Starting phenix.real_space_refine on Fri Mar 6 04:24:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjq_25929/03_2026/7tjq_25929.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjq_25929/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tjq_25929/03_2026/7tjq_25929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjq_25929/03_2026/7tjq_25929.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjq_25929/03_2026/7tjq_25929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjq_25929/03_2026/7tjq_25929.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.25, per 1000 atoms: 0.21 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: 1.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.99 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: 5.47 Time building geometry restraints manager: 2.30 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: 11873 17.97 - 35.93: 664 35.93 - 53.90: 144 53.90 - 71.87: 63 71.87 - 89.83: 18 Dihedral angle restraints: 12762 sinusoidal: 5082 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 12759 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: 7.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.970 Find NCS groups from input model: 0.350 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 13.284 89.834 7716 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 covalent geometry : bond 0.00432 (20928) covalent geometry : angle 0.77074 (28386) SS BOND : bond 0.00522 ( 48) SS BOND : angle 1.31106 ( 96) hydrogen bonds : bond 0.17746 ( 985) hydrogen bonds : angle 8.25894 ( 2604) link_BETA1-4 : bond 0.00980 ( 6) link_BETA1-4 : angle 3.86069 ( 18) link_NAG-ASN : bond 0.00544 ( 6) link_NAG-ASN : angle 3.23244 ( 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 : 0.724 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: 0.1675 time to fit residues: 153.3949 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 : 0.727 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 206 GLN ** 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 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 = 0.119061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105959 restraints weight = 28195.130| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.89 r_work: 0.3172 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20988 Z= 0.211 Angle : 0.677 8.478 28518 Z= 0.368 Chirality : 0.047 0.221 3261 Planarity : 0.005 0.049 3618 Dihedral : 6.932 59.635 3180 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.19 % Allowed : 10.93 % Favored : 86.88 % 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: 0.43 (0.25), 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 0.007 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 0.007 0.001 HIS G 368 Details of bonding type rmsd covalent geometry : bond 0.00472 (20928) covalent geometry : angle 0.66709 (28386) SS BOND : bond 0.00404 ( 48) SS BOND : angle 1.36646 ( 96) hydrogen bonds : bond 0.05065 ( 985) hydrogen bonds : angle 6.22965 ( 2604) link_BETA1-4 : bond 0.00459 ( 6) link_BETA1-4 : angle 2.55328 ( 18) link_NAG-ASN : bond 0.00653 ( 6) link_NAG-ASN : angle 2.89202 ( 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 589 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 540 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 THR cc_start: 0.7836 (t) cc_final: 0.7474 (t) REVERT: C 70 GLU cc_start: 0.7278 (tp30) cc_final: 0.6842 (tp30) REVERT: C 71 LEU cc_start: 0.7886 (tp) cc_final: 0.7649 (tp) REVERT: C 75 LYS cc_start: 0.8314 (mtpp) cc_final: 0.8102 (mtmm) REVERT: C 79 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7313 (mtm-85) REVERT: C 81 LEU cc_start: 0.8186 (tp) cc_final: 0.7936 (tp) REVERT: C 82 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7867 (mtt90) REVERT: C 133 GLU cc_start: 0.7259 (tp30) cc_final: 0.6776 (tp30) REVERT: C 194 SER cc_start: 0.7645 (p) cc_final: 0.7422 (t) REVERT: C 248 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7508 (mtp85) REVERT: C 343 VAL cc_start: 0.8533 (p) cc_final: 0.8273 (m) REVERT: C 399 ILE cc_start: 0.8063 (mm) cc_final: 0.7811 (mt) REVERT: C 412 ASN cc_start: 0.7983 (p0) cc_final: 0.7734 (p0) REVERT: E 74 THR cc_start: 0.8160 (m) cc_final: 0.7505 (p) REVERT: F 62 ASP cc_start: 0.7831 (m-30) cc_final: 0.7295 (m-30) REVERT: F 133 GLU cc_start: 0.7453 (tp30) cc_final: 0.6789 (tp30) REVERT: F 163 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7332 (mtm-85) REVERT: F 166 LYS cc_start: 0.7822 (ttpt) cc_final: 0.7613 (ttpt) REVERT: F 174 THR cc_start: 0.8376 (m) cc_final: 0.8151 (m) REVERT: F 189 MET cc_start: 0.7483 (mmt) cc_final: 0.6935 (mmt) REVERT: F 192 SER cc_start: 0.7770 (m) cc_final: 0.7238 (p) REVERT: F 205 ARG cc_start: 0.7405 (ttp80) cc_final: 0.6929 (ttp80) REVERT: F 206 GLN cc_start: 0.7513 (mt0) cc_final: 0.7210 (mt0) REVERT: F 245 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7701 (mm) REVERT: F 343 VAL cc_start: 0.8452 (p) cc_final: 0.8097 (m) REVERT: F 408 SER cc_start: 0.8182 (m) cc_final: 0.7804 (p) REVERT: F 464 PHE cc_start: 0.8063 (m-80) cc_final: 0.7789 (m-80) REVERT: G 20 LYS cc_start: 0.8310 (tttt) cc_final: 0.8040 (tttm) REVERT: G 37 SER cc_start: 0.8139 (p) cc_final: 0.7932 (p) REVERT: G 40 ARG cc_start: 0.7903 (tmm160) cc_final: 0.7598 (tmm160) REVERT: G 73 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8222 (mp) REVERT: G 129 ARG cc_start: 0.7596 (ttp-170) cc_final: 0.7146 (ttp-170) REVERT: G 131 GLU cc_start: 0.7742 (tt0) cc_final: 0.7182 (tt0) REVERT: G 163 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7425 (mtm-85) REVERT: G 177 ILE cc_start: 0.7822 (mt) cc_final: 0.7557 (mt) REVERT: G 192 SER cc_start: 0.7744 (m) cc_final: 0.7295 (p) REVERT: G 197 ASN cc_start: 0.8501 (p0) cc_final: 0.7786 (p0) REVERT: G 198 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7168 (ttm-80) REVERT: G 205 ARG cc_start: 0.7374 (ttp80) cc_final: 0.7125 (ttp80) REVERT: G 206 GLN cc_start: 0.7486 (mt0) cc_final: 0.7268 (mt0) REVERT: G 219 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7737 (mmmm) REVERT: G 223 THR cc_start: 0.8378 (m) cc_final: 0.7841 (p) REVERT: G 280 ASP cc_start: 0.7545 (t70) cc_final: 0.7283 (t70) REVERT: G 343 VAL cc_start: 0.8429 (p) cc_final: 0.8082 (m) REVERT: G 353 ASN cc_start: 0.7545 (p0) cc_final: 0.7049 (p0) REVERT: G 413 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8023 (mm-40) REVERT: G 454 ASP cc_start: 0.7482 (m-30) cc_final: 0.7234 (m-30) REVERT: J 7 SER cc_start: 0.7881 (p) cc_final: 0.7674 (t) REVERT: J 28 THR cc_start: 0.8623 (m) cc_final: 0.8117 (p) REVERT: J 71 SER cc_start: 0.8090 (p) cc_final: 0.7864 (m) REVERT: L 79 GLN cc_start: 0.7553 (mm110) cc_final: 0.7234 (mm-40) REVERT: M 27 SER cc_start: 0.8095 (p) cc_final: 0.7825 (p) REVERT: M 98 SER cc_start: 0.8263 (p) cc_final: 0.7998 (m) REVERT: N 52 SER cc_start: 0.8498 (p) cc_final: 0.8268 (t) REVERT: O 27 SER cc_start: 0.8363 (p) cc_final: 0.8019 (t) outliers start: 49 outliers final: 30 residues processed: 562 average time/residue: 0.1609 time to fit residues: 133.2372 Evaluate side-chains 550 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 518 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 129 ARG 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 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 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 73 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 156 ARG 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 K residue 5 THR Chi-restraints excluded: chain M residue 67 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 176 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 39 optimal weight: 0.0980 chunk 107 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN E 92 ASN F 195 GLN F 206 GLN F 272 GLN G 139 ASN G 202 ASN G 346 GLN G 351 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN N 35 ASN O 28 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104246 restraints weight = 28385.550| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.89 r_work: 0.3152 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1918 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= 0.180 Angle : 0.605 9.178 28518 Z= 0.325 Chirality : 0.045 0.189 3261 Planarity : 0.004 0.040 3618 Dihedral : 6.381 59.613 3167 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.50 % Allowed : 12.27 % Favored : 85.23 % 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: -0.03 (0.16), residues: 2643 helix: 0.57 (0.25), residues: 420 sheet: -0.20 (0.16), residues: 954 loop : 0.11 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 329 TYR 0.023 0.002 TYR K 51 PHE 0.018 0.002 PHE J 29 TRP 0.021 0.002 TRP H 50 HIS 0.007 0.001 HIS G 368 Details of bonding type rmsd covalent geometry : bond 0.00401 (20928) covalent geometry : angle 0.59566 (28386) SS BOND : bond 0.00331 ( 48) SS BOND : angle 1.18089 ( 96) hydrogen bonds : bond 0.04259 ( 985) hydrogen bonds : angle 5.84449 ( 2604) link_BETA1-4 : bond 0.00407 ( 6) link_BETA1-4 : angle 2.24612 ( 18) link_NAG-ASN : bond 0.00277 ( 6) link_NAG-ASN : angle 2.68456 ( 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 585 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 529 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8394 (m-80) cc_final: 0.8148 (m-80) REVERT: B 102 THR cc_start: 0.8079 (t) cc_final: 0.7727 (t) REVERT: C 70 GLU cc_start: 0.7199 (tp30) cc_final: 0.6765 (tp30) REVERT: C 71 LEU cc_start: 0.7782 (tp) cc_final: 0.7560 (tp) REVERT: C 81 LEU cc_start: 0.8199 (tp) cc_final: 0.7966 (tp) REVERT: C 133 GLU cc_start: 0.7316 (tp30) cc_final: 0.6868 (tp30) REVERT: C 144 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7784 (p) REVERT: C 163 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7680 (mtm-85) REVERT: C 174 THR cc_start: 0.8316 (m) cc_final: 0.8089 (t) REVERT: C 175 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7517 (ttp-170) REVERT: C 189 MET cc_start: 0.7443 (tpp) cc_final: 0.7081 (mpp) REVERT: C 195 GLN cc_start: 0.8031 (mt0) cc_final: 0.7718 (mt0) REVERT: C 229 ARG cc_start: 0.7386 (mtp85) cc_final: 0.7054 (ttm-80) REVERT: C 233 ASN cc_start: 0.6683 (t0) cc_final: 0.6403 (m110) REVERT: C 245 LEU cc_start: 0.7914 (mt) cc_final: 0.7686 (mm) REVERT: C 248 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7406 (mtp-110) REVERT: C 253 ARG cc_start: 0.7745 (ttp-110) cc_final: 0.7411 (ttm110) REVERT: C 343 VAL cc_start: 0.8518 (p) cc_final: 0.8290 (m) REVERT: C 412 ASN cc_start: 0.7949 (p0) cc_final: 0.7658 (p0) REVERT: D 71 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8127 (pmt-80) REVERT: E 74 THR cc_start: 0.8101 (m) cc_final: 0.7460 (p) REVERT: F 62 ASP cc_start: 0.7780 (m-30) cc_final: 0.7275 (m-30) REVERT: F 133 GLU cc_start: 0.7446 (tp30) cc_final: 0.6786 (tp30) REVERT: F 163 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7438 (mtm-85) REVERT: F 166 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7555 (ttpt) REVERT: F 175 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7350 (ttp-170) REVERT: F 189 MET cc_start: 0.7388 (mmt) cc_final: 0.6952 (mmt) REVERT: F 343 VAL cc_start: 0.8449 (p) cc_final: 0.8105 (m) REVERT: F 401 LYS cc_start: 0.8253 (ttpp) cc_final: 0.8014 (ttpp) REVERT: F 408 SER cc_start: 0.8218 (m) cc_final: 0.7893 (t) REVERT: G 20 LYS cc_start: 0.8376 (tttt) cc_final: 0.8092 (tttp) REVERT: G 70 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6715 (mp0) REVERT: G 75 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7872 (mtpt) REVERT: G 131 GLU cc_start: 0.7732 (tt0) cc_final: 0.7201 (tt0) REVERT: G 163 ARG cc_start: 0.7698 (ttm-80) cc_final: 0.7366 (mtm-85) REVERT: G 177 ILE cc_start: 0.7787 (mt) cc_final: 0.7546 (mt) REVERT: G 178 ASN cc_start: 0.7885 (t0) cc_final: 0.7661 (t0) REVERT: G 192 SER cc_start: 0.7740 (m) cc_final: 0.7290 (p) REVERT: G 197 ASN cc_start: 0.8482 (p0) cc_final: 0.7813 (p0) REVERT: G 198 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7243 (ttm-80) REVERT: G 205 ARG cc_start: 0.7381 (ttp80) cc_final: 0.7170 (ttp80) REVERT: G 223 THR cc_start: 0.8413 (m) cc_final: 0.7909 (p) REVERT: G 280 ASP cc_start: 0.7593 (t70) cc_final: 0.7279 (t70) REVERT: G 329 ARG cc_start: 0.7835 (ttm110) cc_final: 0.7458 (ttm-80) REVERT: G 343 VAL cc_start: 0.8427 (p) cc_final: 0.8130 (m) REVERT: G 353 ASN cc_start: 0.7676 (p0) cc_final: 0.7157 (p0) REVERT: G 454 ASP cc_start: 0.7438 (m-30) cc_final: 0.7192 (m-30) REVERT: G 464 PHE cc_start: 0.8110 (m-80) cc_final: 0.7707 (m-80) REVERT: J 7 SER cc_start: 0.7861 (p) cc_final: 0.7627 (t) REVERT: J 71 SER cc_start: 0.8078 (p) cc_final: 0.7839 (m) REVERT: J 85 SER cc_start: 0.8510 (m) cc_final: 0.7845 (t) REVERT: K 50 ILE cc_start: 0.8368 (mm) cc_final: 0.8081 (mm) REVERT: L 79 GLN cc_start: 0.7583 (mm110) cc_final: 0.7242 (mm-40) REVERT: M 27 SER cc_start: 0.8086 (p) cc_final: 0.7839 (p) REVERT: M 98 SER cc_start: 0.8226 (p) cc_final: 0.7972 (m) REVERT: N 31 SER cc_start: 0.8167 (m) cc_final: 0.7927 (p) REVERT: O 27 SER cc_start: 0.8331 (p) cc_final: 0.8036 (t) outliers start: 56 outliers final: 38 residues processed: 561 average time/residue: 0.1608 time to fit residues: 133.7805 Evaluate side-chains 559 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 518 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 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 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 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 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 155 VAL Chi-restraints excluded: chain G residue 156 ARG 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 K residue 5 THR 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 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: 0.9990 chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN F 195 GLN F 206 GLN F 422 ASN G 139 ASN G 412 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103960 restraints weight = 28364.020| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.90 r_work: 0.3146 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2233 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 : 0.592 9.054 28518 Z= 0.319 Chirality : 0.045 0.170 3261 Planarity : 0.004 0.041 3618 Dihedral : 6.227 59.928 3167 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.81 % Allowed : 13.39 % Favored : 83.80 % 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: -0.04 (0.16), residues: 2643 helix: 0.57 (0.25), residues: 420 sheet: -0.21 (0.16), residues: 954 loop : 0.10 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 40 TYR 0.025 0.002 TYR L 49 PHE 0.022 0.002 PHE J 29 TRP 0.018 0.002 TRP H 50 HIS 0.006 0.001 HIS G 368 Details of bonding type rmsd covalent geometry : bond 0.00448 (20928) covalent geometry : angle 0.58472 (28386) SS BOND : bond 0.00325 ( 48) SS BOND : angle 1.12022 ( 96) hydrogen bonds : bond 0.04063 ( 985) hydrogen bonds : angle 5.71710 ( 2604) link_BETA1-4 : bond 0.00409 ( 6) link_BETA1-4 : angle 2.10913 ( 18) link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 2.41790 ( 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 586 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 523 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8399 (m-80) cc_final: 0.8125 (m-80) REVERT: B 102 THR cc_start: 0.8173 (t) cc_final: 0.7799 (t) REVERT: C 70 GLU cc_start: 0.7184 (tp30) cc_final: 0.6755 (tp30) REVERT: C 81 LEU cc_start: 0.8241 (tp) cc_final: 0.8010 (tp) REVERT: C 126 LYS cc_start: 0.7744 (mtpp) cc_final: 0.7447 (mttm) REVERT: C 133 GLU cc_start: 0.7385 (tp30) cc_final: 0.6919 (tp30) REVERT: C 144 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7792 (p) REVERT: C 163 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7615 (mtm-85) REVERT: C 166 LYS cc_start: 0.7952 (tttt) cc_final: 0.7723 (tttt) REVERT: C 175 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7472 (ttp-170) REVERT: C 188 LYS cc_start: 0.7476 (tmmm) cc_final: 0.6946 (tmmm) REVERT: C 189 MET cc_start: 0.7448 (tpp) cc_final: 0.6899 (tpp) REVERT: C 192 SER cc_start: 0.8206 (t) cc_final: 0.7769 (p) REVERT: C 195 GLN cc_start: 0.8029 (mt0) cc_final: 0.7808 (mt0) REVERT: C 248 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7541 (mtm180) REVERT: C 250 MET cc_start: 0.6539 (tpp) cc_final: 0.6282 (mmm) REVERT: C 305 GLU cc_start: 0.7468 (tp30) cc_final: 0.6997 (mp0) REVERT: C 343 VAL cc_start: 0.8502 (p) cc_final: 0.8274 (m) REVERT: D 71 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8113 (pmt-80) REVERT: E 74 THR cc_start: 0.8125 (m) cc_final: 0.7529 (p) REVERT: F 62 ASP cc_start: 0.7748 (m-30) cc_final: 0.7225 (m-30) REVERT: F 129 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7095 (mtm110) REVERT: F 133 GLU cc_start: 0.7462 (tp30) cc_final: 0.6783 (tp30) REVERT: F 144 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7901 (t) REVERT: F 163 ARG cc_start: 0.7827 (ttm-80) cc_final: 0.7454 (mtm-85) REVERT: F 166 LYS cc_start: 0.7866 (ttpt) cc_final: 0.7532 (ttpt) REVERT: F 175 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7378 (ttp-170) REVERT: F 189 MET cc_start: 0.7330 (mmt) cc_final: 0.6873 (mmt) REVERT: F 206 GLN cc_start: 0.7391 (mt0) cc_final: 0.7096 (mt0) REVERT: F 250 MET cc_start: 0.6827 (mmm) cc_final: 0.6607 (tmm) REVERT: F 252 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7841 (ttm-80) REVERT: F 343 VAL cc_start: 0.8436 (p) cc_final: 0.8084 (m) REVERT: F 401 LYS cc_start: 0.8293 (ttpp) cc_final: 0.8053 (ttpp) REVERT: F 408 SER cc_start: 0.8195 (m) cc_final: 0.7899 (t) REVERT: F 412 ASN cc_start: 0.8276 (p0) cc_final: 0.8045 (p0) REVERT: F 449 VAL cc_start: 0.8411 (p) cc_final: 0.8190 (m) REVERT: G 20 LYS cc_start: 0.8375 (tttt) cc_final: 0.8128 (tttm) REVERT: G 40 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7735 (ttp80) REVERT: G 70 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: G 131 GLU cc_start: 0.7670 (tt0) cc_final: 0.7249 (tt0) REVERT: G 163 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7378 (mtm-85) REVERT: G 167 ASP cc_start: 0.7503 (m-30) cc_final: 0.7192 (m-30) REVERT: G 177 ILE cc_start: 0.7738 (mt) cc_final: 0.7466 (mt) REVERT: G 192 SER cc_start: 0.7723 (m) cc_final: 0.7263 (p) REVERT: G 197 ASN cc_start: 0.8483 (p0) cc_final: 0.7815 (p0) REVERT: G 198 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7302 (ttm-80) REVERT: G 280 ASP cc_start: 0.7610 (t70) cc_final: 0.7243 (t70) REVERT: G 329 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7609 (mtp85) REVERT: G 343 VAL cc_start: 0.8435 (p) cc_final: 0.8168 (m) REVERT: G 353 ASN cc_start: 0.7704 (p0) cc_final: 0.7244 (p0) REVERT: G 405 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7958 (mmtt) REVERT: G 454 ASP cc_start: 0.7433 (m-30) cc_final: 0.7179 (m-30) REVERT: G 464 PHE cc_start: 0.8079 (m-80) cc_final: 0.7729 (m-80) REVERT: H 100 SER cc_start: 0.8069 (OUTLIER) cc_final: 0.7855 (p) REVERT: J 7 SER cc_start: 0.7867 (p) cc_final: 0.7606 (t) REVERT: J 28 THR cc_start: 0.8582 (m) cc_final: 0.7855 (p) REVERT: J 31 SER cc_start: 0.8145 (m) cc_final: 0.7911 (p) REVERT: J 71 SER cc_start: 0.8081 (p) cc_final: 0.7828 (m) REVERT: K 50 ILE cc_start: 0.8381 (mm) cc_final: 0.8052 (mm) REVERT: M 27 SER cc_start: 0.8066 (p) cc_final: 0.7802 (t) REVERT: M 98 SER cc_start: 0.8255 (p) cc_final: 0.7992 (m) REVERT: N 31 SER cc_start: 0.8203 (m) cc_final: 0.8001 (p) REVERT: N 49 SER cc_start: 0.8685 (p) cc_final: 0.8467 (p) REVERT: O 27 SER cc_start: 0.8306 (p) cc_final: 0.8058 (t) outliers start: 63 outliers final: 45 residues processed: 554 average time/residue: 0.1669 time to fit residues: 138.4940 Evaluate side-chains 561 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 510 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 33 GLU 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 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 129 ARG Chi-restraints excluded: chain F residue 144 THR 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 26 GLU 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 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 L residue 92 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 161 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 234 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN C 422 ASN F 195 GLN F 307 GLN G 139 ASN G 247 ASN G 412 ASN G 413 GLN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** O 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.102427 restraints weight = 28495.280| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.91 r_work: 0.3129 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20988 Z= 0.224 Angle : 0.596 8.677 28518 Z= 0.319 Chirality : 0.046 0.204 3261 Planarity : 0.004 0.042 3618 Dihedral : 6.158 59.887 3166 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.08 % Allowed : 14.59 % Favored : 82.33 % 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: 0.52 (0.25), residues: 420 sheet: -0.26 (0.16), residues: 954 loop : 0.08 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 329 TYR 0.026 0.002 TYR K 51 PHE 0.019 0.002 PHE J 29 TRP 0.017 0.002 TRP O 37 HIS 0.006 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00507 (20928) covalent geometry : angle 0.58813 (28386) SS BOND : bond 0.00352 ( 48) SS BOND : angle 1.08661 ( 96) hydrogen bonds : bond 0.04018 ( 985) hydrogen bonds : angle 5.69662 ( 2604) link_BETA1-4 : bond 0.00359 ( 6) link_BETA1-4 : angle 2.12435 ( 18) link_NAG-ASN : bond 0.00245 ( 6) link_NAG-ASN : angle 2.40182 ( 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 580 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 511 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8374 (m-80) cc_final: 0.8115 (m-80) REVERT: C 70 GLU cc_start: 0.7226 (tp30) cc_final: 0.6926 (tp30) REVERT: C 81 LEU cc_start: 0.8258 (tp) cc_final: 0.8036 (tp) REVERT: C 126 LYS cc_start: 0.7681 (mtpp) cc_final: 0.7352 (mttm) REVERT: C 133 GLU cc_start: 0.7399 (tp30) cc_final: 0.6929 (tp30) REVERT: C 166 LYS cc_start: 0.7941 (tttt) cc_final: 0.7716 (tttt) REVERT: C 188 LYS cc_start: 0.7483 (tmmm) cc_final: 0.6921 (tmmm) REVERT: C 189 MET cc_start: 0.7453 (tpp) cc_final: 0.6911 (tpp) REVERT: C 192 SER cc_start: 0.8179 (t) cc_final: 0.7765 (p) REVERT: C 195 GLN cc_start: 0.8047 (mt0) cc_final: 0.7772 (mt0) REVERT: C 248 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7631 (mtp85) REVERT: C 305 GLU cc_start: 0.7450 (tp30) cc_final: 0.6969 (mp0) REVERT: C 343 VAL cc_start: 0.8466 (p) cc_final: 0.8244 (m) REVERT: D 71 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8035 (pmt-80) REVERT: E 74 THR cc_start: 0.8116 (m) cc_final: 0.7527 (p) REVERT: F 62 ASP cc_start: 0.7749 (m-30) cc_final: 0.7213 (m-30) REVERT: F 129 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7151 (mtm110) REVERT: F 133 GLU cc_start: 0.7495 (tp30) cc_final: 0.6841 (tp30) REVERT: F 175 ARG cc_start: 0.7807 (ttp-170) cc_final: 0.7483 (ttp-170) REVERT: F 189 MET cc_start: 0.7326 (mmt) cc_final: 0.6868 (mmt) REVERT: F 197 ASN cc_start: 0.8353 (p0) cc_final: 0.7787 (p0) REVERT: F 206 GLN cc_start: 0.7418 (mt0) cc_final: 0.7190 (mt0) REVERT: F 250 MET cc_start: 0.6875 (mmm) cc_final: 0.6634 (tmm) REVERT: F 343 VAL cc_start: 0.8413 (p) cc_final: 0.8052 (m) REVERT: F 401 LYS cc_start: 0.8281 (ttpp) cc_final: 0.8048 (ttpp) REVERT: F 408 SER cc_start: 0.8195 (m) cc_final: 0.7922 (t) REVERT: G 20 LYS cc_start: 0.8350 (tttt) cc_final: 0.8119 (tttm) REVERT: G 70 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: G 126 LYS cc_start: 0.7564 (mmtp) cc_final: 0.7080 (mmmm) REVERT: G 129 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6980 (ptp-170) REVERT: G 131 GLU cc_start: 0.7674 (tt0) cc_final: 0.7328 (tt0) REVERT: G 156 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7093 (ptt-90) REVERT: G 163 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7075 (mtm-85) REVERT: G 167 ASP cc_start: 0.7548 (m-30) cc_final: 0.7230 (m-30) REVERT: G 177 ILE cc_start: 0.7702 (mt) cc_final: 0.7416 (mt) REVERT: G 192 SER cc_start: 0.7736 (m) cc_final: 0.7289 (p) REVERT: G 197 ASN cc_start: 0.8500 (p0) cc_final: 0.7834 (p0) REVERT: G 280 ASP cc_start: 0.7641 (t70) cc_final: 0.7277 (t70) REVERT: G 327 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7184 (mt-10) REVERT: G 329 ARG cc_start: 0.7949 (ttm110) cc_final: 0.7663 (mtp85) REVERT: G 343 VAL cc_start: 0.8430 (p) cc_final: 0.8171 (m) REVERT: G 353 ASN cc_start: 0.7699 (p0) cc_final: 0.7228 (p0) REVERT: G 405 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7943 (mmtt) REVERT: G 454 ASP cc_start: 0.7487 (m-30) cc_final: 0.7256 (m-30) REVERT: G 464 PHE cc_start: 0.8078 (m-80) cc_final: 0.7726 (m-80) REVERT: H 100 SER cc_start: 0.8098 (OUTLIER) cc_final: 0.7879 (p) REVERT: I 7 SER cc_start: 0.8058 (p) cc_final: 0.7762 (t) REVERT: J 7 SER cc_start: 0.7895 (p) cc_final: 0.7639 (t) REVERT: J 71 SER cc_start: 0.8086 (p) cc_final: 0.7828 (m) REVERT: K 50 ILE cc_start: 0.8400 (mm) cc_final: 0.8068 (mm) REVERT: M 98 SER cc_start: 0.8250 (p) cc_final: 0.8020 (m) REVERT: O 27 SER cc_start: 0.8287 (p) cc_final: 0.8063 (t) outliers start: 69 outliers final: 51 residues processed: 545 average time/residue: 0.1569 time to fit residues: 127.2667 Evaluate side-chains 550 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 493 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 33 GLU 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 327 GLU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 71 ARG 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 84 VAL Chi-restraints excluded: chain F residue 129 ARG 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 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 133 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 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 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: 0.9980 chunk 168 optimal weight: 0.0670 chunk 44 optimal weight: 0.1980 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: 0.9980 chunk 153 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN F 195 GLN F 233 ASN F 307 GLN F 351 ASN G 139 ASN G 247 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102656 restraints weight = 28405.187| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.92 r_work: 0.3148 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20988 Z= 0.167 Angle : 0.566 8.269 28518 Z= 0.302 Chirality : 0.045 0.235 3261 Planarity : 0.004 0.040 3618 Dihedral : 6.045 59.945 3166 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.86 % Allowed : 15.31 % Favored : 81.84 % 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: -0.00 (0.16), residues: 2643 helix: 0.67 (0.25), residues: 423 sheet: -0.24 (0.16), residues: 954 loop : 0.14 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 329 TYR 0.020 0.002 TYR K 51 PHE 0.018 0.002 PHE J 29 TRP 0.015 0.002 TRP H 50 HIS 0.005 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00372 (20928) covalent geometry : angle 0.55853 (28386) SS BOND : bond 0.00307 ( 48) SS BOND : angle 0.94403 ( 96) hydrogen bonds : bond 0.03750 ( 985) hydrogen bonds : angle 5.56657 ( 2604) link_BETA1-4 : bond 0.00711 ( 6) link_BETA1-4 : angle 2.47769 ( 18) link_NAG-ASN : bond 0.00909 ( 6) link_NAG-ASN : angle 2.34606 ( 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 577 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 513 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8372 (m-80) cc_final: 0.8102 (m-80) REVERT: C 70 GLU cc_start: 0.7151 (tp30) cc_final: 0.6876 (tp30) REVERT: C 81 LEU cc_start: 0.8217 (tp) cc_final: 0.7988 (tp) REVERT: C 166 LYS cc_start: 0.7965 (tttt) cc_final: 0.7755 (tttt) REVERT: C 175 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.7676 (ttp-170) REVERT: C 188 LYS cc_start: 0.7464 (tmmm) cc_final: 0.6906 (tmmm) REVERT: C 189 MET cc_start: 0.7434 (tpp) cc_final: 0.6888 (tpp) REVERT: C 192 SER cc_start: 0.8146 (t) cc_final: 0.7746 (p) REVERT: C 195 GLN cc_start: 0.8037 (mt0) cc_final: 0.7768 (mt0) REVERT: C 248 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7597 (mtp85) REVERT: C 305 GLU cc_start: 0.7449 (tp30) cc_final: 0.6957 (mp0) REVERT: C 343 VAL cc_start: 0.8455 (p) cc_final: 0.8222 (m) REVERT: E 74 THR cc_start: 0.8115 (m) cc_final: 0.7538 (p) REVERT: F 62 ASP cc_start: 0.7728 (m-30) cc_final: 0.7198 (m-30) REVERT: F 126 LYS cc_start: 0.7753 (mmtp) cc_final: 0.7551 (mmmm) REVERT: F 133 GLU cc_start: 0.7467 (tp30) cc_final: 0.6827 (tp30) REVERT: F 163 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7379 (mtm-85) REVERT: F 175 ARG cc_start: 0.7792 (ttp-170) cc_final: 0.7469 (ttp-170) REVERT: F 189 MET cc_start: 0.7310 (mmt) cc_final: 0.6821 (mmt) REVERT: F 206 GLN cc_start: 0.7404 (mt0) cc_final: 0.7163 (mt0) REVERT: F 250 MET cc_start: 0.6910 (mmm) cc_final: 0.6615 (tmm) REVERT: F 294 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7243 (mt-10) REVERT: F 343 VAL cc_start: 0.8393 (p) cc_final: 0.8044 (m) REVERT: F 397 VAL cc_start: 0.7753 (t) cc_final: 0.7435 (m) REVERT: F 401 LYS cc_start: 0.8300 (ttpp) cc_final: 0.8079 (ttpp) REVERT: F 408 SER cc_start: 0.8208 (m) cc_final: 0.7875 (p) REVERT: G 20 LYS cc_start: 0.8361 (tttt) cc_final: 0.8121 (tttm) REVERT: G 21 GLU cc_start: 0.7407 (tt0) cc_final: 0.7204 (tt0) REVERT: G 70 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: G 131 GLU cc_start: 0.7709 (tt0) cc_final: 0.7347 (tt0) REVERT: G 163 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7050 (mtm-85) REVERT: G 167 ASP cc_start: 0.7545 (m-30) cc_final: 0.7187 (m-30) REVERT: G 177 ILE cc_start: 0.7656 (mt) cc_final: 0.7397 (mt) REVERT: G 192 SER cc_start: 0.7701 (m) cc_final: 0.7223 (p) REVERT: G 197 ASN cc_start: 0.8521 (p0) cc_final: 0.7859 (p0) REVERT: G 280 ASP cc_start: 0.7624 (t70) cc_final: 0.7243 (t70) REVERT: G 327 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7167 (mt-10) REVERT: G 343 VAL cc_start: 0.8437 (p) cc_final: 0.8187 (m) REVERT: G 353 ASN cc_start: 0.7696 (p0) cc_final: 0.7236 (p0) REVERT: G 405 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7951 (mmtt) REVERT: G 454 ASP cc_start: 0.7486 (m-30) cc_final: 0.7261 (m-30) REVERT: G 464 PHE cc_start: 0.8074 (m-80) cc_final: 0.7735 (m-80) REVERT: H 100 SER cc_start: 0.8089 (OUTLIER) cc_final: 0.7882 (p) REVERT: J 71 SER cc_start: 0.8066 (p) cc_final: 0.7818 (m) REVERT: J 85 SER cc_start: 0.8432 (m) cc_final: 0.7764 (t) REVERT: K 50 ILE cc_start: 0.8355 (mm) cc_final: 0.8054 (mm) REVERT: O 27 SER cc_start: 0.8274 (p) cc_final: 0.8054 (t) outliers start: 64 outliers final: 42 residues processed: 548 average time/residue: 0.1657 time to fit residues: 134.0190 Evaluate side-chains 548 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 504 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 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 327 GLU 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 192 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 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 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 69 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 48 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 250 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 307 GLN G 139 ASN G 247 ASN G 346 GLN G 412 ASN G 413 GLN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN L 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.102358 restraints weight = 28601.162| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.92 r_work: 0.3142 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20988 Z= 0.208 Angle : 0.589 8.314 28518 Z= 0.315 Chirality : 0.046 0.296 3261 Planarity : 0.004 0.041 3618 Dihedral : 6.000 59.592 3166 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.21 % Allowed : 15.57 % Favored : 81.21 % 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: -0.06 (0.16), residues: 2643 helix: 0.58 (0.25), residues: 423 sheet: -0.24 (0.16), residues: 954 loop : 0.10 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 329 TYR 0.027 0.002 TYR F 385 PHE 0.020 0.002 PHE J 29 TRP 0.015 0.002 TRP O 37 HIS 0.005 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00472 (20928) covalent geometry : angle 0.58050 (28386) SS BOND : bond 0.00358 ( 48) SS BOND : angle 1.11802 ( 96) hydrogen bonds : bond 0.03888 ( 985) hydrogen bonds : angle 5.60682 ( 2604) link_BETA1-4 : bond 0.00504 ( 6) link_BETA1-4 : angle 2.23807 ( 18) link_NAG-ASN : bond 0.00474 ( 6) link_NAG-ASN : angle 2.47505 ( 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 575 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 503 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8363 (m-80) cc_final: 0.8108 (m-80) REVERT: C 81 LEU cc_start: 0.8230 (tp) cc_final: 0.7990 (tp) REVERT: C 163 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7660 (mtm-85) REVERT: C 166 LYS cc_start: 0.7942 (tttt) cc_final: 0.7709 (tttt) REVERT: C 175 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7689 (ttp-170) REVERT: C 188 LYS cc_start: 0.7423 (tmmm) cc_final: 0.6861 (tmmm) REVERT: C 189 MET cc_start: 0.7446 (tpp) cc_final: 0.6900 (tpp) REVERT: C 192 SER cc_start: 0.8178 (t) cc_final: 0.7734 (p) REVERT: C 195 GLN cc_start: 0.8044 (mt0) cc_final: 0.7782 (mt0) REVERT: C 248 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7509 (mtp180) REVERT: C 305 GLU cc_start: 0.7440 (tp30) cc_final: 0.6932 (mp0) REVERT: C 329 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7910 (ttm-80) REVERT: C 343 VAL cc_start: 0.8440 (p) cc_final: 0.8216 (m) REVERT: C 412 ASN cc_start: 0.8010 (p0) cc_final: 0.7762 (p0) REVERT: E 74 THR cc_start: 0.8117 (m) cc_final: 0.7555 (p) REVERT: F 21 GLU cc_start: 0.7389 (tp30) cc_final: 0.7133 (tp30) REVERT: F 62 ASP cc_start: 0.7701 (m-30) cc_final: 0.7186 (m-30) REVERT: F 126 LYS cc_start: 0.7777 (mmtp) cc_final: 0.7575 (mmmm) REVERT: F 129 ARG cc_start: 0.7416 (ttp80) cc_final: 0.6801 (ttp80) REVERT: F 133 GLU cc_start: 0.7478 (tp30) cc_final: 0.6840 (tp30) REVERT: F 163 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7416 (mtm-85) REVERT: F 175 ARG cc_start: 0.7761 (ttp-170) cc_final: 0.7316 (ttp-170) REVERT: F 189 MET cc_start: 0.7273 (mmt) cc_final: 0.6853 (mmt) REVERT: F 206 GLN cc_start: 0.7449 (mt0) cc_final: 0.7185 (mt0) REVERT: F 250 MET cc_start: 0.6956 (mmm) cc_final: 0.6688 (tmm) REVERT: F 294 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7249 (mt-10) REVERT: F 343 VAL cc_start: 0.8375 (p) cc_final: 0.8030 (m) REVERT: F 401 LYS cc_start: 0.8275 (ttpp) cc_final: 0.8044 (ttpp) REVERT: F 408 SER cc_start: 0.8223 (m) cc_final: 0.7975 (t) REVERT: F 454 ASP cc_start: 0.7547 (m-30) cc_final: 0.7336 (m-30) REVERT: G 20 LYS cc_start: 0.8351 (tttt) cc_final: 0.8111 (tttm) REVERT: G 70 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: G 131 GLU cc_start: 0.7730 (tt0) cc_final: 0.7397 (tt0) REVERT: G 156 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7130 (ptt-90) REVERT: G 163 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7055 (mtm-85) REVERT: G 167 ASP cc_start: 0.7544 (m-30) cc_final: 0.7166 (m-30) REVERT: G 177 ILE cc_start: 0.7627 (mt) cc_final: 0.7360 (mt) REVERT: G 178 ASN cc_start: 0.7957 (t0) cc_final: 0.7632 (t0) REVERT: G 192 SER cc_start: 0.7717 (m) cc_final: 0.7252 (p) REVERT: G 197 ASN cc_start: 0.8524 (p0) cc_final: 0.7855 (p0) REVERT: G 280 ASP cc_start: 0.7635 (t70) cc_final: 0.7267 (t70) REVERT: G 343 VAL cc_start: 0.8432 (p) cc_final: 0.8195 (m) REVERT: G 353 ASN cc_start: 0.7707 (p0) cc_final: 0.7258 (p0) REVERT: G 405 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7951 (mmtt) REVERT: G 454 ASP cc_start: 0.7523 (m-30) cc_final: 0.7302 (m-30) REVERT: G 464 PHE cc_start: 0.8057 (m-80) cc_final: 0.7768 (m-80) REVERT: H 100 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7894 (p) REVERT: J 71 SER cc_start: 0.8068 (p) cc_final: 0.7823 (m) REVERT: J 85 SER cc_start: 0.8442 (m) cc_final: 0.7780 (t) REVERT: K 50 ILE cc_start: 0.8386 (mm) cc_final: 0.8053 (mm) REVERT: O 27 SER cc_start: 0.8287 (p) cc_final: 0.8079 (t) outliers start: 72 outliers final: 56 residues processed: 543 average time/residue: 0.1569 time to fit residues: 126.9755 Evaluate side-chains 565 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 506 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 92 ASN Chi-restraints excluded: chain C residue 174 THR 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 327 GLU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 390 CYS 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 192 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 73 LEU 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 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 53 TYR 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 I residue 85 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 L residue 60 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 18 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 107 optimal weight: 0.7980 chunk 249 optimal weight: 0.0570 chunk 91 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 307 GLN G 46 ASN G 139 ASN G 247 ASN G 413 GLN ** 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 = 0.3453 r_free = 0.3453 target = 0.117149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104096 restraints weight = 28338.478| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.90 r_work: 0.3155 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20988 Z= 0.162 Angle : 0.560 8.106 28518 Z= 0.299 Chirality : 0.044 0.282 3261 Planarity : 0.004 0.053 3618 Dihedral : 5.901 58.663 3166 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.03 % Allowed : 15.93 % Favored : 81.04 % 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 (0.17), residues: 2643 helix: 1.01 (0.25), residues: 405 sheet: -0.26 (0.17), residues: 927 loop : 0.21 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 129 TYR 0.019 0.002 TYR K 51 PHE 0.016 0.002 PHE J 29 TRP 0.015 0.002 TRP H 50 HIS 0.004 0.001 HIS G 368 Details of bonding type rmsd covalent geometry : bond 0.00363 (20928) covalent geometry : angle 0.55163 (28386) SS BOND : bond 0.00418 ( 48) SS BOND : angle 1.07151 ( 96) hydrogen bonds : bond 0.03642 ( 985) hydrogen bonds : angle 5.51178 ( 2604) link_BETA1-4 : bond 0.00475 ( 6) link_BETA1-4 : angle 2.09929 ( 18) link_NAG-ASN : bond 0.00610 ( 6) link_NAG-ASN : angle 2.64017 ( 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 582 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 514 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 70 GLU cc_start: 0.7143 (tp30) cc_final: 0.6888 (tp30) REVERT: C 81 LEU cc_start: 0.8217 (tp) cc_final: 0.7983 (tp) REVERT: C 126 LYS cc_start: 0.7652 (mtpp) cc_final: 0.7347 (mttm) REVERT: C 163 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7588 (mtm-85) REVERT: C 166 LYS cc_start: 0.7947 (tttt) cc_final: 0.7747 (tttt) REVERT: C 175 ARG cc_start: 0.7844 (ttp-170) cc_final: 0.7637 (ttp-170) REVERT: C 189 MET cc_start: 0.7450 (tpp) cc_final: 0.7128 (tpp) REVERT: C 192 SER cc_start: 0.8150 (t) cc_final: 0.7722 (p) REVERT: C 195 GLN cc_start: 0.8039 (mt0) cc_final: 0.7776 (mt0) REVERT: C 305 GLU cc_start: 0.7431 (tp30) cc_final: 0.6944 (mp0) REVERT: C 329 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7918 (ttm-80) REVERT: C 343 VAL cc_start: 0.8449 (p) cc_final: 0.8225 (m) REVERT: C 412 ASN cc_start: 0.8018 (p0) cc_final: 0.7762 (p0) REVERT: C 450 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8132 (mmtt) REVERT: E 74 THR cc_start: 0.8101 (m) cc_final: 0.7544 (p) REVERT: F 21 GLU cc_start: 0.7336 (tp30) cc_final: 0.7111 (tp30) REVERT: F 62 ASP cc_start: 0.7673 (m-30) cc_final: 0.7171 (m-30) REVERT: F 126 LYS cc_start: 0.7763 (mmtp) cc_final: 0.7544 (mmmm) REVERT: F 129 ARG cc_start: 0.7462 (ttp80) cc_final: 0.6347 (ttp80) REVERT: F 133 GLU cc_start: 0.7480 (tp30) cc_final: 0.6827 (tp30) REVERT: F 163 ARG cc_start: 0.7732 (mtm-85) cc_final: 0.7409 (mtm-85) REVERT: F 175 ARG cc_start: 0.7756 (ttp-170) cc_final: 0.7347 (ttp-170) REVERT: F 178 ASN cc_start: 0.8004 (t0) cc_final: 0.7666 (t0) REVERT: F 189 MET cc_start: 0.7279 (mmt) cc_final: 0.6872 (mmt) REVERT: F 206 GLN cc_start: 0.7403 (mt0) cc_final: 0.7154 (mt0) REVERT: F 236 THR cc_start: 0.7949 (p) cc_final: 0.7735 (p) REVERT: F 250 MET cc_start: 0.6952 (mmm) cc_final: 0.6673 (tmm) REVERT: F 294 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7267 (mt-10) REVERT: F 343 VAL cc_start: 0.8380 (p) cc_final: 0.8037 (m) REVERT: F 397 VAL cc_start: 0.7727 (t) cc_final: 0.7408 (m) REVERT: F 401 LYS cc_start: 0.8245 (ttpp) cc_final: 0.8022 (ttpp) REVERT: F 408 SER cc_start: 0.8226 (m) cc_final: 0.7940 (p) REVERT: F 454 ASP cc_start: 0.7546 (m-30) cc_final: 0.7341 (m-30) REVERT: G 20 LYS cc_start: 0.8360 (tttt) cc_final: 0.8145 (tttm) REVERT: G 70 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: G 128 ILE cc_start: 0.7511 (mt) cc_final: 0.7093 (mt) REVERT: G 131 GLU cc_start: 0.7698 (tt0) cc_final: 0.7362 (tt0) REVERT: G 156 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7099 (ptt-90) REVERT: G 163 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7100 (mtm-85) REVERT: G 167 ASP cc_start: 0.7560 (m-30) cc_final: 0.7153 (m-30) REVERT: G 177 ILE cc_start: 0.7619 (mt) cc_final: 0.7372 (mt) REVERT: G 178 ASN cc_start: 0.7964 (t0) cc_final: 0.7632 (t0) REVERT: G 192 SER cc_start: 0.7702 (m) cc_final: 0.7222 (p) REVERT: G 197 ASN cc_start: 0.8525 (p0) cc_final: 0.7829 (p0) REVERT: G 280 ASP cc_start: 0.7623 (t70) cc_final: 0.7256 (t70) REVERT: G 329 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7580 (ttm-80) REVERT: G 343 VAL cc_start: 0.8430 (p) cc_final: 0.8200 (m) REVERT: G 353 ASN cc_start: 0.7704 (p0) cc_final: 0.7269 (p0) REVERT: G 405 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7963 (mmtt) REVERT: G 454 ASP cc_start: 0.7512 (m-30) cc_final: 0.7292 (m-30) REVERT: H 53 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6096 (t80) REVERT: J 71 SER cc_start: 0.8060 (p) cc_final: 0.7813 (m) REVERT: J 85 SER cc_start: 0.8427 (m) cc_final: 0.7762 (t) REVERT: K 50 ILE cc_start: 0.8353 (mm) cc_final: 0.8006 (mm) outliers start: 68 outliers final: 56 residues processed: 548 average time/residue: 0.1572 time to fit residues: 128.9742 Evaluate side-chains 571 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 512 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 92 ASN Chi-restraints excluded: chain C residue 33 GLU 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 327 GLU 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 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 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 73 LEU 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 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 53 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 85 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 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 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=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: 0.9980 chunk 96 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN F 195 GLN F 307 GLN G 46 ASN G 139 ASN G 247 ASN G 412 ASN G 422 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103059 restraints weight = 28190.946| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.90 r_work: 0.3137 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20988 Z= 0.275 Angle : 0.628 8.477 28518 Z= 0.337 Chirality : 0.048 0.262 3261 Planarity : 0.005 0.045 3618 Dihedral : 6.129 59.852 3166 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.95 % Allowed : 16.60 % Favored : 80.46 % 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: -0.14 (0.16), residues: 2643 helix: 0.63 (0.25), residues: 405 sheet: -0.33 (0.17), residues: 918 loop : 0.02 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 129 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 0.005 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00630 (20928) covalent geometry : angle 0.61911 (28386) SS BOND : bond 0.00430 ( 48) SS BOND : angle 1.30259 ( 96) hydrogen bonds : bond 0.04148 ( 985) hydrogen bonds : angle 5.73451 ( 2604) link_BETA1-4 : bond 0.00440 ( 6) link_BETA1-4 : angle 2.05712 ( 18) link_NAG-ASN : bond 0.00423 ( 6) link_NAG-ASN : angle 2.73467 ( 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 582 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 516 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 81 LEU cc_start: 0.8247 (tp) cc_final: 0.8020 (tp) REVERT: C 163 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7597 (mtm-85) REVERT: C 166 LYS cc_start: 0.7923 (tttt) cc_final: 0.7709 (tttt) REVERT: C 189 MET cc_start: 0.7487 (tpp) cc_final: 0.7180 (tpp) REVERT: C 192 SER cc_start: 0.8218 (t) cc_final: 0.7758 (p) REVERT: C 195 GLN cc_start: 0.8062 (mt0) cc_final: 0.7819 (mt0) REVERT: C 305 GLU cc_start: 0.7405 (tp30) cc_final: 0.6864 (mp0) REVERT: C 329 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7886 (ttm-80) REVERT: C 343 VAL cc_start: 0.8412 (p) cc_final: 0.8189 (m) REVERT: C 412 ASN cc_start: 0.7965 (p0) cc_final: 0.7626 (p0) REVERT: C 450 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8134 (mmtt) REVERT: E 74 THR cc_start: 0.8124 (m) cc_final: 0.7618 (p) REVERT: F 21 GLU cc_start: 0.7318 (tp30) cc_final: 0.7061 (tp30) REVERT: F 62 ASP cc_start: 0.7667 (m-30) cc_final: 0.7182 (m-30) REVERT: F 133 GLU cc_start: 0.7472 (tp30) cc_final: 0.6799 (tp30) REVERT: F 163 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7434 (mtm-85) REVERT: F 175 ARG cc_start: 0.7742 (ttp-170) cc_final: 0.7348 (ttp-170) REVERT: F 178 ASN cc_start: 0.8008 (t0) cc_final: 0.7670 (t0) REVERT: F 189 MET cc_start: 0.7325 (mmt) cc_final: 0.6836 (mmt) REVERT: F 206 GLN cc_start: 0.7449 (mt0) cc_final: 0.7161 (mt0) REVERT: F 250 MET cc_start: 0.7004 (mmm) cc_final: 0.6659 (tmm) REVERT: F 294 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7267 (mt-10) REVERT: F 343 VAL cc_start: 0.8365 (p) cc_final: 0.8040 (m) REVERT: F 378 LEU cc_start: 0.8142 (mt) cc_final: 0.7824 (mp) REVERT: F 401 LYS cc_start: 0.8235 (ttpp) cc_final: 0.8012 (ttpp) REVERT: F 408 SER cc_start: 0.8228 (m) cc_final: 0.7955 (p) REVERT: F 412 ASN cc_start: 0.8127 (p0) cc_final: 0.7809 (p0) REVERT: F 454 ASP cc_start: 0.7564 (m-30) cc_final: 0.7352 (m-30) REVERT: G 20 LYS cc_start: 0.8331 (tttt) cc_final: 0.8128 (tttm) REVERT: G 70 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: G 128 ILE cc_start: 0.7577 (mt) cc_final: 0.7152 (mt) REVERT: G 129 ARG cc_start: 0.7541 (ttp80) cc_final: 0.7272 (ptm-80) REVERT: G 131 GLU cc_start: 0.7714 (tt0) cc_final: 0.7407 (tt0) REVERT: G 156 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7172 (ptt-90) REVERT: G 163 ARG cc_start: 0.7825 (ttm-80) cc_final: 0.7040 (mtm-85) REVERT: G 167 ASP cc_start: 0.7536 (m-30) cc_final: 0.7110 (m-30) REVERT: G 177 ILE cc_start: 0.7626 (mt) cc_final: 0.7354 (mt) REVERT: G 178 ASN cc_start: 0.7987 (t0) cc_final: 0.7757 (t0) REVERT: G 192 SER cc_start: 0.7758 (m) cc_final: 0.7307 (p) REVERT: G 280 ASP cc_start: 0.7646 (t70) cc_final: 0.7292 (t70) REVERT: G 329 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7641 (tpp-160) REVERT: G 343 VAL cc_start: 0.8369 (p) cc_final: 0.8116 (m) REVERT: G 353 ASN cc_start: 0.7657 (p0) cc_final: 0.7230 (p0) REVERT: G 405 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7958 (mmtt) REVERT: G 454 ASP cc_start: 0.7552 (m-30) cc_final: 0.7346 (m-30) REVERT: J 71 SER cc_start: 0.8083 (p) cc_final: 0.7826 (m) REVERT: K 50 ILE cc_start: 0.8415 (mm) cc_final: 0.8071 (mm) REVERT: L 79 GLN cc_start: 0.7717 (mm110) cc_final: 0.7276 (mm110) outliers start: 66 outliers final: 60 residues processed: 545 average time/residue: 0.1540 time to fit residues: 126.2758 Evaluate side-chains 562 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 500 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 92 ASN 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 327 GLU 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 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 84 VAL 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 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 73 LEU 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 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 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 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 L residue 74 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 256 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.0170 chunk 64 optimal weight: 0.9990 chunk 198 optimal weight: 0.0970 chunk 216 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 chunk 160 optimal weight: 0.0770 chunk 43 optimal weight: 0.7980 chunk 240 optimal weight: 0.6980 overall best weight: 0.1972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 272 GLN C 455 GLN F 195 GLN F 307 GLN F 332 HIS G 206 GLN ** 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 = 0.3470 r_free = 0.3470 target = 0.118230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105158 restraints weight = 28214.667| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.89 r_work: 0.3168 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 20988 Z= 0.113 Angle : 0.548 12.955 28518 Z= 0.290 Chirality : 0.044 0.226 3261 Planarity : 0.004 0.035 3618 Dihedral : 5.779 59.335 3166 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.83 % Allowed : 18.03 % 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: 0.11 (0.17), residues: 2643 helix: 1.16 (0.26), residues: 405 sheet: -0.28 (0.17), residues: 930 loop : 0.17 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 129 TYR 0.017 0.001 TYR C 385 PHE 0.011 0.001 PHE J 111 TRP 0.019 0.001 TRP H 50 HIS 0.004 0.001 HIS G 368 Details of bonding type rmsd covalent geometry : bond 0.00245 (20928) covalent geometry : angle 0.54048 (28386) SS BOND : bond 0.00265 ( 48) SS BOND : angle 0.78680 ( 96) hydrogen bonds : bond 0.03374 ( 985) hydrogen bonds : angle 5.41139 ( 2604) link_BETA1-4 : bond 0.00602 ( 6) link_BETA1-4 : angle 2.04559 ( 18) link_NAG-ASN : bond 0.00771 ( 6) link_NAG-ASN : angle 2.90045 ( 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 548 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 507 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: B 89 GLN cc_start: 0.8279 (tt0) cc_final: 0.8050 (tt0) REVERT: C 48 PHE cc_start: 0.8458 (m-80) cc_final: 0.8252 (m-80) REVERT: C 70 GLU cc_start: 0.7123 (tp30) cc_final: 0.6873 (tp30) REVERT: C 81 LEU cc_start: 0.8198 (tp) cc_final: 0.7959 (tp) REVERT: C 163 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7327 (mtm-85) REVERT: C 189 MET cc_start: 0.7433 (tpp) cc_final: 0.7108 (tpp) REVERT: C 192 SER cc_start: 0.8100 (t) cc_final: 0.7695 (p) REVERT: C 195 GLN cc_start: 0.8019 (mt0) cc_final: 0.7700 (mt0) REVERT: C 248 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7451 (mtp180) REVERT: C 305 GLU cc_start: 0.7405 (tp30) cc_final: 0.6923 (mp0) REVERT: C 307 GLN cc_start: 0.8506 (mt0) cc_final: 0.8297 (mt0) REVERT: C 343 VAL cc_start: 0.8446 (p) cc_final: 0.8212 (m) REVERT: C 412 ASN cc_start: 0.7967 (p0) cc_final: 0.7712 (p0) REVERT: E 74 THR cc_start: 0.8174 (m) cc_final: 0.7628 (p) REVERT: F 21 GLU cc_start: 0.7245 (tp30) cc_final: 0.7030 (tp30) REVERT: F 62 ASP cc_start: 0.7657 (m-30) cc_final: 0.7152 (m-30) REVERT: F 129 ARG cc_start: 0.7476 (ttp80) cc_final: 0.7234 (ttp80) REVERT: F 133 GLU cc_start: 0.7439 (tp30) cc_final: 0.6780 (tp30) REVERT: F 163 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.7450 (mtm-85) REVERT: F 175 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7299 (ttp-170) REVERT: F 178 ASN cc_start: 0.8029 (t0) cc_final: 0.7676 (t0) REVERT: F 189 MET cc_start: 0.7265 (mmt) cc_final: 0.6864 (mmt) REVERT: F 250 MET cc_start: 0.6981 (mmm) cc_final: 0.6685 (tmm) REVERT: F 280 ASP cc_start: 0.7781 (t0) cc_final: 0.7519 (t70) REVERT: F 343 VAL cc_start: 0.8381 (p) cc_final: 0.8048 (m) REVERT: F 397 VAL cc_start: 0.7730 (t) cc_final: 0.7423 (m) REVERT: F 401 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7917 (ttpp) REVERT: F 408 SER cc_start: 0.8196 (m) cc_final: 0.7949 (p) REVERT: F 412 ASN cc_start: 0.8041 (p0) cc_final: 0.7692 (p0) REVERT: G 70 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: G 128 ILE cc_start: 0.7438 (mt) cc_final: 0.7063 (mt) REVERT: G 131 GLU cc_start: 0.7712 (tt0) cc_final: 0.7428 (tt0) REVERT: G 156 ARG cc_start: 0.7523 (ptm-80) cc_final: 0.7054 (ptt-90) REVERT: G 163 ARG cc_start: 0.7687 (ttm-80) cc_final: 0.7014 (mtm-85) REVERT: G 167 ASP cc_start: 0.7495 (m-30) cc_final: 0.7051 (m-30) REVERT: G 177 ILE cc_start: 0.7519 (mt) cc_final: 0.7306 (mt) REVERT: G 178 ASN cc_start: 0.7978 (t0) cc_final: 0.7756 (t0) REVERT: G 192 SER cc_start: 0.7691 (m) cc_final: 0.7198 (p) REVERT: G 197 ASN cc_start: 0.8479 (p0) cc_final: 0.7853 (p0) REVERT: G 280 ASP cc_start: 0.7624 (t70) cc_final: 0.7252 (t70) REVERT: G 307 GLN cc_start: 0.8446 (mt0) cc_final: 0.8230 (mt0) REVERT: G 343 VAL cc_start: 0.8436 (p) cc_final: 0.8209 (m) REVERT: G 353 ASN cc_start: 0.7642 (p0) cc_final: 0.7234 (p0) REVERT: G 405 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7930 (mmtt) REVERT: G 454 ASP cc_start: 0.7501 (m-30) cc_final: 0.7277 (m-30) REVERT: J 71 SER cc_start: 0.8118 (p) cc_final: 0.7862 (m) REVERT: K 50 ILE cc_start: 0.8291 (mm) cc_final: 0.7994 (mm) REVERT: L 79 GLN cc_start: 0.7689 (mm110) cc_final: 0.7244 (mm110) REVERT: L 102 THR cc_start: 0.8307 (t) cc_final: 0.8067 (p) outliers start: 41 outliers final: 33 residues processed: 532 average time/residue: 0.1546 time to fit residues: 123.1644 Evaluate side-chains 525 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 491 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL 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 327 GLU 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 92 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 155 VAL 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 144 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 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 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain O residue 26 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: 0.9980 chunk 92 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 122 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 195 GLN F 206 GLN F 307 GLN G 139 ASN G 195 GLN G 202 ASN G 247 ASN G 351 ASN G 412 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103507 restraints weight = 28345.551| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.90 r_work: 0.3137 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20988 Z= 0.264 Angle : 0.620 8.158 28518 Z= 0.331 Chirality : 0.047 0.226 3261 Planarity : 0.004 0.055 3618 Dihedral : 6.033 59.487 3166 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.74 % Allowed : 17.89 % Favored : 80.37 % 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: -0.08 (0.17), residues: 2643 helix: 0.87 (0.25), residues: 402 sheet: -0.32 (0.17), residues: 927 loop : 0.01 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 129 TYR 0.030 0.003 TYR G 319 PHE 0.023 0.002 PHE K 101 TRP 0.018 0.002 TRP O 37 HIS 0.005 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00605 (20928) covalent geometry : angle 0.61054 (28386) SS BOND : bond 0.00446 ( 48) SS BOND : angle 1.20154 ( 96) hydrogen bonds : bond 0.04000 ( 985) hydrogen bonds : angle 5.64124 ( 2604) link_BETA1-4 : bond 0.00493 ( 6) link_BETA1-4 : angle 2.07207 ( 18) link_NAG-ASN : bond 0.00454 ( 6) link_NAG-ASN : angle 3.17725 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5267.43 seconds wall clock time: 90 minutes 59.31 seconds (5459.31 seconds total)