Starting phenix.real_space_refine on Sun Jul 5 13:20:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tjq_25929/07_2026/7tjq_25929.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjq_25929/07_2026/7tjq_25929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tjq_25929/07_2026/7tjq_25929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjq_25929/07_2026/7tjq_25929.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tjq_25929/07_2026/7tjq_25929.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tjq_25929/07_2026/7tjq_25929.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tjq_25929/07_2026/7tjq_25929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjq_25929/07_2026/7tjq_25929.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9645 atoms to isotropic. 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 129 5.16 5 C 12867 2.51 5 N 3516 2.21 5 O 4026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20538 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3265 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3265 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3265 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "K" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "L" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "N" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "O" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.62, per 1000 atoms: 0.22 Number of scatterers: 20538 At special positions: 0 Unit cell: (162.81, 148.23, 106.11, 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 129 16.00 O 4026 8.00 N 3516 7.00 C 12867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 100B" distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 322 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 153 " distance=2.04 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 463 " distance=2.02 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 100B" distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 407 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 110 " - pdb=" SG CYS F 322 " distance=2.03 Simple disulfide: pdb=" SG CYS F 127 " - pdb=" SG CYS F 153 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 283 " - pdb=" SG CYS F 311 " distance=2.03 Simple disulfide: pdb=" SG CYS F 292 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 326 " - pdb=" SG CYS F 335 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 365 " - pdb=" SG CYS F 463 " distance=2.02 Simple disulfide: pdb=" SG CYS F 384 " - pdb=" SG CYS F 390 " distance=2.03 Simple disulfide: pdb=" SG CYS G 28 " - pdb=" SG CYS G 407 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 182 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 322 " distance=2.03 Simple disulfide: pdb=" SG CYS G 127 " - pdb=" SG CYS G 153 " distance=2.04 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 283 " - pdb=" SG CYS G 311 " distance=2.03 Simple disulfide: pdb=" SG CYS G 292 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 326 " - pdb=" SG CYS G 335 " distance=2.03 Simple disulfide: pdb=" SG CYS G 350 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 365 " - pdb=" SG CYS G 463 " distance=2.02 Simple disulfide: pdb=" SG CYS G 384 " - pdb=" SG CYS G 390 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.04 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 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG P 1 " - " ASN A 96 " " NAG Q 1 " - " ASN C 172 " " NAG R 1 " - " ASN D 96 " " NAG S 1 " - " ASN F 172 " " NAG T 1 " - " ASN G 172 " " NAG U 1 " - " ASN H 96 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 871.3 milliseconds 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4902 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 55 sheets defined 21.4% alpha, 41.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.740A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.030A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 65 through 84 removed outlier: 3.512A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 129 removed outlier: 3.714A pdb=" N ILE C 108 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 186 through 197 removed outlier: 4.164A pdb=" N ALA C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.658A pdb=" N ARG C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 247 Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 344 through 351 Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 460 through 463 No H-bonds generated for 'chain 'C' and resid 460 through 463' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.701A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'F' and resid 54 through 58 Processing helix chain 'F' and resid 65 through 84 Processing helix chain 'F' and resid 104 through 129 removed outlier: 3.862A pdb=" N ILE F 108 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 141 Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 186 through 197 removed outlier: 4.189A pdb=" N ALA F 190 " --> pdb=" O ASP F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 210 Processing helix chain 'F' and resid 223 through 234 removed outlier: 3.763A pdb=" N ARG F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 247 Processing helix chain 'F' and resid 247 through 255 Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 344 through 352 Processing helix chain 'F' and resid 441 through 446 Processing helix chain 'F' and resid 461 through 463 No H-bonds generated for 'chain 'F' and resid 461 through 463' Processing helix chain 'G' and resid 65 through 84 removed outlier: 3.606A pdb=" N THR G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 129 removed outlier: 3.777A pdb=" N ILE G 108 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 141 Processing helix chain 'G' and resid 163 through 172 Processing helix chain 'G' and resid 172 through 177 Processing helix chain 'G' and resid 178 through 181 Processing helix chain 'G' and resid 187 through 197 Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 223 through 234 Processing helix chain 'G' and resid 237 through 247 Processing helix chain 'G' and resid 247 through 255 Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 344 through 347 Processing helix chain 'G' and resid 348 through 353 Processing helix chain 'G' and resid 441 through 446 Processing helix chain 'G' and resid 460 through 463 No H-bonds generated for 'chain 'G' and resid 460 through 463' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.679A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 81 through 85 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.540A pdb=" N ASP A 10 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.540A pdb=" N ASP A 10 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG A 94 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TYR A 100D" --> pdb=" O SER A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.185A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.948A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 327 through 329 removed outlier: 3.826A pdb=" N GLY C 34 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS C 283 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU C 36 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR C 281 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 38 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE C 279 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP C 309 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR C 317 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AA9, first strand: chain 'C' and resid 146 through 150 removed outlier: 9.400A pdb=" N TRP C 43 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N LEU C 158 " --> pdb=" O TRP C 43 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR C 45 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR C 160 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 47 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL C 162 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR C 49 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL C 262 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE C 268 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 291 through 294 removed outlier: 7.009A pdb=" N CYS C 365 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE C 456 " --> pdb=" O CYS C 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 372 through 376 Processing sheet with id=AB3, first strand: chain 'C' and resid 398 through 402 removed outlier: 6.909A pdb=" N ILE C 392 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLN C 402 " --> pdb=" O CYS C 390 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N CYS C 390 " --> pdb=" O GLN C 402 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 447 through 448 removed outlier: 4.412A pdb=" N ASP C 447 " --> pdb=" O GLU C 465 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.672A pdb=" N ASP D 10 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.672A pdb=" N ASP D 10 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR D 100D" --> pdb=" O SER D 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.570A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.988A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 327 through 329 removed outlier: 3.901A pdb=" N GLY F 34 " --> pdb=" O CYS F 283 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS F 283 " --> pdb=" O GLY F 34 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU F 36 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR F 281 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL F 38 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE F 279 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TRP F 309 " --> pdb=" O TYR F 320 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR F 317 " --> pdb=" O VAL F 343 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 327 through 329 removed outlier: 6.349A pdb=" N GLU F 21 " --> pdb=" O HIS F 435 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE F 437 " --> pdb=" O GLU F 21 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR F 23 " --> pdb=" O ILE F 437 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 146 through 150 removed outlier: 8.285A pdb=" N ARG F 156 " --> pdb=" O TRP F 43 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR F 45 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N MET F 270 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU F 259 " --> pdb=" O MET F 270 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN F 272 " --> pdb=" O GLY F 257 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLY F 257 " --> pdb=" O GLN F 272 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY F 257 " --> pdb=" O THR F 214 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 291 through 295 removed outlier: 6.956A pdb=" N CYS F 365 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE F 456 " --> pdb=" O CYS F 365 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 372 through 376 Processing sheet with id=AC7, first strand: chain 'F' and resid 398 through 402 removed outlier: 6.940A pdb=" N ILE F 392 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN F 402 " --> pdb=" O CYS F 390 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N CYS F 390 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 327 through 329 removed outlier: 4.006A pdb=" N GLY G 34 " --> pdb=" O CYS G 283 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS G 283 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU G 36 " --> pdb=" O THR G 281 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N THR G 281 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL G 38 " --> pdb=" O ILE G 279 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE G 279 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TRP G 309 " --> pdb=" O TYR G 320 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR G 317 " --> pdb=" O VAL G 343 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 327 through 329 removed outlier: 3.503A pdb=" N SER G 29 " --> pdb=" O LEU G 24 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 146 through 150 removed outlier: 9.388A pdb=" N TRP G 43 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N LEU G 158 " --> pdb=" O TRP G 43 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR G 45 " --> pdb=" O LEU G 158 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR G 160 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL G 47 " --> pdb=" O THR G 160 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL G 162 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR G 49 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER G 266 " --> pdb=" O VAL G 262 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL G 262 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE G 268 " --> pdb=" O ILE G 260 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 257 " --> pdb=" O THR G 214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 291 through 294 removed outlier: 7.064A pdb=" N CYS G 365 " --> pdb=" O PHE G 456 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE G 456 " --> pdb=" O CYS G 365 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 372 through 376 Processing sheet with id=AD4, first strand: chain 'G' and resid 398 through 402 removed outlier: 6.945A pdb=" N ILE G 392 " --> pdb=" O ILE G 400 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLN G 402 " --> pdb=" O CYS G 390 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N CYS G 390 " --> pdb=" O GLN G 402 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 447 through 448 removed outlier: 4.615A pdb=" N ASP G 447 " --> pdb=" O GLU G 465 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.528A pdb=" N ASP H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.528A pdb=" N ASP H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR H 100D" --> pdb=" O SER H 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.012A pdb=" N SER I 33 " --> pdb=" O ALA I 99 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N MET I 34 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.076A pdb=" N CYS I 96 " --> pdb=" O TRP I 114 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TRP I 114 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG I 98 " --> pdb=" O ASP I 112 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.810A pdb=" N SER J 33 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 12 removed outlier: 7.054A pdb=" N CYS J 96 " --> pdb=" O TRP J 114 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TRP J 114 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG J 98 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 9 through 11 removed outlier: 6.494A pdb=" N VAL K 10 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 9 through 11 removed outlier: 6.494A pdb=" N VAL K 10 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.961A pdb=" N GLY L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.472A pdb=" N VAL M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.472A pdb=" N VAL M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AF5, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AF6, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.840A pdb=" N SER N 33 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.027A pdb=" N CYS N 96 " --> pdb=" O TRP N 114 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TRP N 114 " --> pdb=" O CYS N 96 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG N 98 " --> pdb=" O ASP N 112 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.436A pdb=" N VAL O 10 " --> pdb=" O THR O 108 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.436A pdb=" N VAL O 10 " --> pdb=" O THR O 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 18 through 23 1058 hydrogen bonds defined for protein. 2604 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.61 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6688 1.35 - 1.47: 5186 1.47 - 1.59: 8892 1.59 - 1.71: 0 1.71 - 1.83: 162 Bond restraints: 20928 Sorted by residual: bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.21e+00 bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.57e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.31e+00 ... (remaining 20923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 26888 1.63 - 3.26: 1354 3.26 - 4.89: 116 4.89 - 6.53: 22 6.53 - 8.16: 6 Bond angle restraints: 28386 Sorted by residual: angle pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 113.90 122.06 -8.16 1.80e+00 3.09e-01 2.05e+01 angle pdb=" C ASP O 52 " pdb=" N ASN O 53 " pdb=" CA ASN O 53 " ideal model delta sigma weight residual 121.54 128.35 -6.81 1.91e+00 2.74e-01 1.27e+01 angle pdb=" CA TYR E 49 " pdb=" CB TYR E 49 " pdb=" CG TYR E 49 " ideal model delta sigma weight residual 113.90 120.25 -6.35 1.80e+00 3.09e-01 1.24e+01 angle pdb=" CA TYR K 51 " pdb=" CB TYR K 51 " pdb=" CG TYR K 51 " ideal model delta sigma weight residual 113.90 119.98 -6.08 1.80e+00 3.09e-01 1.14e+01 angle pdb=" C ASP M 52 " pdb=" N ASN M 53 " pdb=" CA ASN M 53 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 ... (remaining 28381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11639 17.97 - 35.93: 658 35.93 - 53.90: 141 53.90 - 71.87: 54 71.87 - 89.83: 18 Dihedral angle restraints: 12510 sinusoidal: 4830 harmonic: 7680 Sorted by residual: dihedral pdb=" CA ASN A 96 " pdb=" C ASN A 96 " pdb=" N CYS A 97 " pdb=" CA CYS A 97 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASN D 96 " pdb=" C ASN D 96 " pdb=" N CYS D 97 " pdb=" CA CYS D 97 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ASN H 96 " pdb=" C ASN H 96 " pdb=" N CYS H 97 " pdb=" CA CYS H 97 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 12507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2328 0.049 - 0.099: 780 0.099 - 0.148: 132 0.148 - 0.197: 17 0.197 - 0.247: 4 Chirality restraints: 3261 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 172 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN G 172 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA TYR L 49 " pdb=" N TYR L 49 " pdb=" C TYR L 49 " pdb=" CB TYR L 49 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3258 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 163 " 0.242 9.50e-02 1.11e+02 1.09e-01 9.39e+00 pdb=" NE ARG C 163 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG C 163 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG C 163 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 163 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 163 " 0.235 9.50e-02 1.11e+02 1.06e-01 8.77e+00 pdb=" NE ARG G 163 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG G 163 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG G 163 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG G 163 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 163 " 0.223 9.50e-02 1.11e+02 1.01e-01 7.94e+00 pdb=" NE ARG F 163 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG F 163 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG F 163 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG F 163 " 0.000 2.00e-02 2.50e+03 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5235 2.81 - 3.33: 19234 3.33 - 3.86: 35070 3.86 - 4.38: 42135 4.38 - 4.90: 73425 Nonbonded interactions: 175099 Sorted by model distance: nonbonded pdb=" OG1 THR I 102 " pdb=" OD2 ASP M 52 " model vdw 2.288 3.040 nonbonded pdb=" ND2 ASN C 412 " pdb=" O VAL C 430 " model vdw 2.336 3.120 nonbonded pdb=" O GLN F 307 " pdb=" OH TYR F 319 " model vdw 2.338 3.040 nonbonded pdb=" OG1 THR N 102 " pdb=" OD2 ASP O 52 " model vdw 2.343 3.040 nonbonded pdb=" OE2 GLU L 50 " pdb=" OH TYR L 91 " model vdw 2.344 3.040 ... (remaining 175094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 6.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.840 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 : 0.004 0.050 20988 Z= 0.192 Angle : 0.783 12.753 28518 Z= 0.444 Chirality : 0.049 0.247 3261 Planarity : 0.008 0.109 3618 Dihedral : 13.251 89.834 7464 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.03 % Allowed : 4.82 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 2643 helix: -0.72 (0.22), residues: 414 sheet: -0.19 (0.17), residues: 936 loop : -0.22 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG C 163 TYR 0.037 0.005 TYR E 49 PHE 0.021 0.002 PHE I 29 TRP 0.040 0.003 TRP D 50 HIS 0.007 0.002 HIS G 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (20928) covalent geometry : angle 0.77074 / 0.44 (28386) SS BOND : bond 0.00522 / 0.34 ( 48) SS BOND : angle 1.31106 / 0.84 ( 96) hydrogen bonds : bond 0.17746 / 11.59 ( 985) hydrogen bonds : angle 8.25894 / 5.58 ( 2604) link_BETA1-4 : bond 0.00980 / 0.48 ( 6) link_BETA1-4 : angle 3.86069 / 2.34 ( 18) link_NAG-ASN : bond 0.00544 / 0.35 ( 6) link_NAG-ASN : angle 3.23244 / 2.21 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 604 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7718 (pmt170) REVERT: B 26 SER cc_start: 0.7874 (p) cc_final: 0.7521 (p) REVERT: B 96 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7713 (mpt180) REVERT: C 79 ARG cc_start: 0.6960 (mtm-85) cc_final: 0.6640 (mtm-85) REVERT: C 81 LEU cc_start: 0.8293 (tp) cc_final: 0.8081 (tp) REVERT: C 133 GLU cc_start: 0.6426 (tp30) cc_final: 0.6203 (tp30) REVERT: C 197 ASN cc_start: 0.8071 (p0) cc_final: 0.7747 (p0) REVERT: C 343 VAL cc_start: 0.8589 (p) cc_final: 0.8247 (m) REVERT: C 399 ILE cc_start: 0.7975 (mm) cc_final: 0.7774 (mt) REVERT: E 74 THR cc_start: 0.7780 (m) cc_final: 0.7345 (p) REVERT: F 62 ASP cc_start: 0.7274 (m-30) cc_final: 0.6901 (m-30) REVERT: F 133 GLU cc_start: 0.6759 (tp30) cc_final: 0.6224 (tp30) REVERT: F 163 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.7160 (mtm-85) REVERT: F 174 THR cc_start: 0.8078 (m) cc_final: 0.7806 (m) REVERT: F 189 MET cc_start: 0.6993 (mmt) cc_final: 0.6465 (mmt) REVERT: F 192 SER cc_start: 0.7605 (m) cc_final: 0.7253 (p) REVERT: F 205 ARG cc_start: 0.6661 (ttp80) cc_final: 0.6311 (ttp80) REVERT: F 223 THR cc_start: 0.8175 (m) cc_final: 0.7843 (p) REVERT: F 256 PHE cc_start: 0.8144 (p90) cc_final: 0.7840 (p90) REVERT: F 343 VAL cc_start: 0.8360 (p) cc_final: 0.8041 (m) REVERT: F 401 LYS cc_start: 0.7600 (tttp) cc_final: 0.7318 (mtpp) REVERT: F 450 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7556 (mmtt) REVERT: F 454 ASP cc_start: 0.6662 (m-30) cc_final: 0.6446 (m-30) REVERT: F 464 PHE cc_start: 0.7962 (m-80) cc_final: 0.7758 (m-80) REVERT: G 20 LYS cc_start: 0.7675 (tttt) cc_final: 0.7443 (tttm) REVERT: G 170 SER cc_start: 0.7712 (p) cc_final: 0.7472 (m) REVERT: G 177 ILE cc_start: 0.7837 (mt) cc_final: 0.7634 (mt) REVERT: G 192 SER cc_start: 0.7664 (m) cc_final: 0.7284 (p) REVERT: G 198 ARG cc_start: 0.7139 (ttm-80) cc_final: 0.6759 (ttm-80) REVERT: G 205 ARG cc_start: 0.6429 (ttp80) cc_final: 0.6177 (ttp80) REVERT: G 219 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7315 (mmmm) REVERT: G 305 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6040 (mt-10) REVERT: G 318 VAL cc_start: 0.8358 (p) cc_final: 0.8113 (t) REVERT: G 343 VAL cc_start: 0.8326 (p) cc_final: 0.7895 (m) REVERT: G 454 ASP cc_start: 0.6747 (m-30) cc_final: 0.6470 (m-30) REVERT: I 52 SER cc_start: 0.8229 (p) cc_final: 0.8013 (t) REVERT: K 50 ILE cc_start: 0.8106 (mm) cc_final: 0.7819 (mm) REVERT: M 27 SER cc_start: 0.7611 (p) cc_final: 0.7375 (p) REVERT: N 52 SER cc_start: 0.8350 (p) cc_final: 0.8098 (t) REVERT: O 27 SER cc_start: 0.8330 (p) cc_final: 0.7976 (p) outliers start: 23 outliers final: 7 residues processed: 621 average time/residue: 0.1763 time to fit residues: 162.4812 Evaluate side-chains 542 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 533 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 258 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 307 GLN G 195 GLN G 272 GLN G 298 ASN G 342 ASN ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN J 35 ASN M 55 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105947 restraints weight = 28225.609| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.89 r_work: 0.3169 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20988 Z= 0.213 Angle : 0.677 8.385 28518 Z= 0.366 Chirality : 0.047 0.219 3261 Planarity : 0.005 0.049 3618 Dihedral : 5.967 54.891 2928 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.01 % Allowed : 11.07 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.16), residues: 2643 helix: 0.41 (0.24), residues: 420 sheet: -0.17 (0.17), residues: 906 loop : -0.02 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 329 TYR 0.026 0.002 TYR K 51 PHE 0.024 0.002 PHE J 29 TRP 0.026 0.002 TRP H 50 HIS 0.008 0.001 HIS G 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (20928) covalent geometry : angle 0.66787 / 0.36 (28386) SS BOND : bond 0.00411 / 0.26 ( 48) SS BOND : angle 1.34752 / 0.83 ( 96) hydrogen bonds : bond 0.04824 / 3.11 ( 985) hydrogen bonds : angle 6.17053 / 4.15 ( 2604) link_BETA1-4 : bond 0.00514 / 0.29 ( 6) link_BETA1-4 : angle 2.22431 / 1.42 ( 18) link_NAG-ASN : bond 0.00671 / 0.36 ( 6) link_NAG-ASN : angle 2.86263 / 1.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 537 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 THR cc_start: 0.7853 (t) cc_final: 0.7487 (t) REVERT: C 70 GLU cc_start: 0.7271 (tp30) cc_final: 0.6799 (tp30) REVERT: C 71 LEU cc_start: 0.7873 (tp) cc_final: 0.7631 (tp) REVERT: C 79 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.7344 (mtm-85) REVERT: C 81 LEU cc_start: 0.8175 (tp) cc_final: 0.7934 (tp) REVERT: C 82 ARG cc_start: 0.8071 (mtt90) cc_final: 0.7851 (mtt90) REVERT: C 133 GLU cc_start: 0.7265 (tp30) cc_final: 0.6755 (tp30) REVERT: C 175 ARG cc_start: 0.7786 (ttp-170) cc_final: 0.7541 (ttp-170) REVERT: C 194 SER cc_start: 0.7642 (p) cc_final: 0.7415 (t) REVERT: C 245 LEU cc_start: 0.7874 (mt) cc_final: 0.7653 (mm) REVERT: C 248 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7533 (mtp85) REVERT: C 253 ARG cc_start: 0.7702 (ttp-110) cc_final: 0.7470 (ttp-110) REVERT: C 343 VAL cc_start: 0.8539 (p) cc_final: 0.8269 (m) REVERT: C 399 ILE cc_start: 0.8062 (mm) cc_final: 0.7841 (mt) REVERT: C 412 ASN cc_start: 0.7991 (p0) cc_final: 0.7748 (p0) REVERT: C 413 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7907 (mm110) REVERT: E 74 THR cc_start: 0.8136 (m) cc_final: 0.7476 (p) REVERT: F 62 ASP cc_start: 0.7826 (m-30) cc_final: 0.7305 (m-30) REVERT: F 133 GLU cc_start: 0.7444 (tp30) cc_final: 0.6775 (tp30) REVERT: F 166 LYS cc_start: 0.7850 (ttpt) cc_final: 0.7610 (ttpt) REVERT: F 189 MET cc_start: 0.7460 (mmt) cc_final: 0.6948 (mmt) REVERT: F 192 SER cc_start: 0.7757 (m) cc_final: 0.7214 (p) REVERT: F 206 GLN cc_start: 0.7487 (mt0) cc_final: 0.7137 (mt0) REVERT: F 245 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7704 (mm) REVERT: F 343 VAL cc_start: 0.8460 (p) cc_final: 0.8111 (m) REVERT: F 408 SER cc_start: 0.8200 (m) cc_final: 0.7817 (p) REVERT: F 464 PHE cc_start: 0.8056 (m-80) cc_final: 0.7792 (m-80) REVERT: G 20 LYS cc_start: 0.8312 (tttt) cc_final: 0.8046 (tttm) REVERT: G 40 ARG cc_start: 0.7894 (tmm160) cc_final: 0.7590 (tmm160) REVERT: G 129 ARG cc_start: 0.7587 (ttp-170) cc_final: 0.7116 (ttp-170) REVERT: G 131 GLU cc_start: 0.7754 (tt0) cc_final: 0.7191 (tt0) REVERT: G 163 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.7405 (mtm-85) REVERT: G 177 ILE cc_start: 0.7834 (mt) cc_final: 0.7566 (mt) REVERT: G 192 SER cc_start: 0.7730 (m) cc_final: 0.7259 (p) REVERT: G 197 ASN cc_start: 0.8513 (p0) cc_final: 0.7797 (p0) REVERT: G 198 ARG cc_start: 0.7922 (ttm-80) cc_final: 0.7173 (ttm-80) REVERT: G 205 ARG cc_start: 0.7373 (ttp80) cc_final: 0.7121 (ttp80) REVERT: G 206 GLN cc_start: 0.7479 (mt0) cc_final: 0.7170 (mt0) REVERT: G 219 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7749 (mmmm) REVERT: G 223 THR cc_start: 0.8384 (m) cc_final: 0.7854 (p) REVERT: G 250 MET cc_start: 0.6581 (tpp) cc_final: 0.6313 (mmm) REVERT: G 280 ASP cc_start: 0.7548 (t70) cc_final: 0.7290 (t70) REVERT: G 343 VAL cc_start: 0.8439 (p) cc_final: 0.8094 (m) REVERT: G 353 ASN cc_start: 0.7547 (p0) cc_final: 0.7047 (p0) REVERT: G 413 GLN cc_start: 0.8281 (mm-40) cc_final: 0.8028 (mm-40) REVERT: G 454 ASP cc_start: 0.7470 (m-30) cc_final: 0.7224 (m-30) REVERT: J 7 SER cc_start: 0.7881 (p) cc_final: 0.7665 (t) REVERT: J 28 THR cc_start: 0.8621 (m) cc_final: 0.8102 (p) REVERT: J 71 SER cc_start: 0.8093 (p) cc_final: 0.7870 (m) REVERT: L 79 GLN cc_start: 0.7573 (mm110) cc_final: 0.7256 (mm-40) REVERT: M 27 SER cc_start: 0.8097 (p) cc_final: 0.7834 (p) REVERT: M 98 SER cc_start: 0.8268 (p) cc_final: 0.8012 (m) REVERT: N 52 SER cc_start: 0.8474 (p) cc_final: 0.8241 (t) REVERT: O 27 SER cc_start: 0.8355 (p) cc_final: 0.8012 (t) outliers start: 45 outliers final: 27 residues processed: 559 average time/residue: 0.1594 time to fit residues: 131.8693 Evaluate side-chains 539 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 511 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 342 ASN Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 176 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 222 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 226 optimal weight: 2.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN F 195 GLN F 206 GLN F 272 GLN G 139 ASN G 202 ASN G 342 ASN G 351 ASN G 413 GLN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN O 28 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103991 restraints weight = 28394.870| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.88 r_work: 0.3144 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20988 Z= 0.213 Angle : 0.624 9.114 28518 Z= 0.336 Chirality : 0.046 0.178 3261 Planarity : 0.005 0.042 3618 Dihedral : 5.425 41.489 2915 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.86 % Allowed : 12.00 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2643 helix: 0.46 (0.24), residues: 420 sheet: -0.22 (0.16), residues: 954 loop : 0.05 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 248 TYR 0.026 0.002 TYR K 51 PHE 0.020 0.002 PHE J 29 TRP 0.020 0.002 TRP H 50 HIS 0.006 0.001 HIS G 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (20928) covalent geometry : angle 0.61529 / 0.33 (28386) SS BOND : bond 0.00415 / 0.27 ( 48) SS BOND : angle 1.26571 / 0.81 ( 96) hydrogen bonds : bond 0.04455 / 2.87 ( 985) hydrogen bonds : angle 5.89944 / 3.98 ( 2604) link_BETA1-4 : bond 0.00409 / 0.20 ( 6) link_BETA1-4 : angle 1.92283 / 1.24 ( 18) link_NAG-ASN : bond 0.00334 / 0.21 ( 6) link_NAG-ASN : angle 2.85319 / 1.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 531 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8415 (m-80) cc_final: 0.8189 (m-80) REVERT: B 102 THR cc_start: 0.8100 (t) cc_final: 0.7762 (t) REVERT: C 70 GLU cc_start: 0.7173 (tp30) cc_final: 0.6734 (tp30) REVERT: C 71 LEU cc_start: 0.7835 (tp) cc_final: 0.7594 (tp) REVERT: C 81 LEU cc_start: 0.8213 (tp) cc_final: 0.7986 (tp) REVERT: C 133 GLU cc_start: 0.7361 (tp30) cc_final: 0.6896 (tp30) REVERT: C 144 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7807 (p) REVERT: C 163 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7664 (mtm-85) REVERT: C 174 THR cc_start: 0.8342 (m) cc_final: 0.8098 (m) REVERT: C 175 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7483 (ttp-170) REVERT: C 189 MET cc_start: 0.7448 (tpp) cc_final: 0.7136 (tpp) REVERT: C 192 SER cc_start: 0.8204 (t) cc_final: 0.7738 (p) REVERT: C 194 SER cc_start: 0.7650 (p) cc_final: 0.7449 (t) REVERT: C 195 GLN cc_start: 0.8025 (mt0) cc_final: 0.7742 (mt0) REVERT: C 229 ARG cc_start: 0.7412 (mtp85) cc_final: 0.7058 (ttm-80) REVERT: C 233 ASN cc_start: 0.6745 (t0) cc_final: 0.6489 (m110) REVERT: C 248 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7369 (mtp180) REVERT: C 253 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7523 (ttm110) REVERT: C 343 VAL cc_start: 0.8531 (p) cc_final: 0.8299 (m) REVERT: C 399 ILE cc_start: 0.8054 (mm) cc_final: 0.7814 (mt) REVERT: C 413 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7912 (mm110) REVERT: D 71 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8085 (pmt-80) REVERT: E 74 THR cc_start: 0.8119 (m) cc_final: 0.7473 (p) REVERT: F 62 ASP cc_start: 0.7772 (m-30) cc_final: 0.7243 (m-30) REVERT: F 133 GLU cc_start: 0.7438 (tp30) cc_final: 0.6777 (tp30) REVERT: F 163 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7382 (mtm-85) REVERT: F 166 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7535 (ttpt) REVERT: F 189 MET cc_start: 0.7394 (mmt) cc_final: 0.6899 (mmt) REVERT: F 206 GLN cc_start: 0.7408 (mt0) cc_final: 0.7160 (mt0) REVERT: F 343 VAL cc_start: 0.8440 (p) cc_final: 0.8092 (m) REVERT: F 401 LYS cc_start: 0.8245 (ttpp) cc_final: 0.7995 (ttpp) REVERT: F 408 SER cc_start: 0.8200 (m) cc_final: 0.7880 (t) REVERT: F 411 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7997 (p) REVERT: G 20 LYS cc_start: 0.8351 (tttt) cc_final: 0.8078 (tttp) REVERT: G 70 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: G 75 LYS cc_start: 0.8153 (mtmm) cc_final: 0.7913 (mtpt) REVERT: G 131 GLU cc_start: 0.7735 (tt0) cc_final: 0.7211 (tt0) REVERT: G 156 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7127 (ptt-90) REVERT: G 163 ARG cc_start: 0.7698 (ttm-80) cc_final: 0.7413 (mtm-85) REVERT: G 177 ILE cc_start: 0.7797 (mt) cc_final: 0.7533 (mt) REVERT: G 192 SER cc_start: 0.7749 (m) cc_final: 0.7295 (p) REVERT: G 197 ASN cc_start: 0.8484 (p0) cc_final: 0.7805 (p0) REVERT: G 205 ARG cc_start: 0.7378 (ttp80) cc_final: 0.7155 (ttp80) REVERT: G 223 THR cc_start: 0.8412 (m) cc_final: 0.7908 (p) REVERT: G 248 ARG cc_start: 0.7583 (ttm110) cc_final: 0.7241 (mtp180) REVERT: G 253 ARG cc_start: 0.7641 (ttp-110) cc_final: 0.7434 (ttp80) REVERT: G 280 ASP cc_start: 0.7593 (t70) cc_final: 0.7253 (t70) REVERT: G 343 VAL cc_start: 0.8281 (p) cc_final: 0.8034 (m) REVERT: G 353 ASN cc_start: 0.7660 (p0) cc_final: 0.7143 (p0) REVERT: G 454 ASP cc_start: 0.7450 (m-30) cc_final: 0.7203 (m-30) REVERT: G 464 PHE cc_start: 0.8113 (m-80) cc_final: 0.7699 (m-80) REVERT: J 7 SER cc_start: 0.7883 (p) cc_final: 0.7650 (t) REVERT: J 71 SER cc_start: 0.8089 (p) cc_final: 0.7851 (m) REVERT: J 85 SER cc_start: 0.8517 (m) cc_final: 0.7865 (t) REVERT: K 50 ILE cc_start: 0.8402 (mm) cc_final: 0.8128 (mm) REVERT: L 79 GLN cc_start: 0.7592 (mm110) cc_final: 0.7231 (mm-40) REVERT: M 27 SER cc_start: 0.8076 (p) cc_final: 0.7842 (p) REVERT: M 98 SER cc_start: 0.8238 (p) cc_final: 0.7993 (m) REVERT: N 31 SER cc_start: 0.8190 (m) cc_final: 0.7974 (p) REVERT: O 27 SER cc_start: 0.8338 (p) cc_final: 0.8033 (t) outliers start: 64 outliers final: 44 residues processed: 562 average time/residue: 0.1570 time to fit residues: 133.0587 Evaluate side-chains 563 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 514 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 118 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 206 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 422 ASN G 139 ASN G 307 GLN ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN N 35 ASN O 28 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103599 restraints weight = 28437.654| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.90 r_work: 0.3144 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20988 Z= 0.216 Angle : 0.604 9.120 28518 Z= 0.325 Chirality : 0.045 0.165 3261 Planarity : 0.004 0.045 3618 Dihedral : 5.231 40.719 2915 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.99 % Allowed : 13.03 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2643 helix: 0.48 (0.24), residues: 420 sheet: -0.21 (0.16), residues: 954 loop : 0.06 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 129 TYR 0.025 0.002 TYR L 49 PHE 0.021 0.002 PHE J 29 TRP 0.018 0.002 TRP H 50 HIS 0.006 0.001 HIS C 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (20928) covalent geometry : angle 0.59634 / 0.32 (28386) SS BOND : bond 0.00349 / 0.23 ( 48) SS BOND : angle 1.19680 / 0.78 ( 96) hydrogen bonds : bond 0.04172 / 2.69 ( 985) hydrogen bonds : angle 5.77271 / 3.90 ( 2604) link_BETA1-4 : bond 0.00397 / 0.23 ( 6) link_BETA1-4 : angle 1.77806 / 1.17 ( 18) link_NAG-ASN : bond 0.00285 / 0.20 ( 6) link_NAG-ASN : angle 2.49797 / 1.61 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 509 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8398 (m-80) cc_final: 0.8125 (m-80) REVERT: B 102 THR cc_start: 0.8178 (t) cc_final: 0.7811 (t) REVERT: C 70 GLU cc_start: 0.7195 (tp30) cc_final: 0.6775 (tp30) REVERT: C 81 LEU cc_start: 0.8240 (tp) cc_final: 0.8015 (tp) REVERT: C 133 GLU cc_start: 0.7426 (tp30) cc_final: 0.6981 (tp30) REVERT: C 144 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7811 (p) REVERT: C 163 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7604 (mtm-85) REVERT: C 175 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7460 (ttp-170) REVERT: C 188 LYS cc_start: 0.7446 (tmmm) cc_final: 0.6918 (tmmm) REVERT: C 189 MET cc_start: 0.7429 (tpp) cc_final: 0.6879 (tpp) REVERT: C 192 SER cc_start: 0.8175 (t) cc_final: 0.7754 (p) REVERT: C 195 GLN cc_start: 0.8021 (mt0) cc_final: 0.7760 (mt0) REVERT: C 226 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7379 (mt-10) REVERT: C 229 ARG cc_start: 0.7421 (mtp85) cc_final: 0.6993 (ttm-80) REVERT: C 248 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7537 (mtm180) REVERT: C 305 GLU cc_start: 0.7477 (tp30) cc_final: 0.7009 (mp0) REVERT: C 343 VAL cc_start: 0.8503 (p) cc_final: 0.8267 (m) REVERT: C 399 ILE cc_start: 0.8044 (mm) cc_final: 0.7795 (mt) REVERT: C 412 ASN cc_start: 0.8027 (p0) cc_final: 0.7723 (p0) REVERT: C 413 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7901 (mm-40) REVERT: D 71 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8011 (pmt-80) REVERT: E 74 THR cc_start: 0.8124 (m) cc_final: 0.7514 (p) REVERT: F 62 ASP cc_start: 0.7747 (m-30) cc_final: 0.7224 (m-30) REVERT: F 133 GLU cc_start: 0.7442 (tp30) cc_final: 0.6759 (tp30) REVERT: F 166 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7525 (ttpt) REVERT: F 175 ARG cc_start: 0.7816 (ttp-170) cc_final: 0.7403 (ttp-170) REVERT: F 189 MET cc_start: 0.7330 (mmt) cc_final: 0.6868 (mmt) REVERT: F 206 GLN cc_start: 0.7402 (mt0) cc_final: 0.7165 (mt0) REVERT: F 250 MET cc_start: 0.6841 (mmm) cc_final: 0.6621 (tmm) REVERT: F 252 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7857 (ttm-80) REVERT: F 343 VAL cc_start: 0.8428 (p) cc_final: 0.8072 (m) REVERT: F 401 LYS cc_start: 0.8274 (ttpp) cc_final: 0.8040 (ttpp) REVERT: F 408 SER cc_start: 0.8200 (m) cc_final: 0.7901 (t) REVERT: G 20 LYS cc_start: 0.8356 (tttt) cc_final: 0.8116 (tttm) REVERT: G 40 ARG cc_start: 0.7876 (tmm160) cc_final: 0.7522 (ttp80) REVERT: G 70 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: G 75 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7934 (mtpt) REVERT: G 131 GLU cc_start: 0.7748 (tt0) cc_final: 0.7246 (tt0) REVERT: G 156 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7134 (ptt-90) REVERT: G 163 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7216 (mtm-85) REVERT: G 167 ASP cc_start: 0.7499 (m-30) cc_final: 0.7222 (m-30) REVERT: G 177 ILE cc_start: 0.7763 (mt) cc_final: 0.7478 (mt) REVERT: G 192 SER cc_start: 0.7735 (m) cc_final: 0.7275 (p) REVERT: G 197 ASN cc_start: 0.8496 (p0) cc_final: 0.7830 (p0) REVERT: G 205 ARG cc_start: 0.7330 (ttp80) cc_final: 0.7120 (ttp80) REVERT: G 206 GLN cc_start: 0.7577 (mt0) cc_final: 0.7326 (mt0) REVERT: G 223 THR cc_start: 0.8407 (m) cc_final: 0.7866 (p) REVERT: G 248 ARG cc_start: 0.7531 (ttm110) cc_final: 0.7284 (mtp85) REVERT: G 253 ARG cc_start: 0.7693 (ttp-110) cc_final: 0.7485 (ttp80) REVERT: G 280 ASP cc_start: 0.7626 (t70) cc_final: 0.7251 (t70) REVERT: G 343 VAL cc_start: 0.8393 (p) cc_final: 0.8136 (m) REVERT: G 353 ASN cc_start: 0.7680 (p0) cc_final: 0.7212 (p0) REVERT: G 405 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7955 (mmtt) REVERT: G 454 ASP cc_start: 0.7488 (m-30) cc_final: 0.7238 (m-30) REVERT: G 464 PHE cc_start: 0.8088 (m-80) cc_final: 0.7792 (m-80) REVERT: H 100 SER cc_start: 0.8089 (OUTLIER) cc_final: 0.7851 (p) REVERT: I 7 SER cc_start: 0.8072 (p) cc_final: 0.7783 (t) REVERT: J 7 SER cc_start: 0.7885 (p) cc_final: 0.7635 (t) REVERT: J 71 SER cc_start: 0.8089 (p) cc_final: 0.7825 (m) REVERT: K 50 ILE cc_start: 0.8401 (mm) cc_final: 0.8083 (mm) REVERT: M 27 SER cc_start: 0.8039 (p) cc_final: 0.7763 (t) REVERT: M 98 SER cc_start: 0.8247 (p) cc_final: 0.8015 (m) REVERT: N 31 SER cc_start: 0.8187 (m) cc_final: 0.7978 (p) REVERT: O 27 SER cc_start: 0.8309 (p) cc_final: 0.8043 (t) outliers start: 67 outliers final: 48 residues processed: 543 average time/residue: 0.1730 time to fit residues: 139.1730 Evaluate side-chains 556 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 503 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 161 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 213 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN F 195 GLN F 307 GLN G 139 ASN ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN O 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103676 restraints weight = 28255.926| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.90 r_work: 0.3143 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20988 Z= 0.199 Angle : 0.581 8.590 28518 Z= 0.312 Chirality : 0.045 0.161 3261 Planarity : 0.004 0.045 3618 Dihedral : 5.051 39.631 2914 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.03 % Allowed : 14.32 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2643 helix: 0.57 (0.25), residues: 420 sheet: -0.28 (0.16), residues: 954 loop : 0.07 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.023 0.002 TYR L 49 PHE 0.021 0.002 PHE J 29 TRP 0.016 0.002 TRP H 50 HIS 0.006 0.001 HIS C 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (20928) covalent geometry : angle 0.57506 / 0.31 (28386) SS BOND : bond 0.00321 / 0.22 ( 48) SS BOND : angle 1.06565 / 0.69 ( 96) hydrogen bonds : bond 0.03950 / 2.54 ( 985) hydrogen bonds : angle 5.66750 / 3.83 ( 2604) link_BETA1-4 : bond 0.00377 / 0.21 ( 6) link_BETA1-4 : angle 1.69780 / 1.11 ( 18) link_NAG-ASN : bond 0.00292 / 0.22 ( 6) link_NAG-ASN : angle 2.14059 / 1.39 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 502 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8377 (m-80) cc_final: 0.8112 (m-80) REVERT: B 102 THR cc_start: 0.8252 (t) cc_final: 0.7959 (t) REVERT: C 81 LEU cc_start: 0.8249 (tp) cc_final: 0.8027 (tp) REVERT: C 133 GLU cc_start: 0.7464 (tp30) cc_final: 0.6992 (tp30) REVERT: C 163 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7497 (mtm-85) REVERT: C 166 LYS cc_start: 0.7884 (tttt) cc_final: 0.7675 (tttt) REVERT: C 167 ASP cc_start: 0.7497 (m-30) cc_final: 0.7281 (m-30) REVERT: C 188 LYS cc_start: 0.7480 (tmmm) cc_final: 0.6927 (tmmm) REVERT: C 189 MET cc_start: 0.7419 (tpp) cc_final: 0.6864 (tpp) REVERT: C 192 SER cc_start: 0.8147 (t) cc_final: 0.7742 (p) REVERT: C 195 GLN cc_start: 0.8008 (mt0) cc_final: 0.7754 (mt0) REVERT: C 226 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7339 (mt-10) REVERT: C 305 GLU cc_start: 0.7448 (tp30) cc_final: 0.6967 (mp0) REVERT: C 343 VAL cc_start: 0.8458 (p) cc_final: 0.8228 (m) REVERT: C 399 ILE cc_start: 0.8035 (mm) cc_final: 0.7787 (mt) REVERT: E 74 THR cc_start: 0.8113 (m) cc_final: 0.7511 (p) REVERT: F 62 ASP cc_start: 0.7718 (m-30) cc_final: 0.7186 (m-30) REVERT: F 133 GLU cc_start: 0.7452 (tp30) cc_final: 0.6809 (tp30) REVERT: F 175 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.7395 (ttp-170) REVERT: F 189 MET cc_start: 0.7313 (mmt) cc_final: 0.6830 (mmt) REVERT: F 206 GLN cc_start: 0.7462 (mt0) cc_final: 0.7220 (mt0) REVERT: F 250 MET cc_start: 0.6895 (mmm) cc_final: 0.6630 (tmm) REVERT: F 252 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7881 (ttm-80) REVERT: F 343 VAL cc_start: 0.8421 (p) cc_final: 0.8054 (m) REVERT: F 401 LYS cc_start: 0.8280 (ttpp) cc_final: 0.8049 (ttpp) REVERT: F 408 SER cc_start: 0.8202 (m) cc_final: 0.7916 (t) REVERT: G 20 LYS cc_start: 0.8353 (tttt) cc_final: 0.8118 (tttm) REVERT: G 47 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8107 (t) REVERT: G 70 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: G 131 GLU cc_start: 0.7702 (tt0) cc_final: 0.7276 (tt0) REVERT: G 156 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7124 (ptt-90) REVERT: G 163 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7221 (mtm-85) REVERT: G 167 ASP cc_start: 0.7518 (m-30) cc_final: 0.7182 (m-30) REVERT: G 177 ILE cc_start: 0.7700 (mt) cc_final: 0.7437 (mt) REVERT: G 192 SER cc_start: 0.7731 (m) cc_final: 0.7249 (p) REVERT: G 197 ASN cc_start: 0.8500 (p0) cc_final: 0.7845 (p0) REVERT: G 206 GLN cc_start: 0.7566 (mt0) cc_final: 0.7357 (mt0) REVERT: G 223 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.7852 (p) REVERT: G 248 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7266 (mtp85) REVERT: G 253 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.7436 (ttp80) REVERT: G 280 ASP cc_start: 0.7626 (t70) cc_final: 0.7255 (t70) REVERT: G 343 VAL cc_start: 0.8435 (p) cc_final: 0.8179 (m) REVERT: G 353 ASN cc_start: 0.7689 (p0) cc_final: 0.7215 (p0) REVERT: G 405 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7934 (mmtt) REVERT: G 454 ASP cc_start: 0.7487 (m-30) cc_final: 0.7255 (m-30) REVERT: G 464 PHE cc_start: 0.8062 (m-80) cc_final: 0.7787 (m-80) REVERT: H 100 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7882 (p) REVERT: I 7 SER cc_start: 0.8052 (p) cc_final: 0.7756 (t) REVERT: J 7 SER cc_start: 0.7896 (p) cc_final: 0.7635 (t) REVERT: J 71 SER cc_start: 0.8072 (p) cc_final: 0.7825 (m) REVERT: K 50 ILE cc_start: 0.8390 (mm) cc_final: 0.8064 (mm) REVERT: L 79 GLN cc_start: 0.7676 (mm110) cc_final: 0.7160 (mm110) REVERT: M 98 SER cc_start: 0.8257 (p) cc_final: 0.8029 (m) REVERT: O 27 SER cc_start: 0.8295 (p) cc_final: 0.8058 (t) outliers start: 68 outliers final: 48 residues processed: 539 average time/residue: 0.1598 time to fit residues: 128.2816 Evaluate side-chains 548 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 495 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 GLU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 213 optimal weight: 1.9990 chunk 168 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 307 GLN F 195 GLN F 307 GLN G 139 ASN ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN L 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102500 restraints weight = 28244.260| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.88 r_work: 0.3128 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 20988 Z= 0.290 Angle : 0.638 8.890 28518 Z= 0.342 Chirality : 0.048 0.251 3261 Planarity : 0.005 0.050 3618 Dihedral : 5.238 41.657 2914 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.66 % Allowed : 14.77 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2643 helix: 0.21 (0.24), residues: 423 sheet: -0.34 (0.16), residues: 954 loop : -0.07 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 329 TYR 0.032 0.003 TYR K 51 PHE 0.024 0.002 PHE K 101 TRP 0.021 0.002 TRP O 37 HIS 0.007 0.002 HIS C 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.29 (20928) covalent geometry : angle 0.62941 / 0.34 (28386) SS BOND : bond 0.00427 / 0.27 ( 48) SS BOND : angle 1.32390 / 0.84 ( 96) hydrogen bonds : bond 0.04292 / 2.76 ( 985) hydrogen bonds : angle 5.82457 / 3.94 ( 2604) link_BETA1-4 : bond 0.00673 / 0.33 ( 6) link_BETA1-4 : angle 2.05374 / 1.31 ( 18) link_NAG-ASN : bond 0.00317 / 0.17 ( 6) link_NAG-ASN : angle 2.40763 / 1.57 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 518 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8366 (m-80) cc_final: 0.8123 (m-80) REVERT: B 102 THR cc_start: 0.8313 (t) cc_final: 0.8110 (t) REVERT: C 81 LEU cc_start: 0.8260 (tp) cc_final: 0.8042 (tp) REVERT: C 144 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7862 (p) REVERT: C 163 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7536 (mtm-85) REVERT: C 166 LYS cc_start: 0.7904 (tttt) cc_final: 0.7697 (tttt) REVERT: C 167 ASP cc_start: 0.7521 (m-30) cc_final: 0.7309 (m-30) REVERT: C 188 LYS cc_start: 0.7464 (tmmm) cc_final: 0.6909 (tmmm) REVERT: C 189 MET cc_start: 0.7447 (tpp) cc_final: 0.6908 (tpp) REVERT: C 192 SER cc_start: 0.8223 (t) cc_final: 0.7792 (p) REVERT: C 195 GLN cc_start: 0.8044 (mt0) cc_final: 0.7806 (mt0) REVERT: C 343 VAL cc_start: 0.8410 (p) cc_final: 0.8188 (m) REVERT: C 399 ILE cc_start: 0.8039 (mm) cc_final: 0.7792 (mt) REVERT: C 412 ASN cc_start: 0.7988 (p0) cc_final: 0.7647 (p0) REVERT: C 413 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7811 (mm110) REVERT: E 74 THR cc_start: 0.8127 (m) cc_final: 0.7540 (p) REVERT: F 62 ASP cc_start: 0.7689 (m-30) cc_final: 0.7192 (m-30) REVERT: F 129 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7302 (ttp80) REVERT: F 133 GLU cc_start: 0.7466 (tp30) cc_final: 0.6809 (tp30) REVERT: F 175 ARG cc_start: 0.7775 (ttp-170) cc_final: 0.7371 (ttp-170) REVERT: F 189 MET cc_start: 0.7345 (mmt) cc_final: 0.6782 (mmt) REVERT: F 206 GLN cc_start: 0.7485 (mt0) cc_final: 0.7216 (mt0) REVERT: F 250 MET cc_start: 0.6944 (mmm) cc_final: 0.6645 (tmm) REVERT: F 294 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7232 (mt-10) REVERT: F 343 VAL cc_start: 0.8372 (p) cc_final: 0.8037 (m) REVERT: F 378 LEU cc_start: 0.8122 (mt) cc_final: 0.7918 (mp) REVERT: F 401 LYS cc_start: 0.8272 (ttpp) cc_final: 0.8038 (ttpp) REVERT: F 408 SER cc_start: 0.8200 (m) cc_final: 0.7877 (p) REVERT: F 454 ASP cc_start: 0.7555 (m-30) cc_final: 0.7343 (m-30) REVERT: G 20 LYS cc_start: 0.8365 (tttt) cc_final: 0.8127 (tttm) REVERT: G 70 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: G 129 ARG cc_start: 0.7449 (ttp-170) cc_final: 0.7148 (ttp-170) REVERT: G 131 GLU cc_start: 0.7687 (tt0) cc_final: 0.7411 (tt0) REVERT: G 156 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7157 (ptt-90) REVERT: G 163 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7407 (mtm-85) REVERT: G 167 ASP cc_start: 0.7551 (m-30) cc_final: 0.7211 (m-30) REVERT: G 177 ILE cc_start: 0.7665 (mt) cc_final: 0.7382 (mt) REVERT: G 192 SER cc_start: 0.7759 (m) cc_final: 0.7329 (p) REVERT: G 197 ASN cc_start: 0.8493 (p0) cc_final: 0.7834 (p0) REVERT: G 206 GLN cc_start: 0.7612 (mt0) cc_final: 0.7342 (mt0) REVERT: G 223 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.7872 (p) REVERT: G 280 ASP cc_start: 0.7637 (t70) cc_final: 0.7284 (t70) REVERT: G 343 VAL cc_start: 0.8417 (p) cc_final: 0.8163 (m) REVERT: G 353 ASN cc_start: 0.7631 (p0) cc_final: 0.7171 (p0) REVERT: G 405 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7937 (mmtt) REVERT: G 454 ASP cc_start: 0.7541 (m-30) cc_final: 0.7327 (m-30) REVERT: H 100 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7873 (p) REVERT: I 7 SER cc_start: 0.8063 (p) cc_final: 0.7758 (t) REVERT: J 7 SER cc_start: 0.7914 (p) cc_final: 0.7644 (t) REVERT: J 71 SER cc_start: 0.8084 (p) cc_final: 0.7831 (m) REVERT: K 50 ILE cc_start: 0.8431 (mm) cc_final: 0.8103 (mm) REVERT: O 27 SER cc_start: 0.8304 (p) cc_final: 0.8058 (t) outliers start: 82 outliers final: 62 residues processed: 558 average time/residue: 0.1554 time to fit residues: 129.9001 Evaluate side-chains 572 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 505 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 GLU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 48 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 250 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 239 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 272 GLN C 455 GLN F 195 GLN F 307 GLN G 139 ASN G 412 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103607 restraints weight = 28419.934| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.89 r_work: 0.3144 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20988 Z= 0.189 Angle : 0.578 8.134 28518 Z= 0.309 Chirality : 0.045 0.213 3261 Planarity : 0.004 0.047 3618 Dihedral : 4.989 39.748 2914 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.26 % Allowed : 15.75 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2643 helix: 0.55 (0.25), residues: 423 sheet: -0.37 (0.17), residues: 930 loop : -0.03 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 248 TYR 0.021 0.002 TYR K 51 PHE 0.017 0.002 PHE J 29 TRP 0.016 0.002 TRP H 50 HIS 0.005 0.001 HIS G 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (20928) covalent geometry : angle 0.57047 / 0.31 (28386) SS BOND : bond 0.00337 / 0.22 ( 48) SS BOND : angle 1.05463 / 0.66 ( 96) hydrogen bonds : bond 0.03814 / 2.45 ( 985) hydrogen bonds : angle 5.67145 / 3.83 ( 2604) link_BETA1-4 : bond 0.00467 / 0.26 ( 6) link_BETA1-4 : angle 1.81147 / 1.16 ( 18) link_NAG-ASN : bond 0.00514 / 0.30 ( 6) link_NAG-ASN : angle 2.75380 / 1.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 498 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8353 (m-80) cc_final: 0.8117 (m-80) REVERT: C 81 LEU cc_start: 0.8240 (tp) cc_final: 0.8021 (tp) REVERT: C 133 GLU cc_start: 0.7501 (tp30) cc_final: 0.7022 (tp30) REVERT: C 144 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7872 (p) REVERT: C 163 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7500 (mtm-85) REVERT: C 166 LYS cc_start: 0.7879 (tttt) cc_final: 0.7645 (tttt) REVERT: C 167 ASP cc_start: 0.7502 (m-30) cc_final: 0.7296 (m-30) REVERT: C 189 MET cc_start: 0.7435 (tpp) cc_final: 0.7117 (tpp) REVERT: C 192 SER cc_start: 0.8167 (t) cc_final: 0.7761 (p) REVERT: C 195 GLN cc_start: 0.8025 (mt0) cc_final: 0.7782 (mt0) REVERT: C 343 VAL cc_start: 0.8428 (p) cc_final: 0.8184 (m) REVERT: C 399 ILE cc_start: 0.8000 (mm) cc_final: 0.7727 (mt) REVERT: C 412 ASN cc_start: 0.7999 (p0) cc_final: 0.7595 (p0) REVERT: C 413 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7899 (mm110) REVERT: E 74 THR cc_start: 0.8121 (m) cc_final: 0.7551 (p) REVERT: F 62 ASP cc_start: 0.7641 (m-30) cc_final: 0.7135 (m-30) REVERT: F 131 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: F 133 GLU cc_start: 0.7470 (tp30) cc_final: 0.6827 (tp30) REVERT: F 163 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7373 (mtm-85) REVERT: F 175 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7384 (ttp-170) REVERT: F 189 MET cc_start: 0.7323 (mmt) cc_final: 0.6752 (mmt) REVERT: F 206 GLN cc_start: 0.7477 (mt0) cc_final: 0.7158 (mt0) REVERT: F 250 MET cc_start: 0.6984 (mmm) cc_final: 0.6659 (tmm) REVERT: F 294 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7238 (mt-10) REVERT: F 343 VAL cc_start: 0.8375 (p) cc_final: 0.8040 (m) REVERT: F 378 LEU cc_start: 0.8133 (mt) cc_final: 0.7817 (mp) REVERT: F 401 LYS cc_start: 0.8244 (ttpp) cc_final: 0.8021 (ttpp) REVERT: F 408 SER cc_start: 0.8204 (m) cc_final: 0.7870 (p) REVERT: G 20 LYS cc_start: 0.8352 (tttt) cc_final: 0.8124 (tttm) REVERT: G 70 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6645 (mp0) REVERT: G 131 GLU cc_start: 0.7700 (tt0) cc_final: 0.7341 (tt0) REVERT: G 156 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7039 (ptt-90) REVERT: G 163 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7201 (mtm-85) REVERT: G 167 ASP cc_start: 0.7522 (m-30) cc_final: 0.7143 (m-30) REVERT: G 177 ILE cc_start: 0.7630 (mt) cc_final: 0.7353 (mt) REVERT: G 178 ASN cc_start: 0.7927 (t0) cc_final: 0.7721 (t0) REVERT: G 192 SER cc_start: 0.7732 (m) cc_final: 0.7262 (p) REVERT: G 197 ASN cc_start: 0.8530 (p0) cc_final: 0.7836 (p0) REVERT: G 206 GLN cc_start: 0.7585 (mt0) cc_final: 0.7297 (mt0) REVERT: G 223 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.7890 (p) REVERT: G 248 ARG cc_start: 0.7463 (ttm110) cc_final: 0.7218 (mtp85) REVERT: G 280 ASP cc_start: 0.7620 (t70) cc_final: 0.7246 (t70) REVERT: G 343 VAL cc_start: 0.8415 (p) cc_final: 0.8177 (m) REVERT: G 353 ASN cc_start: 0.7620 (p0) cc_final: 0.7173 (p0) REVERT: G 405 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7946 (mmtt) REVERT: G 454 ASP cc_start: 0.7539 (m-30) cc_final: 0.7318 (m-30) REVERT: H 100 SER cc_start: 0.8102 (OUTLIER) cc_final: 0.7884 (p) REVERT: I 7 SER cc_start: 0.8041 (p) cc_final: 0.7742 (t) REVERT: J 71 SER cc_start: 0.8062 (p) cc_final: 0.7814 (m) REVERT: K 50 ILE cc_start: 0.8374 (mm) cc_final: 0.8025 (mm) REVERT: O 27 SER cc_start: 0.8294 (p) cc_final: 0.8060 (t) outliers start: 73 outliers final: 52 residues processed: 536 average time/residue: 0.1594 time to fit residues: 127.6143 Evaluate side-chains 555 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 497 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 107 optimal weight: 1.9990 chunk 249 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 123 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 196 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 195 GLN G 46 ASN G 139 ASN G 413 GLN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** M 28 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 = 0.3454 r_free = 0.3454 target = 0.117215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104215 restraints weight = 28334.392| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.89 r_work: 0.3152 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20988 Z= 0.164 Angle : 0.562 8.016 28518 Z= 0.300 Chirality : 0.044 0.205 3261 Planarity : 0.004 0.041 3618 Dihedral : 4.854 38.499 2914 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.95 % Allowed : 16.42 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2643 helix: 0.81 (0.25), residues: 420 sheet: -0.34 (0.17), residues: 930 loop : -0.00 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 253 TYR 0.019 0.002 TYR K 51 PHE 0.016 0.002 PHE J 29 TRP 0.016 0.002 TRP H 50 HIS 0.005 0.001 HIS G 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (20928) covalent geometry : angle 0.55337 / 0.30 (28386) SS BOND : bond 0.00349 / 0.23 ( 48) SS BOND : angle 0.95581 / 0.61 ( 96) hydrogen bonds : bond 0.03667 / 2.36 ( 985) hydrogen bonds : angle 5.57475 / 3.76 ( 2604) link_BETA1-4 : bond 0.00408 / 0.22 ( 6) link_BETA1-4 : angle 1.81411 / 1.16 ( 18) link_NAG-ASN : bond 0.00446 / 0.22 ( 6) link_NAG-ASN : angle 2.97361 / 1.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 504 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8354 (m-80) cc_final: 0.8113 (m-80) REVERT: C 81 LEU cc_start: 0.8202 (tp) cc_final: 0.7988 (tp) REVERT: C 126 LYS cc_start: 0.7617 (mttm) cc_final: 0.7412 (mttm) REVERT: C 133 GLU cc_start: 0.7480 (tp30) cc_final: 0.7006 (tp30) REVERT: C 163 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7521 (mtm-85) REVERT: C 166 LYS cc_start: 0.7873 (tttt) cc_final: 0.7648 (tttt) REVERT: C 167 ASP cc_start: 0.7485 (m-30) cc_final: 0.7258 (m-30) REVERT: C 189 MET cc_start: 0.7424 (tpp) cc_final: 0.7114 (tpp) REVERT: C 192 SER cc_start: 0.8152 (t) cc_final: 0.7731 (p) REVERT: C 195 GLN cc_start: 0.8005 (mt0) cc_final: 0.7759 (mt0) REVERT: C 248 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7372 (mtp180) REVERT: C 343 VAL cc_start: 0.8426 (p) cc_final: 0.8195 (m) REVERT: C 413 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7825 (mm110) REVERT: E 74 THR cc_start: 0.8113 (m) cc_final: 0.7550 (p) REVERT: F 62 ASP cc_start: 0.7649 (m-30) cc_final: 0.7148 (m-30) REVERT: F 131 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: F 133 GLU cc_start: 0.7454 (tp30) cc_final: 0.6764 (tp30) REVERT: F 163 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7386 (mtm-85) REVERT: F 171 LYS cc_start: 0.7627 (mttm) cc_final: 0.7310 (mttm) REVERT: F 175 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7399 (ttp-170) REVERT: F 178 ASN cc_start: 0.7989 (t0) cc_final: 0.7660 (t0) REVERT: F 189 MET cc_start: 0.7304 (mmt) cc_final: 0.6743 (mmt) REVERT: F 206 GLN cc_start: 0.7456 (mt0) cc_final: 0.7151 (mt0) REVERT: F 250 MET cc_start: 0.7008 (mmm) cc_final: 0.6670 (tmm) REVERT: F 294 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7240 (mt-10) REVERT: F 343 VAL cc_start: 0.8376 (p) cc_final: 0.8036 (m) REVERT: F 401 LYS cc_start: 0.8246 (ttpp) cc_final: 0.8032 (ttpp) REVERT: F 408 SER cc_start: 0.8238 (m) cc_final: 0.7924 (p) REVERT: F 454 ASP cc_start: 0.7555 (m-30) cc_final: 0.7352 (m-30) REVERT: G 20 LYS cc_start: 0.8337 (tttt) cc_final: 0.8099 (tttm) REVERT: G 70 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6632 (mp0) REVERT: G 129 ARG cc_start: 0.7431 (ttp-170) cc_final: 0.7204 (ttp-170) REVERT: G 131 GLU cc_start: 0.7693 (tt0) cc_final: 0.7364 (tt0) REVERT: G 156 ARG cc_start: 0.7451 (ptm-80) cc_final: 0.7053 (ptt-90) REVERT: G 163 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7165 (mtm-85) REVERT: G 167 ASP cc_start: 0.7516 (m-30) cc_final: 0.7112 (m-30) REVERT: G 177 ILE cc_start: 0.7593 (mt) cc_final: 0.7338 (mt) REVERT: G 178 ASN cc_start: 0.7942 (t0) cc_final: 0.7732 (t0) REVERT: G 192 SER cc_start: 0.7705 (m) cc_final: 0.7200 (p) REVERT: G 206 GLN cc_start: 0.7567 (mt0) cc_final: 0.7269 (mt0) REVERT: G 223 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.7873 (p) REVERT: G 244 MET cc_start: 0.7427 (mtm) cc_final: 0.7217 (mtm) REVERT: G 248 ARG cc_start: 0.7479 (ttm110) cc_final: 0.7208 (mtp85) REVERT: G 280 ASP cc_start: 0.7617 (t70) cc_final: 0.7242 (t70) REVERT: G 343 VAL cc_start: 0.8396 (p) cc_final: 0.8162 (m) REVERT: G 353 ASN cc_start: 0.7623 (p0) cc_final: 0.7179 (p0) REVERT: G 405 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7947 (mmtt) REVERT: G 454 ASP cc_start: 0.7543 (m-30) cc_final: 0.7313 (m-30) REVERT: J 71 SER cc_start: 0.8050 (p) cc_final: 0.7804 (m) REVERT: J 85 SER cc_start: 0.8433 (m) cc_final: 0.7768 (t) REVERT: K 50 ILE cc_start: 0.8353 (mm) cc_final: 0.8069 (mm) outliers start: 66 outliers final: 52 residues processed: 540 average time/residue: 0.1603 time to fit residues: 128.8022 Evaluate side-chains 550 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 495 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 GLU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 182 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 195 GLN G 412 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104379 restraints weight = 28110.259| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.78 r_work: 0.3168 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20988 Z= 0.274 Angle : 0.626 8.398 28518 Z= 0.335 Chirality : 0.047 0.216 3261 Planarity : 0.005 0.047 3618 Dihedral : 5.081 41.006 2914 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.99 % Allowed : 16.87 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.16), residues: 2643 helix: 0.70 (0.25), residues: 402 sheet: -0.40 (0.17), residues: 921 loop : -0.13 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 253 TYR 0.030 0.003 TYR K 51 PHE 0.023 0.002 PHE J 29 TRP 0.019 0.002 TRP O 37 HIS 0.006 0.002 HIS G 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.27 (20928) covalent geometry : angle 0.61680 / 0.33 (28386) SS BOND : bond 0.00423 / 0.28 ( 48) SS BOND : angle 1.20726 / 0.78 ( 96) hydrogen bonds : bond 0.04140 / 2.67 ( 985) hydrogen bonds : angle 5.75802 / 3.88 ( 2604) link_BETA1-4 : bond 0.00449 / 0.23 ( 6) link_BETA1-4 : angle 1.84247 / 1.18 ( 18) link_NAG-ASN : bond 0.00353 / 0.18 ( 6) link_NAG-ASN : angle 3.05224 / 1.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 519 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.7314 (mtt90) REVERT: C 81 LEU cc_start: 0.8278 (tp) cc_final: 0.8041 (tp) REVERT: C 110 CYS cc_start: 0.6454 (OUTLIER) cc_final: 0.6176 (m) REVERT: C 144 THR cc_start: 0.8147 (t) cc_final: 0.7845 (p) REVERT: C 163 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7498 (mtm-85) REVERT: C 166 LYS cc_start: 0.7855 (tttt) cc_final: 0.7620 (tttt) REVERT: C 167 ASP cc_start: 0.7481 (m-30) cc_final: 0.7258 (m-30) REVERT: C 189 MET cc_start: 0.7428 (tpp) cc_final: 0.7126 (tpp) REVERT: C 192 SER cc_start: 0.8207 (t) cc_final: 0.7759 (p) REVERT: C 195 GLN cc_start: 0.8009 (mt0) cc_final: 0.7765 (mt0) REVERT: C 248 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7392 (mtp180) REVERT: C 343 VAL cc_start: 0.8398 (p) cc_final: 0.8183 (m) REVERT: C 412 ASN cc_start: 0.7943 (p0) cc_final: 0.7597 (p0) REVERT: C 413 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7914 (mm110) REVERT: E 74 THR cc_start: 0.8119 (m) cc_final: 0.7612 (p) REVERT: F 133 GLU cc_start: 0.7460 (tp30) cc_final: 0.6810 (tp30) REVERT: F 163 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7351 (mtm-85) REVERT: F 171 LYS cc_start: 0.7629 (mttm) cc_final: 0.7413 (mttm) REVERT: F 175 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.7361 (ttp-170) REVERT: F 178 ASN cc_start: 0.7957 (t0) cc_final: 0.7640 (t0) REVERT: F 189 MET cc_start: 0.7318 (mmt) cc_final: 0.6733 (mmt) REVERT: F 206 GLN cc_start: 0.7507 (mt0) cc_final: 0.7241 (mt0) REVERT: F 280 ASP cc_start: 0.7969 (t70) cc_final: 0.7609 (t70) REVERT: F 294 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7189 (mt-10) REVERT: F 343 VAL cc_start: 0.8398 (p) cc_final: 0.8077 (m) REVERT: F 408 SER cc_start: 0.8218 (m) cc_final: 0.7934 (p) REVERT: G 20 LYS cc_start: 0.8238 (tttt) cc_final: 0.8025 (tttm) REVERT: G 70 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: G 129 ARG cc_start: 0.7466 (ttp-170) cc_final: 0.7151 (ttp-170) REVERT: G 131 GLU cc_start: 0.7659 (tt0) cc_final: 0.7376 (tt0) REVERT: G 156 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7145 (ptt-90) REVERT: G 163 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7262 (mtm-85) REVERT: G 167 ASP cc_start: 0.7489 (m-30) cc_final: 0.7093 (m-30) REVERT: G 177 ILE cc_start: 0.7622 (mt) cc_final: 0.7324 (mt) REVERT: G 178 ASN cc_start: 0.7946 (t0) cc_final: 0.7734 (t0) REVERT: G 192 SER cc_start: 0.7753 (m) cc_final: 0.7321 (p) REVERT: G 197 ASN cc_start: 0.8512 (p0) cc_final: 0.7876 (p0) REVERT: G 223 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.7886 (p) REVERT: G 280 ASP cc_start: 0.7614 (t70) cc_final: 0.7261 (t70) REVERT: G 343 VAL cc_start: 0.8415 (p) cc_final: 0.8196 (m) REVERT: G 353 ASN cc_start: 0.7595 (p0) cc_final: 0.7160 (p0) REVERT: G 405 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7956 (mmtt) REVERT: G 454 ASP cc_start: 0.7570 (m-30) cc_final: 0.7366 (m-30) REVERT: J 71 SER cc_start: 0.8074 (p) cc_final: 0.7810 (m) REVERT: K 50 ILE cc_start: 0.8420 (mm) cc_final: 0.8089 (mm) REVERT: L 79 GLN cc_start: 0.7721 (mm110) cc_final: 0.7282 (mm110) REVERT: L 102 THR cc_start: 0.8357 (t) cc_final: 0.8109 (p) outliers start: 67 outliers final: 57 residues processed: 553 average time/residue: 0.1756 time to fit residues: 144.0952 Evaluate side-chains 575 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 514 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 GLU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 256 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.0030 chunk 64 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 195 GLN F 312 GLN G 139 ASN G 413 GLN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** M 28 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 = 0.3455 r_free = 0.3455 target = 0.117329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104216 restraints weight = 28284.728| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.91 r_work: 0.3156 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20988 Z= 0.164 Angle : 0.574 9.571 28518 Z= 0.305 Chirality : 0.045 0.201 3261 Planarity : 0.004 0.042 3618 Dihedral : 4.871 38.706 2914 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.68 % Allowed : 17.63 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.17), residues: 2643 helix: 0.99 (0.25), residues: 402 sheet: -0.34 (0.17), residues: 927 loop : -0.02 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 248 TYR 0.019 0.002 TYR G 269 PHE 0.016 0.002 PHE J 29 TRP 0.017 0.002 TRP H 50 HIS 0.004 0.001 HIS G 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (20928) covalent geometry : angle 0.56565 / 0.30 (28386) SS BOND : bond 0.00323 / 0.22 ( 48) SS BOND : angle 0.93856 / 0.61 ( 96) hydrogen bonds : bond 0.03706 / 2.40 ( 985) hydrogen bonds : angle 5.60287 / 3.77 ( 2604) link_BETA1-4 : bond 0.00432 / 0.23 ( 6) link_BETA1-4 : angle 1.78264 / 1.13 ( 18) link_NAG-ASN : bond 0.00527 / 0.34 ( 6) link_NAG-ASN : angle 3.13168 / 1.96 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 504 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 70 GLU cc_start: 0.7158 (tp30) cc_final: 0.6920 (tp30) REVERT: C 81 LEU cc_start: 0.8217 (tp) cc_final: 0.7994 (tp) REVERT: C 133 GLU cc_start: 0.7471 (tp30) cc_final: 0.7000 (tp30) REVERT: C 144 THR cc_start: 0.8138 (t) cc_final: 0.7848 (p) REVERT: C 163 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7477 (mtm-85) REVERT: C 166 LYS cc_start: 0.7868 (tttt) cc_final: 0.7641 (tttt) REVERT: C 167 ASP cc_start: 0.7468 (m-30) cc_final: 0.7236 (m-30) REVERT: C 189 MET cc_start: 0.7424 (tpp) cc_final: 0.7128 (tpp) REVERT: C 192 SER cc_start: 0.8157 (t) cc_final: 0.7733 (p) REVERT: C 248 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7360 (mtp180) REVERT: C 343 VAL cc_start: 0.8411 (p) cc_final: 0.8172 (m) REVERT: C 412 ASN cc_start: 0.7939 (p0) cc_final: 0.7586 (p0) REVERT: C 413 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7891 (mm110) REVERT: E 74 THR cc_start: 0.8186 (m) cc_final: 0.7623 (p) REVERT: F 62 ASP cc_start: 0.7629 (m-30) cc_final: 0.7154 (m-30) REVERT: F 133 GLU cc_start: 0.7451 (tp30) cc_final: 0.6790 (tp30) REVERT: F 163 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7358 (mtm-85) REVERT: F 171 LYS cc_start: 0.7616 (mttm) cc_final: 0.7305 (mttm) REVERT: F 175 ARG cc_start: 0.7805 (ttp-170) cc_final: 0.7397 (ttp-170) REVERT: F 178 ASN cc_start: 0.7958 (t0) cc_final: 0.7632 (t0) REVERT: F 189 MET cc_start: 0.7310 (mmt) cc_final: 0.6732 (mmt) REVERT: F 206 GLN cc_start: 0.7468 (mt0) cc_final: 0.7198 (mt0) REVERT: F 280 ASP cc_start: 0.7946 (t70) cc_final: 0.7595 (t70) REVERT: F 294 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7262 (mt-10) REVERT: F 343 VAL cc_start: 0.8359 (p) cc_final: 0.8028 (m) REVERT: F 401 LYS cc_start: 0.8288 (ttpp) cc_final: 0.8010 (ptmm) REVERT: F 408 SER cc_start: 0.8232 (m) cc_final: 0.7954 (p) REVERT: G 128 ILE cc_start: 0.7503 (mt) cc_final: 0.7135 (mt) REVERT: G 129 ARG cc_start: 0.7482 (ttp-170) cc_final: 0.7118 (ttp-170) REVERT: G 131 GLU cc_start: 0.7699 (tt0) cc_final: 0.7385 (tt0) REVERT: G 156 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7079 (ptt-90) REVERT: G 163 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7231 (mtm-85) REVERT: G 167 ASP cc_start: 0.7564 (m-30) cc_final: 0.7143 (m-30) REVERT: G 177 ILE cc_start: 0.7600 (mt) cc_final: 0.7331 (mt) REVERT: G 178 ASN cc_start: 0.7954 (t0) cc_final: 0.7732 (t0) REVERT: G 192 SER cc_start: 0.7712 (m) cc_final: 0.7241 (p) REVERT: G 197 ASN cc_start: 0.8536 (p0) cc_final: 0.7871 (p0) REVERT: G 206 GLN cc_start: 0.7560 (mt0) cc_final: 0.7315 (mt0) REVERT: G 223 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.7884 (p) REVERT: G 244 MET cc_start: 0.7430 (mtm) cc_final: 0.7221 (mtm) REVERT: G 280 ASP cc_start: 0.7614 (t70) cc_final: 0.7238 (t70) REVERT: G 343 VAL cc_start: 0.8389 (p) cc_final: 0.8167 (m) REVERT: G 353 ASN cc_start: 0.7603 (p0) cc_final: 0.7167 (p0) REVERT: G 405 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7945 (mmtt) REVERT: G 454 ASP cc_start: 0.7572 (m-30) cc_final: 0.7357 (m-30) REVERT: J 71 SER cc_start: 0.8087 (p) cc_final: 0.7814 (m) REVERT: K 50 ILE cc_start: 0.8371 (mm) cc_final: 0.8025 (mm) REVERT: L 79 GLN cc_start: 0.7703 (mm110) cc_final: 0.7254 (mm110) REVERT: L 102 THR cc_start: 0.8336 (t) cc_final: 0.8100 (p) outliers start: 60 outliers final: 54 residues processed: 534 average time/residue: 0.1648 time to fit residues: 130.4621 Evaluate side-chains 560 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 504 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 GLU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 12 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 123 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 GLN F 195 GLN G 139 ASN G 202 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** M 28 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 = 0.3448 r_free = 0.3448 target = 0.116724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103708 restraints weight = 28456.898| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.90 r_work: 0.3148 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20988 Z= 0.191 Angle : 0.580 8.178 28518 Z= 0.309 Chirality : 0.045 0.220 3261 Planarity : 0.004 0.042 3618 Dihedral : 4.870 38.287 2914 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.72 % Allowed : 17.72 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2643 helix: 1.01 (0.25), residues: 402 sheet: -0.34 (0.17), residues: 927 loop : -0.05 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 248 TYR 0.023 0.002 TYR F 385 PHE 0.017 0.002 PHE J 29 TRP 0.016 0.002 TRP H 50 HIS 0.004 0.001 HIS G 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (20928) covalent geometry : angle 0.57088 / 0.31 (28386) SS BOND : bond 0.00389 / 0.27 ( 48) SS BOND : angle 1.15676 / 0.86 ( 96) hydrogen bonds : bond 0.03743 / 2.42 ( 985) hydrogen bonds : angle 5.59045 / 3.76 ( 2604) link_BETA1-4 : bond 0.00407 / 0.22 ( 6) link_BETA1-4 : angle 1.74463 / 1.11 ( 18) link_NAG-ASN : bond 0.00394 / 0.25 ( 6) link_NAG-ASN : angle 3.09095 / 1.94 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5744.63 seconds wall clock time: 99 minutes 3.10 seconds (5943.10 seconds total)