Starting phenix.real_space_refine on Wed Jun 18 00:52:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iyg_35821/06_2025/8iyg_35821.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iyg_35821/06_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_35821/06_2025/8iyg_35821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iyg_35821/06_2025/8iyg_35821.map" model { file = "/net/cci-nas-00/data/ceres_data/8iyg_35821/06_2025/8iyg_35821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iyg_35821/06_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-5710/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: 13.08, per 1000 atoms: 0.64 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: 5.34 Conformation dependent library (CDL) restraints added in 2.2 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: 1.65 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: 5.36 Time building geometry restraints manager: 6.28 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: 1.210 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: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 44.320 Find NCS groups from input model: 1.230 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: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.560 ------------------------------------------------------------------------------- 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 : 2.509 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: 1.1348 time to fit residues: 1098.6789 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 : 2.292 ------------------------------------------------------------------------------- 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 ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 ASN H 268 ASN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 ASN ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.144006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.105011 restraints weight = 33606.463| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.00 r_work: 0.3318 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3588 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 8.167 28548 Z= 0.304 Chirality : 0.038 0.152 3396 Planarity : 0.004 0.033 3144 Dihedral : 8.541 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 0.04180 ( 1416) hydrogen bonds : angle 3.05252 ( 4212) SS BOND : bond 0.00605 ( 36) SS BOND : angle 1.40580 ( 72) covalent geometry : bond 0.00306 (21024) covalent geometry : angle 0.62202 (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 : 2.992 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8726 (tp40) cc_final: 0.8006 (tp40) REVERT: A 253 PHE cc_start: 0.7987 (t80) cc_final: 0.7713 (t80) REVERT: A 257 MET cc_start: 0.8814 (mmm) cc_final: 0.8426 (mmm) REVERT: A 278 ARG cc_start: 0.8698 (mmp-170) cc_final: 0.8384 (mmp80) REVERT: B 43 GLU cc_start: 0.8317 (tt0) cc_final: 0.7731 (tm-30) REVERT: B 59 GLN cc_start: 0.8873 (tp40) cc_final: 0.8277 (tp40) REVERT: B 230 GLU cc_start: 0.8379 (mp0) cc_final: 0.8145 (mm-30) REVERT: B 278 ARG cc_start: 0.8661 (mmp80) cc_final: 0.8436 (mmp80) REVERT: C 43 GLU cc_start: 0.8210 (tt0) cc_final: 0.7983 (tt0) REVERT: C 59 GLN cc_start: 0.8804 (tp40) cc_final: 0.8041 (tp40) REVERT: C 78 TYR cc_start: 0.8597 (t80) cc_final: 0.8393 (t80) REVERT: C 230 GLU cc_start: 0.8243 (mp0) cc_final: 0.7983 (mp0) REVERT: D 59 GLN cc_start: 0.8713 (tp40) cc_final: 0.7993 (tp40) REVERT: D 253 PHE cc_start: 0.7974 (t80) cc_final: 0.7701 (t80) REVERT: D 257 MET cc_start: 0.8799 (mmm) cc_final: 0.8417 (mmm) REVERT: D 278 ARG cc_start: 0.8692 (mmp-170) cc_final: 0.8381 (mmp80) REVERT: E 43 GLU cc_start: 0.8293 (tt0) cc_final: 0.7715 (tm-30) REVERT: E 230 GLU cc_start: 0.8347 (mp0) cc_final: 0.8106 (mm-30) REVERT: E 253 PHE cc_start: 0.8158 (t80) cc_final: 0.7945 (t80) REVERT: E 278 ARG cc_start: 0.8729 (mmp-170) cc_final: 0.8482 (mmp80) REVERT: F 43 GLU cc_start: 0.8199 (tt0) cc_final: 0.7971 (tt0) REVERT: F 59 GLN cc_start: 0.8813 (tp40) cc_final: 0.8049 (tp40) REVERT: F 230 GLU cc_start: 0.8266 (mp0) cc_final: 0.8004 (mp0) REVERT: G 43 GLU cc_start: 0.8218 (tt0) cc_final: 0.7987 (tt0) REVERT: G 59 GLN cc_start: 0.8788 (tp40) cc_final: 0.8021 (tp40) REVERT: G 78 TYR cc_start: 0.8572 (t80) cc_final: 0.8361 (t80) REVERT: G 230 GLU cc_start: 0.8223 (mp0) cc_final: 0.7967 (mp0) REVERT: H 59 GLN cc_start: 0.8712 (tp40) cc_final: 0.8006 (tp40) REVERT: H 253 PHE cc_start: 0.7938 (t80) cc_final: 0.7677 (t80) REVERT: H 257 MET cc_start: 0.8803 (mmm) cc_final: 0.8420 (mmm) REVERT: H 278 ARG cc_start: 0.8705 (mmp-170) cc_final: 0.8391 (mmp80) REVERT: I 43 GLU cc_start: 0.8294 (tt0) cc_final: 0.7717 (tm-30) REVERT: I 59 GLN cc_start: 0.8854 (tp40) cc_final: 0.8262 (tp40) REVERT: I 230 GLU cc_start: 0.8373 (mp0) cc_final: 0.8143 (mm-30) REVERT: I 253 PHE cc_start: 0.8129 (t80) cc_final: 0.7923 (t80) REVERT: I 278 ARG cc_start: 0.8669 (mmp80) cc_final: 0.8446 (mmp80) REVERT: J 21 MET cc_start: 0.7983 (pmm) cc_final: 0.7782 (pmm) REVERT: J 59 GLN cc_start: 0.8741 (tp40) cc_final: 0.8406 (tp40) REVERT: J 278 ARG cc_start: 0.8710 (mmp-170) cc_final: 0.8406 (mmp80) REVERT: K 59 GLN cc_start: 0.8698 (tp40) cc_final: 0.7981 (tp40) REVERT: K 253 PHE cc_start: 0.7944 (t80) cc_final: 0.7684 (t80) REVERT: K 257 MET cc_start: 0.8810 (mmm) cc_final: 0.8412 (mmm) REVERT: K 278 ARG cc_start: 0.8685 (mmp-170) cc_final: 0.8382 (mmp80) REVERT: K 285 ARG cc_start: 0.7509 (mmm160) cc_final: 0.7237 (mmp-170) REVERT: L 43 GLU cc_start: 0.8311 (tt0) cc_final: 0.7722 (tm-30) REVERT: L 59 GLN cc_start: 0.8864 (tp40) cc_final: 0.8281 (tp40) REVERT: L 230 GLU cc_start: 0.8373 (mp0) cc_final: 0.8146 (mm-30) REVERT: L 253 PHE cc_start: 0.8190 (t80) cc_final: 0.7980 (t80) outliers start: 38 outliers final: 28 residues processed: 469 average time/residue: 1.5487 time to fit residues: 819.7942 Evaluate side-chains 408 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 380 time to evaluate : 2.276 ------------------------------------------------------------------------------- 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: 8.9990 chunk 163 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 268 ASN B 75 HIS ** 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 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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.138069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098515 restraints weight = 34058.593| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.96 r_work: 0.3200 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21060 Z= 0.127 Angle : 0.588 7.249 28548 Z= 0.291 Chirality : 0.038 0.154 3396 Planarity : 0.004 0.029 3144 Dihedral : 7.727 48.759 6732 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 1.85 % Allowed : 20.36 % Favored : 77.79 % 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: 4.06 (0.18), residues: 2196 helix: 3.62 (0.11), residues: 1680 sheet: 0.30 (0.38), residues: 204 loop : -1.48 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 277 HIS 0.002 0.001 HIS H 75 PHE 0.010 0.001 PHE E 33 TYR 0.021 0.002 TYR E 96 ARG 0.010 0.001 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 1416) hydrogen bonds : angle 2.98310 ( 4212) SS BOND : bond 0.00118 ( 36) SS BOND : angle 1.50832 ( 72) covalent geometry : bond 0.00289 (21024) covalent geometry : angle 0.58380 (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 457 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 420 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8020 (ptp90) cc_final: 0.7748 (ptt-90) REVERT: A 59 GLN cc_start: 0.8843 (tp40) cc_final: 0.8054 (tp40) REVERT: A 217 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8418 (tt0) REVERT: A 253 PHE cc_start: 0.8238 (t80) cc_final: 0.7883 (t80) REVERT: A 257 MET cc_start: 0.8817 (mmm) cc_final: 0.8413 (mmm) REVERT: A 278 ARG cc_start: 0.8679 (mmp-170) cc_final: 0.8377 (mmp80) REVERT: B 43 GLU cc_start: 0.8373 (tt0) cc_final: 0.7803 (tm-30) REVERT: B 230 GLU cc_start: 0.8491 (mp0) cc_final: 0.8247 (mm-30) REVERT: B 281 LYS cc_start: 0.9117 (tppt) cc_final: 0.8853 (mmmm) REVERT: C 21 MET cc_start: 0.7887 (pmm) cc_final: 0.7672 (pmm) REVERT: C 43 GLU cc_start: 0.8399 (tt0) cc_final: 0.8151 (tt0) REVERT: C 59 GLN cc_start: 0.8938 (tp40) cc_final: 0.8112 (tp40) REVERT: C 230 GLU cc_start: 0.8412 (mp0) cc_final: 0.8004 (pm20) REVERT: D 24 ARG cc_start: 0.7972 (ptt-90) cc_final: 0.7721 (ptt-90) REVERT: D 59 GLN cc_start: 0.8838 (tp40) cc_final: 0.8028 (tp40) REVERT: D 78 TYR cc_start: 0.8780 (t80) cc_final: 0.8580 (t80) REVERT: D 217 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8387 (tt0) REVERT: D 253 PHE cc_start: 0.8227 (t80) cc_final: 0.7875 (t80) REVERT: D 257 MET cc_start: 0.8812 (mmm) cc_final: 0.8414 (mmm) REVERT: D 278 ARG cc_start: 0.8707 (mmp-170) cc_final: 0.8415 (mmp80) REVERT: E 24 ARG cc_start: 0.8013 (ptt-90) cc_final: 0.7801 (ptt-90) REVERT: E 43 GLU cc_start: 0.8423 (tt0) cc_final: 0.7886 (tm-30) REVERT: E 217 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8323 (tt0) REVERT: E 230 GLU cc_start: 0.8477 (mp0) cc_final: 0.8266 (mm-30) REVERT: F 21 MET cc_start: 0.7908 (pmm) cc_final: 0.7686 (pmm) REVERT: F 59 GLN cc_start: 0.8957 (tp40) cc_final: 0.8129 (tp40) REVERT: F 230 GLU cc_start: 0.8428 (mp0) cc_final: 0.8015 (pm20) REVERT: F 285 ARG cc_start: 0.7718 (mmm160) cc_final: 0.7498 (mmp-170) REVERT: G 230 GLU cc_start: 0.8366 (mp0) cc_final: 0.7963 (pm20) REVERT: H 59 GLN cc_start: 0.8840 (tp40) cc_final: 0.8044 (tp40) REVERT: H 78 TYR cc_start: 0.8764 (t80) cc_final: 0.8552 (t80) REVERT: H 217 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8354 (tt0) REVERT: H 253 PHE cc_start: 0.8223 (t80) cc_final: 0.7893 (t80) REVERT: H 257 MET cc_start: 0.8804 (mmm) cc_final: 0.8413 (mmm) REVERT: H 278 ARG cc_start: 0.8706 (mmp-170) cc_final: 0.8432 (mmp80) REVERT: I 24 ARG cc_start: 0.8027 (ptt-90) cc_final: 0.7809 (ptt-90) REVERT: I 43 GLU cc_start: 0.8398 (tt0) cc_final: 0.7907 (tm-30) REVERT: I 59 GLN cc_start: 0.8980 (tp40) cc_final: 0.8295 (tp40) REVERT: I 230 GLU cc_start: 0.8494 (mp0) cc_final: 0.8280 (mm-30) REVERT: I 281 LYS cc_start: 0.9144 (tppt) cc_final: 0.8885 (mmmm) REVERT: J 59 GLN cc_start: 0.8910 (tp40) cc_final: 0.8457 (tp40) REVERT: J 230 GLU cc_start: 0.8399 (mp0) cc_final: 0.8046 (pm20) REVERT: J 278 ARG cc_start: 0.8726 (mmp-170) cc_final: 0.8459 (mmp80) REVERT: J 285 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7512 (mmp-170) REVERT: K 59 GLN cc_start: 0.8828 (tp40) cc_final: 0.8043 (tp40) REVERT: K 78 TYR cc_start: 0.8775 (t80) cc_final: 0.8562 (t80) REVERT: K 217 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8350 (tt0) REVERT: K 253 PHE cc_start: 0.8215 (t80) cc_final: 0.7866 (t80) REVERT: K 257 MET cc_start: 0.8821 (mmm) cc_final: 0.8379 (mmm) REVERT: K 278 ARG cc_start: 0.8724 (mmp-170) cc_final: 0.8489 (mmp80) REVERT: L 43 GLU cc_start: 0.8339 (tt0) cc_final: 0.7878 (tm-30) REVERT: L 59 GLN cc_start: 0.8985 (tp40) cc_final: 0.8307 (tp40) REVERT: L 217 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8291 (tt0) REVERT: L 230 GLU cc_start: 0.8483 (mp0) cc_final: 0.8258 (mm-30) REVERT: L 281 LYS cc_start: 0.9178 (tppt) cc_final: 0.8565 (mmmm) outliers start: 37 outliers final: 24 residues processed: 441 average time/residue: 1.6923 time to fit residues: 838.6890 Evaluate side-chains 412 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 388 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 272 LEU 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 37 ILE Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 92 CYS 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 282 LEU Chi-restraints excluded: chain J residue 92 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 142 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN A 268 ASN B 217 GLN D 207 ASN D 268 ASN H 207 ASN H 268 ASN I 82 GLN K 207 ASN K 268 ASN L 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.135675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096570 restraints weight = 34012.669| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.90 r_work: 0.3168 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21060 Z= 0.139 Angle : 0.642 14.457 28548 Z= 0.317 Chirality : 0.039 0.253 3396 Planarity : 0.004 0.033 3144 Dihedral : 7.242 49.102 6732 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.40 % Allowed : 22.11 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.95 (0.18), residues: 2196 helix: 3.59 (0.11), residues: 1680 sheet: -0.24 (0.37), residues: 204 loop : -1.38 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 277 HIS 0.002 0.001 HIS K 75 PHE 0.010 0.001 PHE I 33 TYR 0.026 0.002 TYR I 96 ARG 0.012 0.001 ARG I 285 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 1416) hydrogen bonds : angle 3.02743 ( 4212) SS BOND : bond 0.00649 ( 36) SS BOND : angle 1.99329 ( 72) covalent geometry : bond 0.00326 (21024) covalent geometry : angle 0.63493 (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 434 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 386 time to evaluate : 2.665 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8895 (tp40) cc_final: 0.8070 (tp40) REVERT: A 217 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8531 (tt0) REVERT: A 253 PHE cc_start: 0.8424 (t80) cc_final: 0.8078 (t80) REVERT: A 257 MET cc_start: 0.8822 (mmm) cc_final: 0.8376 (mmm) REVERT: A 278 ARG cc_start: 0.8751 (mmp-170) cc_final: 0.8529 (mmp80) REVERT: B 24 ARG cc_start: 0.8133 (ptp90) cc_final: 0.7739 (ptp90) REVERT: B 43 GLU cc_start: 0.8407 (tt0) cc_final: 0.7951 (tm-30) REVERT: B 48 ASP cc_start: 0.9033 (p0) cc_final: 0.8739 (p0) REVERT: B 230 GLU cc_start: 0.8579 (mp0) cc_final: 0.8355 (mm-30) REVERT: B 281 LYS cc_start: 0.9134 (tppt) cc_final: 0.8751 (mmmm) REVERT: C 48 ASP cc_start: 0.8980 (p0) cc_final: 0.8771 (p0) REVERT: C 59 GLN cc_start: 0.8988 (tp40) cc_final: 0.8120 (tp40) REVERT: C 239 GLU cc_start: 0.8333 (tt0) cc_final: 0.8109 (tt0) REVERT: D 59 GLN cc_start: 0.8849 (tp40) cc_final: 0.8049 (tp40) REVERT: D 217 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8416 (tt0) REVERT: D 253 PHE cc_start: 0.8415 (t80) cc_final: 0.8057 (t80) REVERT: D 257 MET cc_start: 0.8825 (mmm) cc_final: 0.8385 (mmm) REVERT: D 278 ARG cc_start: 0.8761 (mmp-170) cc_final: 0.8554 (mmp80) REVERT: E 24 ARG cc_start: 0.8026 (ptt-90) cc_final: 0.7807 (ptt-90) REVERT: E 43 GLU cc_start: 0.8543 (tt0) cc_final: 0.8028 (tm-30) REVERT: E 48 ASP cc_start: 0.9014 (p0) cc_final: 0.8667 (p0) REVERT: E 230 GLU cc_start: 0.8540 (mp0) cc_final: 0.8300 (mm-30) REVERT: F 59 GLN cc_start: 0.9011 (tp40) cc_final: 0.8124 (tp40) REVERT: F 210 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8738 (tp30) REVERT: F 230 GLU cc_start: 0.8450 (mp0) cc_final: 0.8029 (pm20) REVERT: G 230 GLU cc_start: 0.8435 (mp0) cc_final: 0.8051 (pm20) REVERT: H 59 GLN cc_start: 0.8876 (tp40) cc_final: 0.8057 (tp40) REVERT: H 217 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8394 (tt0) REVERT: H 253 PHE cc_start: 0.8402 (t80) cc_final: 0.8065 (t80) REVERT: H 257 MET cc_start: 0.8818 (mmm) cc_final: 0.8382 (mmm) REVERT: H 278 ARG cc_start: 0.8769 (mmp-170) cc_final: 0.8567 (mmp80) REVERT: I 24 ARG cc_start: 0.8046 (ptt-90) cc_final: 0.7807 (ptt-90) REVERT: I 43 GLU cc_start: 0.8546 (tt0) cc_final: 0.8031 (tm-30) REVERT: I 48 ASP cc_start: 0.8970 (p0) cc_final: 0.8639 (p0) REVERT: I 59 GLN cc_start: 0.8943 (tp40) cc_final: 0.8201 (tp40) REVERT: I 230 GLU cc_start: 0.8553 (mp0) cc_final: 0.8330 (mm-30) REVERT: I 281 LYS cc_start: 0.9178 (tppt) cc_final: 0.8718 (mmmm) REVERT: J 48 ASP cc_start: 0.8983 (p0) cc_final: 0.8759 (p0) REVERT: J 59 GLN cc_start: 0.8972 (tp40) cc_final: 0.8546 (tp40) REVERT: J 239 GLU cc_start: 0.8352 (tt0) cc_final: 0.7700 (tt0) REVERT: J 278 ARG cc_start: 0.8750 (mmp-170) cc_final: 0.8538 (mmp80) REVERT: K 59 GLN cc_start: 0.8826 (tp40) cc_final: 0.8027 (tp40) REVERT: K 217 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8380 (tt0) REVERT: K 253 PHE cc_start: 0.8404 (t80) cc_final: 0.8014 (t80) REVERT: K 257 MET cc_start: 0.8833 (mmm) cc_final: 0.8400 (mmm) REVERT: K 278 ARG cc_start: 0.8782 (mmp-170) cc_final: 0.8577 (mmp80) REVERT: L 24 ARG cc_start: 0.8004 (ptt-90) cc_final: 0.7786 (ptt-90) REVERT: L 43 GLU cc_start: 0.8489 (tt0) cc_final: 0.7985 (tm-30) REVERT: L 48 ASP cc_start: 0.8959 (p0) cc_final: 0.8604 (p0) REVERT: L 59 GLN cc_start: 0.8938 (tp40) cc_final: 0.8201 (tp40) REVERT: L 230 GLU cc_start: 0.8545 (mp0) cc_final: 0.8318 (mm-30) outliers start: 48 outliers final: 17 residues processed: 408 average time/residue: 2.0599 time to fit residues: 954.7325 Evaluate side-chains 384 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 367 time to evaluate : 3.571 ------------------------------------------------------------------------------- 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 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 91 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 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: 0.9980 chunk 159 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 40 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 138 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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** A 268 ASN B 217 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN E 217 GLN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 268 ASN I 82 GLN I 217 GLN K 207 ASN K 268 ASN L 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.137018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097759 restraints weight = 33960.941| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.94 r_work: 0.3196 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21060 Z= 0.122 Angle : 0.612 13.056 28548 Z= 0.301 Chirality : 0.038 0.171 3396 Planarity : 0.004 0.035 3144 Dihedral : 6.892 50.770 6732 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 2.25 % Allowed : 22.95 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.08 (0.18), residues: 2196 helix: 3.66 (0.11), residues: 1680 sheet: 0.57 (0.45), residues: 132 loop : -1.41 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 277 HIS 0.001 0.000 HIS I 274 PHE 0.009 0.001 PHE F 81 TYR 0.019 0.001 TYR I 96 ARG 0.009 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 1416) hydrogen bonds : angle 2.93840 ( 4212) SS BOND : bond 0.00473 ( 36) SS BOND : angle 1.67605 ( 72) covalent geometry : bond 0.00275 (21024) covalent geometry : angle 0.60737 (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 457 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 412 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.9023 (p0) cc_final: 0.8788 (p0) REVERT: A 59 GLN cc_start: 0.8874 (tp40) cc_final: 0.8063 (tp40) REVERT: A 210 GLU cc_start: 0.9068 (tp30) cc_final: 0.8808 (mm-30) REVERT: A 217 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8408 (tt0) REVERT: A 230 GLU cc_start: 0.8232 (mp0) cc_final: 0.7950 (mt-10) REVERT: A 253 PHE cc_start: 0.8371 (t80) cc_final: 0.7968 (t80) REVERT: A 257 MET cc_start: 0.8790 (mmm) cc_final: 0.8341 (mmm) REVERT: B 20 THR cc_start: 0.7382 (p) cc_final: 0.6995 (p) REVERT: B 43 GLU cc_start: 0.8572 (tt0) cc_final: 0.8070 (tm-30) REVERT: B 48 ASP cc_start: 0.9052 (p0) cc_final: 0.8696 (p0) REVERT: B 230 GLU cc_start: 0.8501 (mp0) cc_final: 0.8204 (mm-30) REVERT: B 239 GLU cc_start: 0.8439 (tt0) cc_final: 0.8213 (tt0) REVERT: B 281 LYS cc_start: 0.9116 (tppt) cc_final: 0.8741 (mmmm) REVERT: C 48 ASP cc_start: 0.9010 (p0) cc_final: 0.8661 (p0) REVERT: C 59 GLN cc_start: 0.8990 (tp40) cc_final: 0.8138 (tp40) REVERT: C 230 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7727 (mm-30) REVERT: C 239 GLU cc_start: 0.8110 (tt0) cc_final: 0.7601 (tt0) REVERT: D 48 ASP cc_start: 0.9029 (p0) cc_final: 0.8803 (p0) REVERT: D 59 GLN cc_start: 0.8897 (tp40) cc_final: 0.8018 (tp40) REVERT: D 210 GLU cc_start: 0.9079 (tp30) cc_final: 0.8778 (mm-30) REVERT: D 217 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8422 (tt0) REVERT: D 253 PHE cc_start: 0.8381 (t80) cc_final: 0.7984 (t80) REVERT: D 257 MET cc_start: 0.8793 (mmm) cc_final: 0.8346 (mmm) REVERT: E 24 ARG cc_start: 0.8070 (ptt-90) cc_final: 0.7843 (ptt-90) REVERT: E 43 GLU cc_start: 0.8577 (tt0) cc_final: 0.8043 (tm-30) REVERT: E 48 ASP cc_start: 0.9013 (p0) cc_final: 0.8705 (p0) REVERT: E 52 MET cc_start: 0.9229 (mmt) cc_final: 0.9012 (mmp) REVERT: E 230 GLU cc_start: 0.8501 (mp0) cc_final: 0.8206 (mm-30) REVERT: F 48 ASP cc_start: 0.8864 (p0) cc_final: 0.8525 (p0) REVERT: F 59 GLN cc_start: 0.9000 (tp40) cc_final: 0.8137 (tp40) REVERT: F 230 GLU cc_start: 0.8420 (mp0) cc_final: 0.8003 (pm20) REVERT: F 239 GLU cc_start: 0.8332 (tt0) cc_final: 0.8129 (tt0) REVERT: G 48 ASP cc_start: 0.8822 (p0) cc_final: 0.8534 (p0) REVERT: G 210 GLU cc_start: 0.9010 (tp30) cc_final: 0.8580 (tp30) REVERT: G 230 GLU cc_start: 0.8362 (mp0) cc_final: 0.7938 (pm20) REVERT: H 48 ASP cc_start: 0.9014 (p0) cc_final: 0.8786 (p0) REVERT: H 59 GLN cc_start: 0.8860 (tp40) cc_final: 0.8059 (tp40) REVERT: H 68 ASP cc_start: 0.8349 (t70) cc_final: 0.8101 (t0) REVERT: H 210 GLU cc_start: 0.9044 (tp30) cc_final: 0.8788 (mm-30) REVERT: H 217 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8462 (tt0) REVERT: H 253 PHE cc_start: 0.8323 (t80) cc_final: 0.7936 (t80) REVERT: H 257 MET cc_start: 0.8764 (mmm) cc_final: 0.8321 (mmm) REVERT: I 24 ARG cc_start: 0.8029 (ptt-90) cc_final: 0.7771 (ptt-90) REVERT: I 43 GLU cc_start: 0.8615 (tt0) cc_final: 0.8067 (tm-30) REVERT: I 48 ASP cc_start: 0.8997 (p0) cc_final: 0.8686 (p0) REVERT: I 52 MET cc_start: 0.9223 (mmt) cc_final: 0.9020 (mmp) REVERT: I 59 GLN cc_start: 0.8860 (tp40) cc_final: 0.8126 (tp40) REVERT: I 230 GLU cc_start: 0.8498 (mp0) cc_final: 0.8204 (mm-30) REVERT: I 281 LYS cc_start: 0.9115 (tppt) cc_final: 0.8742 (mmmm) REVERT: J 48 ASP cc_start: 0.8967 (p0) cc_final: 0.8628 (p0) REVERT: J 59 GLN cc_start: 0.8939 (tp40) cc_final: 0.8611 (tp40) REVERT: J 230 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7925 (mt-10) REVERT: K 24 ARG cc_start: 0.7905 (ptt-90) cc_final: 0.7663 (ptt-90) REVERT: K 48 ASP cc_start: 0.9026 (p0) cc_final: 0.8807 (p0) REVERT: K 59 GLN cc_start: 0.8905 (tp40) cc_final: 0.8037 (tp40) REVERT: K 210 GLU cc_start: 0.9080 (tp30) cc_final: 0.8829 (mm-30) REVERT: K 217 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8453 (tt0) REVERT: K 253 PHE cc_start: 0.8364 (t80) cc_final: 0.7968 (t80) REVERT: K 257 MET cc_start: 0.8799 (mmm) cc_final: 0.8355 (mmm) REVERT: L 24 ARG cc_start: 0.7957 (ptt-90) cc_final: 0.7734 (ptt-90) REVERT: L 43 GLU cc_start: 0.8558 (tt0) cc_final: 0.8049 (tm-30) REVERT: L 48 ASP cc_start: 0.8980 (p0) cc_final: 0.8658 (p0) REVERT: L 52 MET cc_start: 0.9228 (mmt) cc_final: 0.9011 (mmp) REVERT: L 59 GLN cc_start: 0.8846 (tp40) cc_final: 0.8128 (tp40) REVERT: L 230 GLU cc_start: 0.8487 (mp0) cc_final: 0.8195 (mm-30) outliers start: 45 outliers final: 20 residues processed: 444 average time/residue: 1.4704 time to fit residues: 737.0517 Evaluate side-chains 386 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 365 time to evaluate : 2.963 ------------------------------------------------------------------------------- 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 230 GLU Chi-restraints excluded: chain C residue 272 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 272 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: 0.8980 chunk 206 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 46 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** A 268 ASN B 217 GLN B 268 ASN D 268 ASN E 217 GLN E 268 ASN H 268 ASN I 82 GLN I 217 GLN I 268 ASN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 ASN L 82 GLN L 217 GLN L 268 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.136235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.097339 restraints weight = 34024.258| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.90 r_work: 0.3186 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21060 Z= 0.134 Angle : 0.658 14.556 28548 Z= 0.324 Chirality : 0.039 0.266 3396 Planarity : 0.003 0.031 3144 Dihedral : 6.763 51.815 6732 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.54 % Allowed : 24.25 % Favored : 73.20 % 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: 4.08 (0.18), residues: 2196 helix: 3.66 (0.11), residues: 1680 sheet: 1.45 (0.43), residues: 120 loop : -1.66 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 277 HIS 0.002 0.000 HIS K 75 PHE 0.014 0.001 PHE D 81 TYR 0.016 0.001 TYR L 96 ARG 0.009 0.001 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 1416) hydrogen bonds : angle 2.98428 ( 4212) SS BOND : bond 0.00986 ( 36) SS BOND : angle 2.18114 ( 72) covalent geometry : bond 0.00316 (21024) covalent geometry : angle 0.64944 (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 455 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 404 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.9021 (p0) cc_final: 0.8731 (p0) REVERT: A 59 GLN cc_start: 0.8911 (tp40) cc_final: 0.8559 (tp40) REVERT: A 210 GLU cc_start: 0.9069 (tp30) cc_final: 0.8752 (mm-30) REVERT: A 253 PHE cc_start: 0.8391 (t80) cc_final: 0.7953 (t80) REVERT: A 257 MET cc_start: 0.8781 (mmm) cc_final: 0.8332 (mmm) REVERT: B 43 GLU cc_start: 0.8555 (tt0) cc_final: 0.8081 (tm-30) REVERT: B 48 ASP cc_start: 0.9014 (p0) cc_final: 0.8749 (p0) REVERT: B 54 VAL cc_start: 0.8980 (t) cc_final: 0.8768 (m) REVERT: B 281 LYS cc_start: 0.9127 (tppt) cc_final: 0.8752 (mmmm) REVERT: C 48 ASP cc_start: 0.8983 (p0) cc_final: 0.8725 (p0) REVERT: C 59 GLN cc_start: 0.8947 (tp40) cc_final: 0.8134 (tp40) REVERT: C 230 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7808 (mm-30) REVERT: C 239 GLU cc_start: 0.8205 (tt0) cc_final: 0.7709 (tt0) REVERT: D 48 ASP cc_start: 0.9062 (p0) cc_final: 0.8777 (p0) REVERT: D 59 GLN cc_start: 0.8962 (tp40) cc_final: 0.8517 (tp40) REVERT: D 210 GLU cc_start: 0.9070 (tp30) cc_final: 0.8758 (mm-30) REVERT: D 253 PHE cc_start: 0.8362 (t80) cc_final: 0.7960 (t80) REVERT: D 257 MET cc_start: 0.8777 (mmm) cc_final: 0.8345 (mmm) REVERT: E 24 ARG cc_start: 0.8101 (ptt-90) cc_final: 0.7861 (ptt-90) REVERT: E 43 GLU cc_start: 0.8616 (tt0) cc_final: 0.8080 (tm-30) REVERT: E 48 ASP cc_start: 0.9016 (p0) cc_final: 0.8701 (p0) REVERT: E 54 VAL cc_start: 0.8965 (t) cc_final: 0.8745 (m) REVERT: E 230 GLU cc_start: 0.8450 (mp0) cc_final: 0.8247 (mp0) REVERT: F 48 ASP cc_start: 0.8869 (p0) cc_final: 0.8526 (p0) REVERT: F 59 GLN cc_start: 0.8967 (tp40) cc_final: 0.8152 (tp40) REVERT: F 230 GLU cc_start: 0.8440 (mp0) cc_final: 0.8003 (pm20) REVERT: G 48 ASP cc_start: 0.8856 (p0) cc_final: 0.8510 (p0) REVERT: G 59 GLN cc_start: 0.8921 (tp40) cc_final: 0.8467 (tp40) REVERT: G 210 GLU cc_start: 0.9031 (tp30) cc_final: 0.8633 (tp30) REVERT: G 230 GLU cc_start: 0.8390 (mp0) cc_final: 0.7952 (pm20) REVERT: H 48 ASP cc_start: 0.9004 (p0) cc_final: 0.8723 (p0) REVERT: H 210 GLU cc_start: 0.9053 (tp30) cc_final: 0.8785 (mm-30) REVERT: H 253 PHE cc_start: 0.8337 (t80) cc_final: 0.7915 (t80) REVERT: H 257 MET cc_start: 0.8760 (mmm) cc_final: 0.8318 (mmm) REVERT: I 43 GLU cc_start: 0.8646 (tt0) cc_final: 0.8162 (tm-30) REVERT: I 48 ASP cc_start: 0.9009 (p0) cc_final: 0.8679 (p0) REVERT: I 54 VAL cc_start: 0.8982 (t) cc_final: 0.8761 (m) REVERT: I 59 GLN cc_start: 0.8837 (tp40) cc_final: 0.8205 (tp40) REVERT: I 198 PHE cc_start: 0.7369 (t80) cc_final: 0.7048 (t80) REVERT: I 230 GLU cc_start: 0.8480 (mp0) cc_final: 0.8253 (mm-30) REVERT: I 281 LYS cc_start: 0.9126 (tppt) cc_final: 0.8752 (mmmm) REVERT: J 48 ASP cc_start: 0.9016 (p0) cc_final: 0.8718 (p0) REVERT: J 59 GLN cc_start: 0.8878 (tp40) cc_final: 0.8589 (tp40) REVERT: J 230 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8097 (mm-30) REVERT: K 48 ASP cc_start: 0.9066 (p0) cc_final: 0.8796 (p0) REVERT: K 210 GLU cc_start: 0.9082 (tp30) cc_final: 0.8776 (mm-30) REVERT: K 217 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8422 (tt0) REVERT: K 253 PHE cc_start: 0.8352 (t80) cc_final: 0.7948 (t80) REVERT: K 257 MET cc_start: 0.8785 (mmm) cc_final: 0.8362 (mmm) REVERT: L 24 ARG cc_start: 0.7944 (ptt-90) cc_final: 0.7723 (ptt-90) REVERT: L 43 GLU cc_start: 0.8532 (tt0) cc_final: 0.8066 (tm-30) REVERT: L 48 ASP cc_start: 0.8987 (p0) cc_final: 0.8651 (p0) REVERT: L 54 VAL cc_start: 0.8966 (t) cc_final: 0.8745 (m) REVERT: L 59 GLN cc_start: 0.8839 (tp40) cc_final: 0.8174 (tp40) REVERT: L 230 GLU cc_start: 0.8470 (mp0) cc_final: 0.8242 (mm-30) outliers start: 51 outliers final: 18 residues processed: 441 average time/residue: 1.6356 time to fit residues: 815.5555 Evaluate side-chains 398 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 380 time to evaluate : 2.116 ------------------------------------------------------------------------------- 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 282 LEU Chi-restraints excluded: chain C residue 91 LEU 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 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 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 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 52 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 210 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 214 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 chunk 207 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 268 ASN B 217 GLN B 268 ASN D 268 ASN E 217 GLN E 268 ASN H 56 ASN H 268 ASN I 82 GLN I 217 GLN I 268 ASN J 56 ASN K 268 ASN L 82 GLN L 217 GLN L 268 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.136418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097862 restraints weight = 33658.086| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.88 r_work: 0.3192 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21060 Z= 0.131 Angle : 0.682 15.987 28548 Z= 0.330 Chirality : 0.038 0.219 3396 Planarity : 0.004 0.056 3144 Dihedral : 6.665 52.406 6732 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.00 % Allowed : 27.40 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.18), residues: 2196 helix: 3.63 (0.12), residues: 1680 sheet: 1.33 (0.42), residues: 120 loop : -1.56 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 277 HIS 0.002 0.000 HIS A 274 PHE 0.018 0.001 PHE J 81 TYR 0.014 0.001 TYR L 96 ARG 0.011 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 1416) hydrogen bonds : angle 3.03884 ( 4212) SS BOND : bond 0.00695 ( 36) SS BOND : angle 1.84632 ( 72) covalent geometry : bond 0.00307 (21024) covalent geometry : angle 0.67666 (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 443 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 403 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.9089 (p0) cc_final: 0.8801 (p0) REVERT: A 59 GLN cc_start: 0.8927 (tp40) cc_final: 0.8543 (tp40) REVERT: A 210 GLU cc_start: 0.9068 (tp30) cc_final: 0.8745 (mm-30) REVERT: A 241 GLU cc_start: 0.8427 (tt0) cc_final: 0.7975 (tt0) REVERT: A 253 PHE cc_start: 0.8406 (t80) cc_final: 0.7981 (t80) REVERT: A 257 MET cc_start: 0.8810 (mmm) cc_final: 0.8346 (mmm) REVERT: B 24 ARG cc_start: 0.8223 (ptt-90) cc_final: 0.7905 (pmt170) REVERT: B 43 GLU cc_start: 0.8521 (tt0) cc_final: 0.8062 (tm-30) REVERT: B 48 ASP cc_start: 0.9065 (p0) cc_final: 0.8785 (p0) REVERT: B 198 PHE cc_start: 0.7381 (t80) cc_final: 0.7051 (t80) REVERT: B 281 LYS cc_start: 0.9126 (tppt) cc_final: 0.8763 (mmmm) REVERT: C 48 ASP cc_start: 0.9042 (p0) cc_final: 0.8767 (p0) REVERT: C 59 GLN cc_start: 0.8985 (tp40) cc_final: 0.8111 (tp40) REVERT: C 230 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7929 (mm-30) REVERT: C 239 GLU cc_start: 0.8047 (tt0) cc_final: 0.7735 (tt0) REVERT: D 48 ASP cc_start: 0.9091 (p0) cc_final: 0.8813 (p0) REVERT: D 59 GLN cc_start: 0.8955 (tp40) cc_final: 0.8502 (tp40) REVERT: D 210 GLU cc_start: 0.9084 (tp30) cc_final: 0.8778 (mm-30) REVERT: D 241 GLU cc_start: 0.8288 (tt0) cc_final: 0.7844 (tt0) REVERT: D 253 PHE cc_start: 0.8383 (t80) cc_final: 0.7961 (t80) REVERT: D 257 MET cc_start: 0.8799 (mmm) cc_final: 0.8337 (mmm) REVERT: E 24 ARG cc_start: 0.8124 (ptt-90) cc_final: 0.7890 (ptt-90) REVERT: E 43 GLU cc_start: 0.8655 (tt0) cc_final: 0.8089 (tm-30) REVERT: E 48 ASP cc_start: 0.9039 (p0) cc_final: 0.8750 (p0) REVERT: E 54 VAL cc_start: 0.8966 (t) cc_final: 0.8759 (m) REVERT: F 48 ASP cc_start: 0.8965 (p0) cc_final: 0.8608 (p0) REVERT: F 59 GLN cc_start: 0.8983 (tp40) cc_final: 0.8134 (tp40) REVERT: F 230 GLU cc_start: 0.8428 (mp0) cc_final: 0.7965 (pm20) REVERT: G 24 ARG cc_start: 0.7937 (ptt-90) cc_final: 0.7729 (pmt170) REVERT: G 48 ASP cc_start: 0.8901 (p0) cc_final: 0.8547 (p0) REVERT: G 59 GLN cc_start: 0.8965 (tp40) cc_final: 0.8471 (tp40) REVERT: G 210 GLU cc_start: 0.9048 (tp30) cc_final: 0.8647 (tp30) REVERT: G 230 GLU cc_start: 0.8375 (mp0) cc_final: 0.7938 (pm20) REVERT: H 48 ASP cc_start: 0.9084 (p0) cc_final: 0.8797 (p0) REVERT: H 241 GLU cc_start: 0.8293 (tt0) cc_final: 0.7835 (tt0) REVERT: H 253 PHE cc_start: 0.8364 (t80) cc_final: 0.7953 (t80) REVERT: H 257 MET cc_start: 0.8786 (mmm) cc_final: 0.8328 (mmm) REVERT: I 48 ASP cc_start: 0.9004 (p0) cc_final: 0.8749 (p0) REVERT: I 54 VAL cc_start: 0.8948 (t) cc_final: 0.8730 (m) REVERT: I 59 GLN cc_start: 0.8948 (tp40) cc_final: 0.8188 (tp40) REVERT: I 198 PHE cc_start: 0.7402 (t80) cc_final: 0.7083 (t80) REVERT: I 281 LYS cc_start: 0.9138 (tppt) cc_final: 0.8763 (mmmm) REVERT: J 48 ASP cc_start: 0.8980 (p0) cc_final: 0.8668 (p0) REVERT: J 59 GLN cc_start: 0.8918 (tp40) cc_final: 0.8589 (tp40) REVERT: J 230 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8017 (mm-30) REVERT: J 239 GLU cc_start: 0.8165 (tt0) cc_final: 0.7831 (tt0) REVERT: K 48 ASP cc_start: 0.9081 (p0) cc_final: 0.8802 (p0) REVERT: K 210 GLU cc_start: 0.9073 (tp30) cc_final: 0.8763 (mm-30) REVERT: K 217 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8395 (tt0) REVERT: K 241 GLU cc_start: 0.8399 (tt0) cc_final: 0.7959 (tt0) REVERT: K 253 PHE cc_start: 0.8368 (t80) cc_final: 0.7947 (t80) REVERT: K 257 MET cc_start: 0.8779 (mmm) cc_final: 0.8351 (mmm) REVERT: L 43 GLU cc_start: 0.8599 (tt0) cc_final: 0.8119 (tm-30) REVERT: L 48 ASP cc_start: 0.9019 (p0) cc_final: 0.8674 (p0) REVERT: L 54 VAL cc_start: 0.8931 (t) cc_final: 0.8715 (m) REVERT: L 59 GLN cc_start: 0.8949 (tp40) cc_final: 0.8145 (tp40) outliers start: 40 outliers final: 12 residues processed: 431 average time/residue: 1.3106 time to fit residues: 637.4780 Evaluate side-chains 396 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 384 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain K residue 282 LEU 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: 4.9990 chunk 127 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 217 GLN B 268 ASN C 56 ASN D 268 ASN E 217 GLN E 268 ASN H 268 ASN I 82 GLN I 217 GLN I 268 ASN J 56 ASN K 268 ASN L 82 GLN L 217 GLN L 268 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.135993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097394 restraints weight = 33921.305| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.90 r_work: 0.3194 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.5178 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= 0.132 Angle : 0.679 14.828 28548 Z= 0.331 Chirality : 0.038 0.188 3396 Planarity : 0.004 0.040 3144 Dihedral : 6.584 52.976 6732 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.70 % Allowed : 28.49 % Favored : 69.81 % 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: 3.63 (0.12), residues: 1680 sheet: 1.21 (0.41), residues: 120 loop : -1.58 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 277 HIS 0.001 0.000 HIS D 75 PHE 0.019 0.001 PHE C 81 TYR 0.013 0.001 TYR J 199 ARG 0.011 0.001 ARG J 278 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 1416) hydrogen bonds : angle 3.06606 ( 4212) SS BOND : bond 0.00631 ( 36) SS BOND : angle 1.70300 ( 72) covalent geometry : bond 0.00309 (21024) covalent geometry : angle 0.67469 (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 434 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 400 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.9127 (p0) cc_final: 0.8811 (p0) REVERT: A 59 GLN cc_start: 0.8927 (tp40) cc_final: 0.8555 (tp40) REVERT: A 210 GLU cc_start: 0.9079 (tp30) cc_final: 0.8758 (mm-30) REVERT: A 241 GLU cc_start: 0.8286 (tt0) cc_final: 0.7946 (tt0) REVERT: A 253 PHE cc_start: 0.8448 (t80) cc_final: 0.8040 (t80) REVERT: A 257 MET cc_start: 0.8829 (mmm) cc_final: 0.8383 (mmm) REVERT: B 43 GLU cc_start: 0.8563 (tt0) cc_final: 0.8117 (tm-30) REVERT: B 48 ASP cc_start: 0.9084 (p0) cc_final: 0.8800 (p0) REVERT: B 59 GLN cc_start: 0.8928 (tp40) cc_final: 0.7963 (tp40) REVERT: B 198 PHE cc_start: 0.7442 (t80) cc_final: 0.7145 (t80) REVERT: B 281 LYS cc_start: 0.9158 (tppt) cc_final: 0.8792 (mmmm) REVERT: C 48 ASP cc_start: 0.9105 (p0) cc_final: 0.8821 (p0) REVERT: C 59 GLN cc_start: 0.9027 (tp40) cc_final: 0.8044 (tp40) REVERT: C 230 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7766 (mm-30) REVERT: C 239 GLU cc_start: 0.8089 (tt0) cc_final: 0.7615 (tt0) REVERT: D 48 ASP cc_start: 0.9126 (p0) cc_final: 0.8819 (p0) REVERT: D 59 GLN cc_start: 0.8970 (tp40) cc_final: 0.8470 (tp40) REVERT: D 241 GLU cc_start: 0.8311 (tt0) cc_final: 0.7962 (tt0) REVERT: D 253 PHE cc_start: 0.8416 (t80) cc_final: 0.8002 (t80) REVERT: D 257 MET cc_start: 0.8815 (mmm) cc_final: 0.8367 (mmm) REVERT: E 24 ARG cc_start: 0.8094 (ptt-90) cc_final: 0.7866 (ptt-90) REVERT: E 43 GLU cc_start: 0.8653 (tt0) cc_final: 0.8100 (tm-30) REVERT: E 48 ASP cc_start: 0.9089 (p0) cc_final: 0.8779 (p0) REVERT: E 59 GLN cc_start: 0.8926 (tp40) cc_final: 0.7925 (tp40) REVERT: F 24 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7929 (pmt170) REVERT: F 48 ASP cc_start: 0.9006 (p0) cc_final: 0.8643 (p0) REVERT: F 59 GLN cc_start: 0.9054 (tp40) cc_final: 0.8070 (tp40) REVERT: F 230 GLU cc_start: 0.8466 (mp0) cc_final: 0.8006 (pm20) REVERT: G 48 ASP cc_start: 0.8954 (p0) cc_final: 0.8597 (p0) REVERT: G 59 GLN cc_start: 0.9043 (tp40) cc_final: 0.8229 (tp40) REVERT: G 210 GLU cc_start: 0.9068 (tp30) cc_final: 0.8665 (tp30) REVERT: G 230 GLU cc_start: 0.8384 (mp0) cc_final: 0.8155 (mm-30) REVERT: H 48 ASP cc_start: 0.9125 (p0) cc_final: 0.8820 (p0) REVERT: H 68 ASP cc_start: 0.8356 (t70) cc_final: 0.8145 (t0) REVERT: H 210 GLU cc_start: 0.9089 (tp30) cc_final: 0.8748 (mm-30) REVERT: H 241 GLU cc_start: 0.8322 (tt0) cc_final: 0.7974 (tt0) REVERT: H 253 PHE cc_start: 0.8417 (t80) cc_final: 0.8019 (t80) REVERT: H 257 MET cc_start: 0.8809 (mmm) cc_final: 0.8369 (mmm) REVERT: I 48 ASP cc_start: 0.9034 (p0) cc_final: 0.8780 (p0) REVERT: I 59 GLN cc_start: 0.8957 (tp40) cc_final: 0.8165 (tp40) REVERT: I 198 PHE cc_start: 0.7434 (t80) cc_final: 0.7120 (t80) REVERT: I 281 LYS cc_start: 0.9148 (tppt) cc_final: 0.8784 (mmmm) REVERT: J 24 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7905 (pmt170) REVERT: J 48 ASP cc_start: 0.9090 (p0) cc_final: 0.8753 (p0) REVERT: J 59 GLN cc_start: 0.8956 (tp40) cc_final: 0.8272 (tp40) REVERT: J 97 SER cc_start: 0.8693 (m) cc_final: 0.8295 (p) REVERT: J 230 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7829 (mt-10) REVERT: J 239 GLU cc_start: 0.8185 (tt0) cc_final: 0.7391 (tt0) REVERT: K 210 GLU cc_start: 0.9080 (tp30) cc_final: 0.8771 (mm-30) REVERT: K 217 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8410 (tt0) REVERT: K 241 GLU cc_start: 0.8331 (tt0) cc_final: 0.7959 (tt0) REVERT: K 253 PHE cc_start: 0.8416 (t80) cc_final: 0.8007 (t80) REVERT: K 257 MET cc_start: 0.8809 (mmm) cc_final: 0.8398 (mmm) REVERT: L 24 ARG cc_start: 0.7990 (ptt-90) cc_final: 0.7722 (ptt-90) REVERT: L 43 GLU cc_start: 0.8607 (tt0) cc_final: 0.8155 (tm-30) REVERT: L 48 ASP cc_start: 0.9029 (p0) cc_final: 0.8756 (p0) REVERT: L 59 GLN cc_start: 0.8955 (tp40) cc_final: 0.8125 (tp40) REVERT: L 68 ASP cc_start: 0.8680 (t70) cc_final: 0.8433 (t0) outliers start: 34 outliers final: 17 residues processed: 429 average time/residue: 1.2864 time to fit residues: 623.6969 Evaluate side-chains 402 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 383 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 282 LEU Chi-restraints excluded: chain D residue 282 LEU 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 G residue 91 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 24 ARG 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 282 LEU 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: 6.9990 chunk 39 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 138 optimal weight: 0.0370 chunk 181 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 217 GLN B 268 ASN C 56 ASN D 268 ASN E 217 GLN E 268 ASN H 268 ASN I 82 GLN I 217 GLN I 268 ASN J 56 ASN K 268 ASN L 82 GLN L 217 GLN L 268 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.136454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098138 restraints weight = 33791.540| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.88 r_work: 0.3197 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.5268 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= 0.131 Angle : 0.696 17.320 28548 Z= 0.337 Chirality : 0.038 0.166 3396 Planarity : 0.004 0.053 3144 Dihedral : 6.484 53.323 6732 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 1.50 % Allowed : 29.19 % Favored : 69.31 % 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: 3.89 (0.18), residues: 2196 helix: 3.56 (0.12), residues: 1692 sheet: 1.09 (0.42), residues: 120 loop : -1.98 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 277 HIS 0.002 0.000 HIS L 274 PHE 0.019 0.001 PHE C 81 TYR 0.014 0.001 TYR C 199 ARG 0.014 0.001 ARG C 278 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 1416) hydrogen bonds : angle 3.06713 ( 4212) SS BOND : bond 0.00637 ( 36) SS BOND : angle 1.54017 ( 72) covalent geometry : bond 0.00305 (21024) covalent geometry : angle 0.69265 (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 444 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 414 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8899 (tp40) cc_final: 0.8515 (tp40) REVERT: A 241 GLU cc_start: 0.8203 (tt0) cc_final: 0.8000 (tt0) REVERT: A 253 PHE cc_start: 0.8421 (t80) cc_final: 0.8007 (t80) REVERT: A 257 MET cc_start: 0.8835 (mmm) cc_final: 0.8383 (mmm) REVERT: B 43 GLU cc_start: 0.8614 (tt0) cc_final: 0.8156 (tm-30) REVERT: B 48 ASP cc_start: 0.9084 (p0) cc_final: 0.8848 (p0) REVERT: B 198 PHE cc_start: 0.7415 (t80) cc_final: 0.7098 (t80) REVERT: C 48 ASP cc_start: 0.9084 (p0) cc_final: 0.8741 (p0) REVERT: C 59 GLN cc_start: 0.8928 (tp40) cc_final: 0.8008 (tp40) REVERT: C 97 SER cc_start: 0.8645 (m) cc_final: 0.8206 (p) REVERT: C 230 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7492 (mm-30) REVERT: C 239 GLU cc_start: 0.8205 (tt0) cc_final: 0.7548 (tt0) REVERT: D 59 GLN cc_start: 0.8876 (tp40) cc_final: 0.8503 (tp40) REVERT: D 253 PHE cc_start: 0.8383 (t80) cc_final: 0.7964 (t80) REVERT: D 257 MET cc_start: 0.8819 (mmm) cc_final: 0.8361 (mmm) REVERT: E 43 GLU cc_start: 0.8627 (tt0) cc_final: 0.8078 (tm-30) REVERT: E 48 ASP cc_start: 0.9067 (p0) cc_final: 0.8824 (p0) REVERT: E 198 PHE cc_start: 0.7444 (t80) cc_final: 0.7122 (t80) REVERT: F 48 ASP cc_start: 0.9089 (p0) cc_final: 0.8739 (p0) REVERT: F 59 GLN cc_start: 0.8992 (tp40) cc_final: 0.8077 (tp40) REVERT: F 97 SER cc_start: 0.8642 (m) cc_final: 0.8211 (p) REVERT: F 230 GLU cc_start: 0.8473 (mp0) cc_final: 0.8021 (pm20) REVERT: G 48 ASP cc_start: 0.8975 (p0) cc_final: 0.8619 (p0) REVERT: G 210 GLU cc_start: 0.9058 (tp30) cc_final: 0.8647 (tp30) REVERT: G 230 GLU cc_start: 0.8284 (mp0) cc_final: 0.7860 (pm20) REVERT: H 241 GLU cc_start: 0.8277 (tt0) cc_final: 0.8056 (tt0) REVERT: H 253 PHE cc_start: 0.8388 (t80) cc_final: 0.7983 (t80) REVERT: H 257 MET cc_start: 0.8812 (mmm) cc_final: 0.8367 (mmm) REVERT: I 48 ASP cc_start: 0.9043 (p0) cc_final: 0.8801 (p0) REVERT: I 59 GLN cc_start: 0.8955 (tp40) cc_final: 0.8170 (tp40) REVERT: I 198 PHE cc_start: 0.7373 (t80) cc_final: 0.7070 (t80) REVERT: J 24 ARG cc_start: 0.7996 (pmt170) cc_final: 0.7672 (pmt170) REVERT: J 48 ASP cc_start: 0.9113 (p0) cc_final: 0.8743 (p0) REVERT: J 59 GLN cc_start: 0.8868 (tp40) cc_final: 0.8550 (tp40) REVERT: J 97 SER cc_start: 0.8679 (m) cc_final: 0.8278 (p) REVERT: J 230 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7855 (mt-10) REVERT: K 48 ASP cc_start: 0.9065 (p0) cc_final: 0.8804 (p0) REVERT: K 217 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8409 (tt0) REVERT: K 241 GLU cc_start: 0.8262 (tt0) cc_final: 0.8049 (tt0) REVERT: K 253 PHE cc_start: 0.8384 (t80) cc_final: 0.7968 (t80) REVERT: K 257 MET cc_start: 0.8808 (mmm) cc_final: 0.8391 (mmm) REVERT: L 43 GLU cc_start: 0.8603 (tt0) cc_final: 0.8156 (tm-30) REVERT: L 48 ASP cc_start: 0.9068 (p0) cc_final: 0.8807 (p0) REVERT: L 59 GLN cc_start: 0.8950 (tp40) cc_final: 0.8118 (tp40) REVERT: L 68 ASP cc_start: 0.8720 (t70) cc_final: 0.8488 (t0) outliers start: 30 outliers final: 14 residues processed: 439 average time/residue: 1.2966 time to fit residues: 643.5645 Evaluate side-chains 402 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 388 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 282 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 G residue 91 LEU 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 K residue 282 LEU Chi-restraints excluded: chain L residue 282 LEU 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: 0.6980 chunk 116 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 104 GLN B 217 GLN B 268 ASN C 56 ASN D 104 GLN D 268 ASN E 56 ASN E 104 GLN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN E 268 ASN H 104 GLN H 268 ASN I 104 GLN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 217 GLN I 268 ASN J 56 ASN K 268 ASN L 56 ASN L 104 GLN L 217 GLN L 268 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.131896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.092630 restraints weight = 34358.146| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.88 r_work: 0.3097 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21060 Z= 0.166 Angle : 0.749 15.790 28548 Z= 0.367 Chirality : 0.040 0.192 3396 Planarity : 0.005 0.070 3144 Dihedral : 6.757 55.465 6732 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.30 % Allowed : 29.99 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.80 (0.18), residues: 2196 helix: 3.46 (0.12), residues: 1692 sheet: 0.13 (0.39), residues: 144 loop : -1.60 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 277 HIS 0.003 0.001 HIS A 75 PHE 0.021 0.001 PHE C 81 TYR 0.013 0.002 TYR G 199 ARG 0.015 0.001 ARG C 278 Details of bonding type rmsd hydrogen bonds : bond 0.05017 ( 1416) hydrogen bonds : angle 3.22911 ( 4212) SS BOND : bond 0.00692 ( 36) SS BOND : angle 2.01941 ( 72) covalent geometry : bond 0.00400 (21024) covalent geometry : angle 0.74321 (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 417 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 391 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8076 (ptp90) cc_final: 0.7867 (ptt-90) REVERT: A 48 ASP cc_start: 0.9081 (p0) cc_final: 0.8828 (p0) REVERT: A 52 MET cc_start: 0.9212 (mmt) cc_final: 0.8891 (mmm) REVERT: A 59 GLN cc_start: 0.8929 (tp40) cc_final: 0.8525 (tp40) REVERT: A 241 GLU cc_start: 0.8410 (tt0) cc_final: 0.8075 (tt0) REVERT: A 253 PHE cc_start: 0.8541 (t80) cc_final: 0.8240 (t80) REVERT: A 257 MET cc_start: 0.8838 (mmm) cc_final: 0.8400 (mmm) REVERT: B 24 ARG cc_start: 0.8198 (ptt-90) cc_final: 0.7934 (pmt170) REVERT: B 43 GLU cc_start: 0.8592 (tt0) cc_final: 0.8130 (tm-30) REVERT: B 48 ASP cc_start: 0.9130 (p0) cc_final: 0.8817 (p0) REVERT: B 217 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: C 48 ASP cc_start: 0.9068 (p0) cc_final: 0.8616 (p0) REVERT: C 59 GLN cc_start: 0.9011 (tp40) cc_final: 0.8047 (tp40) REVERT: C 97 SER cc_start: 0.8709 (m) cc_final: 0.8298 (p) REVERT: C 230 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7748 (mm-30) REVERT: C 239 GLU cc_start: 0.8423 (tt0) cc_final: 0.7783 (tt0) REVERT: D 48 ASP cc_start: 0.9081 (p0) cc_final: 0.8828 (p0) REVERT: D 52 MET cc_start: 0.9224 (mmt) cc_final: 0.8906 (mmm) REVERT: D 59 GLN cc_start: 0.8994 (tp40) cc_final: 0.8522 (tp40) REVERT: D 253 PHE cc_start: 0.8478 (t80) cc_final: 0.8193 (t80) REVERT: D 257 MET cc_start: 0.8842 (mmm) cc_final: 0.8406 (mmm) REVERT: E 24 ARG cc_start: 0.8180 (ptt-90) cc_final: 0.7946 (ptt-90) REVERT: E 48 ASP cc_start: 0.9175 (p0) cc_final: 0.8839 (p0) REVERT: E 239 GLU cc_start: 0.8987 (tt0) cc_final: 0.8026 (tm-30) REVERT: F 48 ASP cc_start: 0.9074 (p0) cc_final: 0.8607 (p0) REVERT: F 97 SER cc_start: 0.8707 (m) cc_final: 0.8299 (p) REVERT: F 230 GLU cc_start: 0.8470 (mp0) cc_final: 0.7972 (pm20) REVERT: G 48 ASP cc_start: 0.9027 (p0) cc_final: 0.8553 (p0) REVERT: G 210 GLU cc_start: 0.9066 (tp30) cc_final: 0.8652 (tp30) REVERT: G 230 GLU cc_start: 0.8496 (mp0) cc_final: 0.8020 (pm20) REVERT: G 279 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7625 (mppt) REVERT: H 48 ASP cc_start: 0.9080 (p0) cc_final: 0.8839 (p0) REVERT: H 52 MET cc_start: 0.9222 (mmt) cc_final: 0.8903 (mmm) REVERT: H 253 PHE cc_start: 0.8438 (t80) cc_final: 0.8185 (t80) REVERT: H 257 MET cc_start: 0.8828 (mmm) cc_final: 0.8399 (mmm) REVERT: I 24 ARG cc_start: 0.8086 (ptt-90) cc_final: 0.7870 (ptt-90) REVERT: I 48 ASP cc_start: 0.9115 (p0) cc_final: 0.8763 (p0) REVERT: I 59 GLN cc_start: 0.8938 (tp40) cc_final: 0.8501 (tp40) REVERT: I 230 GLU cc_start: 0.8373 (mp0) cc_final: 0.8119 (tp30) REVERT: J 24 ARG cc_start: 0.7978 (pmt170) cc_final: 0.7745 (pmt170) REVERT: J 48 ASP cc_start: 0.9113 (p0) cc_final: 0.8697 (p0) REVERT: J 59 GLN cc_start: 0.8965 (tp40) cc_final: 0.8516 (tp40) REVERT: J 97 SER cc_start: 0.8707 (m) cc_final: 0.8304 (p) REVERT: J 230 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8005 (mm-30) REVERT: J 239 GLU cc_start: 0.8366 (tt0) cc_final: 0.7991 (tt0) REVERT: K 24 ARG cc_start: 0.8064 (ptt-90) cc_final: 0.7839 (pmt170) REVERT: K 48 ASP cc_start: 0.9109 (p0) cc_final: 0.8796 (p0) REVERT: K 217 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8508 (tt0) REVERT: K 253 PHE cc_start: 0.8495 (t80) cc_final: 0.8213 (t80) REVERT: K 257 MET cc_start: 0.8831 (mmm) cc_final: 0.8431 (mmm) REVERT: L 24 ARG cc_start: 0.8112 (ptt-90) cc_final: 0.7817 (pmt170) REVERT: L 43 GLU cc_start: 0.8612 (tt0) cc_final: 0.8215 (tm-30) REVERT: L 48 ASP cc_start: 0.9117 (p0) cc_final: 0.8770 (p0) REVERT: L 59 GLN cc_start: 0.8959 (tp40) cc_final: 0.8162 (tp40) REVERT: L 230 GLU cc_start: 0.8409 (mp0) cc_final: 0.8137 (tp30) outliers start: 26 outliers final: 8 residues processed: 408 average time/residue: 1.3531 time to fit residues: 619.8620 Evaluate side-chains 386 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 377 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain J residue 272 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: 3.9990 chunk 190 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 chunk 191 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 268 ASN B 56 ASN B 217 GLN C 56 ASN D 268 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 268 ASN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 217 GLN J 56 ASN K 268 ASN L 217 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.134471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095759 restraints weight = 34151.077| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.89 r_work: 0.3165 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5620 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= 0.142 Angle : 0.738 18.012 28548 Z= 0.359 Chirality : 0.039 0.165 3396 Planarity : 0.005 0.080 3144 Dihedral : 6.594 54.992 6732 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.05 % Allowed : 30.64 % Favored : 68.31 % 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: 3.88 (0.18), residues: 2196 helix: 3.54 (0.12), residues: 1692 sheet: 0.07 (0.40), residues: 144 loop : -1.60 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 277 HIS 0.002 0.001 HIS A 274 PHE 0.021 0.001 PHE C 81 TYR 0.017 0.001 TYR B 218 ARG 0.016 0.001 ARG F 278 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 1416) hydrogen bonds : angle 3.13946 ( 4212) SS BOND : bond 0.00622 ( 36) SS BOND : angle 1.62418 ( 72) covalent geometry : bond 0.00331 (21024) covalent geometry : angle 0.73488 (28476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17989.56 seconds wall clock time: 318 minutes 5.45 seconds (19085.45 seconds total)