 GLN cc_start: 0.9043 (tp40) cc_final: 0.8091 (tp40) REVERT: F 97 SER cc_start: 0.8705 (m) cc_final: 0.8303 (p) REVERT: F 230 GLU cc_start: 0.8488 (mp0) cc_final: 0.8031 (pm20) REVERT: G 48 ASP cc_start: 0.9123 (p0) cc_final: 0.8692 (p0) REVERT: G 59 GLN cc_start: 0.8995 (tp40) cc_final: 0.8039 (tp40) REVERT: G 97 SER cc_start: 0.8712 (m) cc_final: 0.8317 (p) REVERT: G 210 GLU cc_start: 0.9069 (tp30) cc_final: 0.8652 (tp30) REVERT: G 230 GLU cc_start: 0.8453 (mp0) cc_final: 0.8003 (pm20) REVERT: H 43 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: H 48 ASP cc_start: 0.9085 (p0) cc_final: 0.8740 (p0) REVERT: H 68 ASP cc_start: 0.8504 (t70) cc_final: 0.8294 (t0) REVERT: H 241 GLU cc_start: 0.8388 (tt0) cc_final: 0.8073 (tt0) REVERT: H 253 PHE cc_start: 0.8497 (t80) cc_final: 0.8118 (t80) REVERT: H 257 MET cc_start: 0.8842 (mmm) cc_final: 0.8419 (mmm) REVERT: I 24 ARG cc_start: 0.7963 (ptt-90) cc_final: 0.7619 (pmt170) REVERT: I 48 ASP cc_start: 0.9108 (p0) cc_final: 0.8862 (p0) REVERT: I 59 GLN cc_start: 0.8972 (tp40) cc_final: 0.8136 (tp40) REVERT: I 198 PHE cc_start: 0.7451 (t80) cc_final: 0.7170 (t80) REVERT: I 277 TRP cc_start: 0.8344 (t-100) cc_final: 0.8114 (t-100) REVERT: I 281 LYS cc_start: 0.9161 (tppt) cc_final: 0.8697 (mmmm) REVERT: J 48 ASP cc_start: 0.9160 (p0) cc_final: 0.8729 (p0) REVERT: J 59 GLN cc_start: 0.8944 (tp40) cc_final: 0.8491 (tp40) REVERT: J 97 SER cc_start: 0.8700 (m) cc_final: 0.8294 (p) REVERT: J 230 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7789 (mt-10) REVERT: K 48 ASP cc_start: 0.9105 (p0) cc_final: 0.8750 (p0) REVERT: K 52 MET cc_start: 0.9232 (mmt) cc_final: 0.8895 (mmm) REVERT: K 68 ASP cc_start: 0.8490 (t70) cc_final: 0.8284 (t0) REVERT: K 217 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8491 (tt0) REVERT: K 241 GLU cc_start: 0.8365 (tt0) cc_final: 0.7949 (tt0) REVERT: K 253 PHE cc_start: 0.8517 (t80) cc_final: 0.8143 (t80) REVERT: K 257 MET cc_start: 0.8834 (mmm) cc_final: 0.8442 (mmm) REVERT: L 43 GLU cc_start: 0.8610 (tt0) cc_final: 0.8167 (tm-30) REVERT: L 48 ASP cc_start: 0.9172 (p0) cc_final: 0.8879 (p0) REVERT: L 59 GLN cc_start: 0.8968 (tp40) cc_final: 0.8130 (tp40) REVERT: L 230 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7733 (tp30) outliers start: 44 outliers final: 18 residues processed: 435 average time/residue: 1.3557 time to fit residues: 667.2163 Evaluate side-chains 401 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 381 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 91 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 224 SER Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain L residue 224 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 123 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 217 GLN C 56 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 268 ASN J 56 ASN K 104 GLN ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 217 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 = 0.3953 r_free = 0.3953 target = 0.134303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.095585 restraints weight = 34125.467| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.89 r_work: 0.3158 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21060 Z= 0.142 Angle : 0.738 17.387 28548 Z= 0.358 Chirality : 0.039 0.168 3396 Planarity : 0.005 0.079 3144 Dihedral : 6.664 54.897 6732 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.45 % Allowed : 29.44 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.18), residues: 2196 helix: 3.52 (0.12), residues: 1692 sheet: -0.04 (0.40), residues: 144 loop : -1.60 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 277 HIS 0.003 0.001 HIS C 274 PHE 0.021 0.001 PHE C 81 TYR 0.026 0.001 TYR I 96 ARG 0.018 0.001 ARG F 285 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 1416) hydrogen bonds : angle 3.14332 ( 4212) SS BOND : bond 0.00623 ( 36) SS BOND : angle 1.76861 ( 72) covalent geometry : bond 0.00336 (21024) covalent geometry : angle 0.73333 (28476) ********************** 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 422 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 393 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: A 48 ASP cc_start: 0.9160 (p0) cc_final: 0.8843 (p0) REVERT: A 59 GLN cc_start: 0.8918 (tp40) cc_final: 0.8547 (tp40) REVERT: A 241 GLU cc_start: 0.8278 (tt0) cc_final: 0.7977 (tt0) REVERT: A 253 PHE cc_start: 0.8495 (t80) cc_final: 0.8104 (t80) REVERT: A 257 MET cc_start: 0.8852 (mmm) cc_final: 0.8416 (mmm) REVERT: B 24 ARG cc_start: 0.8055 (ptt-90) cc_final: 0.7765 (pmt170) REVERT: B 43 GLU cc_start: 0.8620 (tt0) cc_final: 0.8179 (tm-30) REVERT: B 48 ASP cc_start: 0.9243 (p0) cc_final: 0.8979 (p0) REVERT: B 59 GLN cc_start: 0.8958 (tp40) cc_final: 0.8006 (tp40) REVERT: B 198 PHE cc_start: 0.7436 (t80) cc_final: 0.7138 (t80) REVERT: B 277 TRP cc_start: 0.8291 (t-100) cc_final: 0.8011 (t-100) REVERT: B 281 LYS cc_start: 0.9281 (tppt) cc_final: 0.8823 (mmmm) REVERT: C 48 ASP cc_start: 0.9162 (p0) cc_final: 0.8768 (p0) REVERT: C 59 GLN cc_start: 0.8967 (tp40) cc_final: 0.8021 (tp40) REVERT: C 97 SER cc_start: 0.8726 (m) cc_final: 0.8315 (p) REVERT: C 230 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7965 (mm-30) REVERT: D 48 ASP cc_start: 0.9170 (p0) cc_final: 0.8823 (p0) REVERT: D 52 MET cc_start: 0.9236 (mmt) cc_final: 0.8913 (mmm) REVERT: D 59 GLN cc_start: 0.8997 (tp40) cc_final: 0.8531 (tp40) REVERT: D 241 GLU cc_start: 0.8278 (tt0) cc_final: 0.7926 (tt0) REVERT: D 253 PHE cc_start: 0.8509 (t80) cc_final: 0.8131 (t80) REVERT: D 257 MET cc_start: 0.8856 (mmm) cc_final: 0.8430 (mmm) REVERT: E 48 ASP cc_start: 0.9184 (p0) cc_final: 0.8886 (p0) REVERT: E 230 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7741 (tp30) REVERT: F 48 ASP cc_start: 0.9170 (p0) cc_final: 0.8798 (p0) REVERT: F 59 GLN cc_start: 0.9037 (tp40) cc_final: 0.8097 (tp40) REVERT: F 97 SER cc_start: 0.8714 (m) cc_final: 0.8305 (p) REVERT: F 230 GLU cc_start: 0.8464 (mp0) cc_final: 0.7980 (pm20) REVERT: G 24 ARG cc_start: 0.8080 (ptt-90) cc_final: 0.7829 (pmt170) REVERT: G 48 ASP cc_start: 0.9128 (p0) cc_final: 0.8700 (p0) REVERT: G 59 GLN cc_start: 0.9024 (tp40) cc_final: 0.8072 (tp40) REVERT: G 97 SER cc_start: 0.8715 (m) cc_final: 0.8302 (p) REVERT: G 210 GLU cc_start: 0.9067 (tp30) cc_final: 0.8649 (tp30) REVERT: G 230 GLU cc_start: 0.8445 (mp0) cc_final: 0.7982 (pm20) REVERT: H 24 ARG cc_start: 0.7896 (ptt-90) cc_final: 0.7665 (ptt-90) REVERT: H 43 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: H 48 ASP cc_start: 0.9099 (p0) cc_final: 0.8747 (p0) REVERT: H 241 GLU cc_start: 0.8302 (tt0) cc_final: 0.7961 (tt0) REVERT: H 253 PHE cc_start: 0.8503 (t80) cc_final: 0.8124 (t80) REVERT: H 257 MET cc_start: 0.8851 (mmm) cc_final: 0.8430 (mmm) REVERT: I 48 ASP cc_start: 0.9123 (p0) cc_final: 0.8837 (p0) REVERT: I 59 GLN cc_start: 0.8952 (tp40) cc_final: 0.7999 (tp40) REVERT: I 198 PHE cc_start: 0.7469 (t80) cc_final: 0.7189 (t80) REVERT: I 277 TRP cc_start: 0.8278 (t-100) cc_final: 0.8042 (t-100) REVERT: I 281 LYS cc_start: 0.9258 (tppt) cc_final: 0.8808 (mmmm) REVERT: J 48 ASP cc_start: 0.9157 (p0) cc_final: 0.8782 (p0) REVERT: J 59 GLN cc_start: 0.8905 (tp40) cc_final: 0.8537 (tp40) REVERT: J 97 SER cc_start: 0.8709 (m) cc_final: 0.8301 (p) REVERT: J 230 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7779 (mt-10) REVERT: K 48 ASP cc_start: 0.9188 (p0) cc_final: 0.8827 (p0) REVERT: K 217 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8500 (tt0) REVERT: K 241 GLU cc_start: 0.8305 (tt0) cc_final: 0.7945 (tt0) REVERT: K 253 PHE cc_start: 0.8519 (t80) cc_final: 0.8144 (t80) REVERT: K 257 MET cc_start: 0.8842 (mmm) cc_final: 0.8451 (mmm) REVERT: L 24 ARG cc_start: 0.8256 (ptt-90) cc_final: 0.8024 (pmt170) REVERT: L 43 GLU cc_start: 0.8647 (tt0) cc_final: 0.8206 (tm-30) REVERT: L 48 ASP cc_start: 0.9184 (p0) cc_final: 0.8878 (p0) REVERT: L 59 GLN cc_start: 0.8924 (tp40) cc_final: 0.8131 (tp40) REVERT: L 230 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7764 (tp30) outliers start: 29 outliers final: 13 residues processed: 412 average time/residue: 1.2993 time to fit residues: 603.8026 Evaluate side-chains 401 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 386 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 282 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 5 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 217 GLN C 56 ASN E 104 GLN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 268 ASN J 56 ASN L 104 GLN ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 217 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 = 0.3948 r_free = 0.3948 target = 0.134023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.095434 restraints weight = 34162.009| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.88 r_work: 0.3150 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5609 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= 0.144 Angle : 0.738 16.596 28548 Z= 0.358 Chirality : 0.039 0.165 3396 Planarity : 0.005 0.081 3144 Dihedral : 6.644 55.354 6732 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.40 % Allowed : 30.39 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.18), residues: 2196 helix: 3.48 (0.12), residues: 1692 sheet: -0.11 (0.40), residues: 144 loop : -1.60 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 277 HIS 0.006 0.001 HIS G 274 PHE 0.020 0.001 PHE C 81 TYR 0.024 0.002 TYR A 96 ARG 0.018 0.001 ARG F 285 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 1416) hydrogen bonds : angle 3.14549 ( 4212) SS BOND : bond 0.00622 ( 36) SS BOND : angle 1.74387 ( 72) covalent geometry : bond 0.00341 (21024) covalent geometry : angle 0.73392 (28476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15879.03 seconds wall clock time: 273 minutes 28.22 seconds (16408.22 seconds total)