Starting phenix.real_space_refine on Tue Jun 24 06:59:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjq_25929/06_2025/7tjq_25929.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjq_25929/06_2025/7tjq_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_25929/06_2025/7tjq_25929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjq_25929/06_2025/7tjq_25929.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjq_25929/06_2025/7tjq_25929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjq_25929/06_2025/7tjq_25929.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.18, per 1000 atoms: 0.59 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: 5.11 Conformation dependent library (CDL) restraints added in 2.8 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: 4.08 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: 10.19 Time building geometry restraints manager: 6.09 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: 0.04 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: 7.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.030 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 54.240 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.040 0.003 TRP D 50 HIS 0.007 0.002 HIS G 332 PHE 0.021 0.002 PHE I 29 TYR 0.037 0.005 TYR E 49 ARG 0.025 0.003 ARG C 163 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 6) link_NAG-ASN : angle 3.23244 ( 18) link_BETA1-4 : bond 0.00980 ( 6) link_BETA1-4 : angle 3.86069 ( 18) hydrogen bonds : bond 0.17746 ( 985) hydrogen bonds : angle 8.25894 ( 2604) SS BOND : bond 0.00522 ( 48) SS BOND : angle 1.31106 ( 96) covalent geometry : bond 0.00432 (20928) covalent geometry : angle 0.77074 (28386) *********************** 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 : 2.367 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: 0.8077 (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: 0.7674 (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: 0.3737 time to fit residues: 341.6509 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 : 2.163 ------------------------------------------------------------------------------- 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 220 optimal weight: 3.9990 chunk 197 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 124 optimal weight: 0.0770 chunk 152 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 195 GLN G 272 GLN G 298 ASN ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN J 35 ASN M 55 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106978 restraints weight = 28177.132| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.77 r_work: 0.3196 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20988 Z= 0.182 Angle : 0.660 8.314 28518 Z= 0.356 Chirality : 0.046 0.211 3261 Planarity : 0.005 0.050 3618 Dihedral : 6.823 59.945 3180 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.83 % Allowed : 11.16 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2643 helix: 0.54 (0.25), residues: 420 sheet: -0.16 (0.17), residues: 906 loop : 0.04 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 50 HIS 0.008 0.001 HIS G 368 PHE 0.022 0.002 PHE J 29 TYR 0.024 0.002 TYR K 51 ARG 0.006 0.001 ARG G 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 6) link_NAG-ASN : angle 2.85378 ( 18) link_BETA1-4 : bond 0.00457 ( 6) link_BETA1-4 : angle 2.47357 ( 18) hydrogen bonds : bond 0.04613 ( 985) hydrogen bonds : angle 6.11861 ( 2604) SS BOND : bond 0.00505 ( 48) SS BOND : angle 1.25318 ( 96) covalent geometry : bond 0.00403 (20928) covalent geometry : angle 0.65046 (28386) *********************** 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 576 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 535 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 THR cc_start: 0.7840 (t) cc_final: 0.7475 (t) REVERT: C 70 GLU cc_start: 0.7237 (tp30) cc_final: 0.6759 (tp30) REVERT: C 71 LEU cc_start: 0.7852 (tp) cc_final: 0.7622 (tp) REVERT: C 75 LYS cc_start: 0.8301 (mtpp) cc_final: 0.8092 (mtmm) REVERT: C 79 ARG cc_start: 0.7575 (mtm-85) cc_final: 0.7311 (mtm-85) REVERT: C 81 LEU cc_start: 0.8154 (tp) cc_final: 0.7910 (tp) REVERT: C 82 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7813 (mtt90) REVERT: C 133 GLU cc_start: 0.7240 (tp30) cc_final: 0.6754 (tp30) REVERT: C 175 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7468 (ttp-170) REVERT: C 194 SER cc_start: 0.7627 (p) cc_final: 0.7398 (t) REVERT: C 245 LEU cc_start: 0.7840 (mt) cc_final: 0.7633 (mm) REVERT: C 248 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7463 (mtp85) REVERT: C 343 VAL cc_start: 0.8541 (p) cc_final: 0.8275 (m) REVERT: C 399 ILE cc_start: 0.8056 (mm) cc_final: 0.7832 (mt) REVERT: C 412 ASN cc_start: 0.7988 (p0) cc_final: 0.7721 (p0) REVERT: C 413 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7902 (mm110) REVERT: E 74 THR cc_start: 0.8127 (m) cc_final: 0.7471 (p) REVERT: F 62 ASP cc_start: 0.7843 (m-30) cc_final: 0.7294 (m-30) REVERT: F 133 GLU cc_start: 0.7412 (tp30) cc_final: 0.6748 (tp30) REVERT: F 166 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7566 (ttpt) REVERT: F 189 MET cc_start: 0.7443 (mmt) cc_final: 0.6934 (mmt) REVERT: F 192 SER cc_start: 0.7736 (m) cc_final: 0.7165 (p) REVERT: F 206 GLN cc_start: 0.7477 (mt0) cc_final: 0.7124 (mt0) REVERT: F 256 PHE cc_start: 0.8395 (p90) cc_final: 0.8121 (p90) REVERT: F 343 VAL cc_start: 0.8459 (p) cc_final: 0.8103 (m) REVERT: F 408 SER cc_start: 0.8178 (m) cc_final: 0.7809 (p) REVERT: F 454 ASP cc_start: 0.7364 (m-30) cc_final: 0.7158 (m-30) REVERT: F 464 PHE cc_start: 0.8042 (m-80) cc_final: 0.7780 (m-80) REVERT: G 20 LYS cc_start: 0.8297 (tttt) cc_final: 0.8025 (tttm) REVERT: G 37 SER cc_start: 0.8119 (p) cc_final: 0.7912 (p) REVERT: G 40 ARG cc_start: 0.7867 (tmm160) cc_final: 0.7591 (tmm160) REVERT: G 70 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: G 73 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8202 (mp) REVERT: G 75 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7840 (mtpt) REVERT: G 129 ARG cc_start: 0.7576 (ttp-170) cc_final: 0.7111 (ttp-170) REVERT: G 131 GLU cc_start: 0.7705 (tt0) cc_final: 0.7136 (tt0) REVERT: G 163 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.7374 (mtm-85) REVERT: G 177 ILE cc_start: 0.7815 (mt) cc_final: 0.7571 (mt) REVERT: G 192 SER cc_start: 0.7696 (m) cc_final: 0.7222 (p) REVERT: G 197 ASN cc_start: 0.8498 (p0) cc_final: 0.7784 (p0) REVERT: G 198 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7300 (ttm-80) REVERT: G 205 ARG cc_start: 0.7330 (ttp80) cc_final: 0.7054 (ttp80) REVERT: G 206 GLN cc_start: 0.7457 (mt0) cc_final: 0.7135 (mt0) REVERT: G 219 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7729 (mmmm) REVERT: G 223 THR cc_start: 0.8380 (m) cc_final: 0.7849 (p) REVERT: G 250 MET cc_start: 0.6554 (tpp) cc_final: 0.6293 (mmm) REVERT: G 280 ASP cc_start: 0.7516 (t70) cc_final: 0.7261 (t70) REVERT: G 343 VAL cc_start: 0.8427 (p) cc_final: 0.8057 (m) REVERT: G 454 ASP cc_start: 0.7442 (m-30) cc_final: 0.7183 (m-30) REVERT: J 7 SER cc_start: 0.7865 (p) cc_final: 0.7658 (t) REVERT: J 28 THR cc_start: 0.8608 (m) cc_final: 0.8089 (p) REVERT: J 71 SER cc_start: 0.8070 (p) cc_final: 0.7852 (m) REVERT: L 79 GLN cc_start: 0.7559 (mm110) cc_final: 0.7239 (mm-40) REVERT: M 27 SER cc_start: 0.8084 (p) cc_final: 0.7816 (p) REVERT: N 52 SER cc_start: 0.8451 (p) cc_final: 0.8236 (t) REVERT: O 27 SER cc_start: 0.8359 (p) cc_final: 0.8023 (t) outliers start: 41 outliers final: 19 residues processed: 556 average time/residue: 0.3706 time to fit residues: 302.9103 Evaluate side-chains 534 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 513 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 411 THR 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 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 115 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 219 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 112 optimal weight: 0.0970 chunk 194 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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** E 92 ASN F 195 GLN F 206 GLN F 272 GLN F 353 ASN G 139 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN 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 = 0.3450 r_free = 0.3450 target = 0.116716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103686 restraints weight = 28117.271| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.88 r_work: 0.3133 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20988 Z= 0.240 Angle : 0.641 9.429 28518 Z= 0.345 Chirality : 0.047 0.187 3261 Planarity : 0.005 0.055 3618 Dihedral : 6.447 59.764 3167 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.81 % Allowed : 12.23 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2643 helix: 0.39 (0.24), residues: 420 sheet: -0.22 (0.16), residues: 954 loop : 0.04 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 50 HIS 0.007 0.002 HIS G 368 PHE 0.022 0.002 PHE J 29 TYR 0.029 0.002 TYR K 51 ARG 0.006 0.001 ARG G 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 6) link_NAG-ASN : angle 2.68177 ( 18) link_BETA1-4 : bond 0.00438 ( 6) link_BETA1-4 : angle 2.26206 ( 18) hydrogen bonds : bond 0.04564 ( 985) hydrogen bonds : angle 5.93884 ( 2604) SS BOND : bond 0.00382 ( 48) SS BOND : angle 1.30835 ( 96) covalent geometry : bond 0.00542 (20928) covalent geometry : angle 0.63159 (28386) *********************** 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 589 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 526 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8419 (m-80) cc_final: 0.8208 (m-80) REVERT: B 102 THR cc_start: 0.8104 (t) cc_final: 0.7761 (t) REVERT: C 70 GLU cc_start: 0.7218 (tp30) cc_final: 0.6788 (tp30) REVERT: C 71 LEU cc_start: 0.7827 (tp) cc_final: 0.7590 (tp) REVERT: C 81 LEU cc_start: 0.8226 (tp) cc_final: 0.7998 (tp) REVERT: C 133 GLU cc_start: 0.7343 (tp30) cc_final: 0.6874 (tp30) REVERT: C 144 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7796 (p) REVERT: C 163 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7660 (mtm-85) REVERT: C 174 THR cc_start: 0.8350 (m) cc_final: 0.8105 (m) REVERT: C 175 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7513 (ttp-170) REVERT: C 189 MET cc_start: 0.7466 (tpp) cc_final: 0.7090 (tpp) REVERT: C 192 SER cc_start: 0.8225 (t) cc_final: 0.7747 (p) REVERT: C 195 GLN cc_start: 0.8031 (mt0) cc_final: 0.7732 (mt0) REVERT: C 229 ARG cc_start: 0.7432 (mtp85) cc_final: 0.7075 (ttm-80) REVERT: C 233 ASN cc_start: 0.6800 (t0) cc_final: 0.6538 (m110) REVERT: C 248 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7543 (mtm180) REVERT: C 343 VAL cc_start: 0.8497 (p) cc_final: 0.8258 (m) REVERT: C 399 ILE cc_start: 0.8064 (mm) cc_final: 0.7823 (mt) REVERT: C 413 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7886 (mm110) REVERT: D 71 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8087 (pmt-80) REVERT: E 74 THR cc_start: 0.8114 (m) cc_final: 0.7470 (p) REVERT: F 62 ASP cc_start: 0.7762 (m-30) cc_final: 0.7245 (m-30) REVERT: F 129 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6305 (mtm110) REVERT: F 133 GLU cc_start: 0.7434 (tp30) cc_final: 0.6775 (tp30) REVERT: F 166 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7542 (ttpt) REVERT: F 189 MET cc_start: 0.7384 (mmt) cc_final: 0.6888 (mmt) REVERT: F 206 GLN cc_start: 0.7423 (mt0) cc_final: 0.7187 (mt0) REVERT: F 343 VAL cc_start: 0.8432 (p) cc_final: 0.8085 (m) REVERT: F 401 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7988 (ttpp) REVERT: F 408 SER cc_start: 0.8191 (m) cc_final: 0.7873 (t) REVERT: F 411 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7990 (p) REVERT: F 454 ASP cc_start: 0.7403 (m-30) cc_final: 0.7199 (m-30) REVERT: G 20 LYS cc_start: 0.8356 (tttt) cc_final: 0.8099 (tttm) REVERT: G 40 ARG cc_start: 0.7877 (tmm160) cc_final: 0.7540 (ttp80) REVERT: G 70 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: G 75 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7950 (mtpt) REVERT: G 131 GLU cc_start: 0.7740 (tt0) cc_final: 0.7242 (tt0) REVERT: G 156 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7123 (ptt-90) REVERT: G 163 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7383 (mtm-85) REVERT: G 177 ILE cc_start: 0.7797 (mt) cc_final: 0.7532 (mt) REVERT: G 178 ASN cc_start: 0.7901 (t0) cc_final: 0.7677 (t0) REVERT: G 192 SER cc_start: 0.7745 (m) cc_final: 0.7307 (p) REVERT: G 197 ASN cc_start: 0.8471 (p0) cc_final: 0.7804 (p0) REVERT: G 198 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7266 (ttm-80) REVERT: G 205 ARG cc_start: 0.7362 (ttp80) cc_final: 0.7153 (ttp80) REVERT: G 223 THR cc_start: 0.8416 (m) cc_final: 0.7849 (p) REVERT: G 248 ARG cc_start: 0.7603 (ttm110) cc_final: 0.7288 (mtp85) REVERT: G 253 ARG cc_start: 0.7646 (ttp-110) cc_final: 0.7425 (ttp80) REVERT: G 280 ASP cc_start: 0.7611 (t70) cc_final: 0.7280 (t70) REVERT: G 329 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7512 (ttm-80) REVERT: G 343 VAL cc_start: 0.8415 (p) cc_final: 0.8128 (m) REVERT: G 353 ASN cc_start: 0.7679 (p0) cc_final: 0.7165 (p0) REVERT: G 454 ASP cc_start: 0.7448 (m-30) cc_final: 0.7203 (m-30) REVERT: G 464 PHE cc_start: 0.8111 (m-80) cc_final: 0.7796 (m-80) REVERT: I 7 SER cc_start: 0.8080 (p) cc_final: 0.7811 (t) REVERT: J 7 SER cc_start: 0.7887 (p) cc_final: 0.7648 (t) REVERT: J 71 SER cc_start: 0.8093 (p) cc_final: 0.7850 (m) REVERT: J 85 SER cc_start: 0.8508 (m) cc_final: 0.7854 (t) REVERT: K 50 ILE cc_start: 0.8423 (mm) cc_final: 0.8164 (mm) REVERT: L 79 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7251 (mm-40) REVERT: M 27 SER cc_start: 0.8068 (p) cc_final: 0.7709 (t) REVERT: M 98 SER cc_start: 0.8242 (p) cc_final: 0.7973 (m) REVERT: N 31 SER cc_start: 0.8199 (m) cc_final: 0.7986 (p) outliers start: 63 outliers final: 42 residues processed: 559 average time/residue: 0.3659 time to fit residues: 302.6578 Evaluate side-chains 566 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 518 time to evaluate : 2.254 ------------------------------------------------------------------------------- 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 28 THR 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 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 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 247 optimal weight: 1.9990 chunk 198 optimal weight: 0.0370 chunk 101 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 422 ASN G 139 ASN G 412 ASN G 413 GLN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN N 35 ASN ** O 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104329 restraints weight = 28450.971| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.90 r_work: 0.3152 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2238 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= 0.176 Angle : 0.575 9.024 28518 Z= 0.309 Chirality : 0.045 0.174 3261 Planarity : 0.004 0.055 3618 Dihedral : 6.186 59.870 3167 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.41 % Allowed : 13.74 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 2643 helix: 0.64 (0.25), residues: 420 sheet: -0.21 (0.16), residues: 954 loop : 0.12 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 50 HIS 0.006 0.001 HIS G 368 PHE 0.018 0.002 PHE J 29 TYR 0.022 0.002 TYR L 49 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 6) link_NAG-ASN : angle 2.10924 ( 18) link_BETA1-4 : bond 0.00399 ( 6) link_BETA1-4 : angle 2.16708 ( 18) hydrogen bonds : bond 0.03927 ( 985) hydrogen bonds : angle 5.67753 ( 2604) SS BOND : bond 0.00312 ( 48) SS BOND : angle 0.98693 ( 96) covalent geometry : bond 0.00392 (20928) covalent geometry : angle 0.56866 (28386) *********************** 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 564 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 510 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8388 (m-80) cc_final: 0.8108 (m-80) REVERT: B 102 THR cc_start: 0.8171 (t) cc_final: 0.7802 (t) REVERT: C 70 GLU cc_start: 0.7164 (tp30) cc_final: 0.6751 (tp30) REVERT: C 81 LEU cc_start: 0.8214 (tp) cc_final: 0.7988 (tp) REVERT: C 133 GLU cc_start: 0.7443 (tp30) cc_final: 0.6986 (tp30) REVERT: C 144 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7834 (p) REVERT: C 163 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7610 (mtm-85) REVERT: C 175 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7474 (ttp-170) REVERT: C 188 LYS cc_start: 0.7445 (tmmm) cc_final: 0.6932 (tmmm) REVERT: C 189 MET cc_start: 0.7427 (tpp) cc_final: 0.6837 (tpp) REVERT: C 192 SER cc_start: 0.8154 (t) cc_final: 0.7715 (p) REVERT: C 195 GLN cc_start: 0.8020 (mt0) cc_final: 0.7755 (mt0) REVERT: C 209 ASP cc_start: 0.6966 (m-30) cc_final: 0.6764 (m-30) REVERT: C 226 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7391 (mt-10) REVERT: C 245 LEU cc_start: 0.7937 (mm) cc_final: 0.7729 (mm) REVERT: C 248 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7453 (mtp180) REVERT: C 305 GLU cc_start: 0.7484 (tp30) cc_final: 0.7009 (mp0) REVERT: C 343 VAL cc_start: 0.8510 (p) cc_final: 0.8275 (m) REVERT: C 399 ILE cc_start: 0.8042 (mm) cc_final: 0.7791 (mt) REVERT: C 412 ASN cc_start: 0.8021 (p0) cc_final: 0.7716 (p0) REVERT: C 413 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7882 (mm110) REVERT: D 71 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8057 (pmt-80) REVERT: E 74 THR cc_start: 0.8117 (m) cc_final: 0.7514 (p) REVERT: F 62 ASP cc_start: 0.7735 (m-30) cc_final: 0.7191 (m-30) REVERT: F 129 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6815 (ttp80) REVERT: F 133 GLU cc_start: 0.7477 (tp30) cc_final: 0.6855 (tp30) REVERT: F 163 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7451 (mtm-85) REVERT: F 166 LYS cc_start: 0.7854 (ttpt) cc_final: 0.7544 (ttpt) REVERT: F 175 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7384 (ttp-170) REVERT: F 189 MET cc_start: 0.7318 (mmt) cc_final: 0.6871 (mmt) REVERT: F 250 MET cc_start: 0.6837 (mmm) cc_final: 0.6608 (tmm) REVERT: F 343 VAL cc_start: 0.8429 (p) cc_final: 0.8065 (m) REVERT: F 401 LYS cc_start: 0.8298 (ttpp) cc_final: 0.8064 (ttpp) REVERT: F 408 SER cc_start: 0.8210 (m) cc_final: 0.7920 (t) REVERT: F 411 THR cc_start: 0.8190 (p) cc_final: 0.7985 (p) REVERT: F 449 VAL cc_start: 0.8415 (p) cc_final: 0.8193 (m) REVERT: F 454 ASP cc_start: 0.7428 (m-30) cc_final: 0.7227 (m-30) REVERT: G 20 LYS cc_start: 0.8377 (tttt) cc_final: 0.8129 (tttm) REVERT: G 70 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: G 131 GLU cc_start: 0.7665 (tt0) cc_final: 0.7176 (tt0) REVERT: G 163 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7207 (mtm-85) REVERT: G 167 ASP cc_start: 0.7477 (m-30) cc_final: 0.7159 (m-30) REVERT: G 177 ILE cc_start: 0.7732 (mt) cc_final: 0.7445 (mt) REVERT: G 180 ASN cc_start: 0.7960 (m110) cc_final: 0.7707 (m-40) REVERT: G 192 SER cc_start: 0.7717 (m) cc_final: 0.7199 (p) REVERT: G 205 ARG cc_start: 0.7373 (ttp80) cc_final: 0.7166 (ttp80) REVERT: G 223 THR cc_start: 0.8399 (m) cc_final: 0.7848 (p) REVERT: G 248 ARG cc_start: 0.7519 (ttm110) cc_final: 0.7245 (mtp85) REVERT: G 253 ARG cc_start: 0.7660 (ttp-110) cc_final: 0.7409 (ttp80) REVERT: G 280 ASP cc_start: 0.7628 (t70) cc_final: 0.7268 (t70) REVERT: G 329 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7594 (ttm-80) REVERT: G 343 VAL cc_start: 0.8449 (p) cc_final: 0.8181 (m) REVERT: G 353 ASN cc_start: 0.7680 (p0) cc_final: 0.7223 (p0) REVERT: G 405 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7938 (mmtt) REVERT: G 454 ASP cc_start: 0.7417 (m-30) cc_final: 0.7163 (m-30) REVERT: G 464 PHE cc_start: 0.8075 (m-80) cc_final: 0.7781 (m-80) REVERT: H 100 SER cc_start: 0.8078 (OUTLIER) cc_final: 0.7854 (p) REVERT: J 7 SER cc_start: 0.7895 (p) cc_final: 0.7639 (t) REVERT: J 71 SER cc_start: 0.8085 (p) cc_final: 0.7823 (m) REVERT: K 50 ILE cc_start: 0.8364 (mm) cc_final: 0.8068 (mm) REVERT: L 102 THR cc_start: 0.8230 (t) cc_final: 0.7997 (p) REVERT: M 27 SER cc_start: 0.8048 (p) cc_final: 0.7803 (t) REVERT: M 98 SER cc_start: 0.8268 (p) cc_final: 0.8002 (m) REVERT: N 31 SER cc_start: 0.8148 (m) cc_final: 0.7943 (p) REVERT: N 49 SER cc_start: 0.8683 (p) cc_final: 0.8478 (p) outliers start: 54 outliers final: 40 residues processed: 539 average time/residue: 0.3747 time to fit residues: 299.3849 Evaluate side-chains 549 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 504 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain 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 71 LEU 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 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 155 VAL Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 GLU 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 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 15 optimal weight: 0.5980 chunk 172 optimal weight: 0.2980 chunk 201 optimal weight: 0.0980 chunk 236 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 422 ASN F 195 GLN F 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104777 restraints weight = 28474.671| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.80 r_work: 0.3163 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20988 Z= 0.160 Angle : 0.559 8.671 28518 Z= 0.300 Chirality : 0.044 0.190 3261 Planarity : 0.004 0.059 3618 Dihedral : 6.028 59.894 3166 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.72 % Allowed : 14.41 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2643 helix: 0.74 (0.25), residues: 423 sheet: -0.23 (0.16), residues: 954 loop : 0.17 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 50 HIS 0.005 0.001 HIS C 332 PHE 0.018 0.002 PHE J 29 TYR 0.024 0.002 TYR F 385 ARG 0.005 0.000 ARG F 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 1.97615 ( 18) link_BETA1-4 : bond 0.00365 ( 6) link_BETA1-4 : angle 2.08000 ( 18) hydrogen bonds : bond 0.03743 ( 985) hydrogen bonds : angle 5.57036 ( 2604) SS BOND : bond 0.00331 ( 48) SS BOND : angle 1.11668 ( 96) covalent geometry : bond 0.00360 (20928) covalent geometry : angle 0.55194 (28386) *********************** 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 564 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 503 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8366 (m-80) cc_final: 0.8085 (m-80) REVERT: C 56 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6784 (mt-10) REVERT: C 81 LEU cc_start: 0.8212 (tp) cc_final: 0.7982 (tp) REVERT: C 133 GLU cc_start: 0.7422 (tp30) cc_final: 0.6956 (tp30) REVERT: C 167 ASP cc_start: 0.7451 (m-30) cc_final: 0.7235 (m-30) REVERT: C 188 LYS cc_start: 0.7462 (tmmm) cc_final: 0.6902 (tmmm) REVERT: C 189 MET cc_start: 0.7402 (tpp) cc_final: 0.6817 (tpp) REVERT: C 192 SER cc_start: 0.8097 (t) cc_final: 0.7684 (p) REVERT: C 195 GLN cc_start: 0.7991 (mt0) cc_final: 0.7725 (mt0) REVERT: C 206 GLN cc_start: 0.7600 (mt0) cc_final: 0.7331 (mt0) REVERT: C 226 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7342 (mt-10) REVERT: C 248 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7613 (mtp85) REVERT: C 252 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7599 (ttm-80) REVERT: C 305 GLU cc_start: 0.7455 (tp30) cc_final: 0.6973 (mp0) REVERT: C 343 VAL cc_start: 0.8495 (p) cc_final: 0.8266 (m) REVERT: C 399 ILE cc_start: 0.8034 (mm) cc_final: 0.7770 (mt) REVERT: C 413 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7844 (mm110) REVERT: E 74 THR cc_start: 0.8095 (m) cc_final: 0.7497 (p) REVERT: F 62 ASP cc_start: 0.7723 (m-30) cc_final: 0.7205 (m-30) REVERT: F 133 GLU cc_start: 0.7471 (tp30) cc_final: 0.6819 (tp30) REVERT: F 163 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7426 (mtm-85) REVERT: F 166 LYS cc_start: 0.7837 (ttpt) cc_final: 0.7504 (ttpt) REVERT: F 175 ARG cc_start: 0.7767 (ttp-170) cc_final: 0.7345 (ttp-170) REVERT: F 189 MET cc_start: 0.7273 (mmt) cc_final: 0.6810 (mmt) REVERT: F 250 MET cc_start: 0.6867 (mmm) cc_final: 0.6595 (tmm) REVERT: F 343 VAL cc_start: 0.8411 (p) cc_final: 0.8058 (m) REVERT: F 401 LYS cc_start: 0.8256 (ttpp) cc_final: 0.8012 (ttpp) REVERT: F 408 SER cc_start: 0.8149 (m) cc_final: 0.7893 (t) REVERT: F 449 VAL cc_start: 0.8403 (p) cc_final: 0.8176 (m) REVERT: G 20 LYS cc_start: 0.8365 (tttt) cc_final: 0.8133 (tttm) REVERT: G 70 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: G 128 ILE cc_start: 0.7617 (mt) cc_final: 0.7250 (mt) REVERT: G 131 GLU cc_start: 0.7643 (tt0) cc_final: 0.7165 (tt0) REVERT: G 156 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7099 (ptt-90) REVERT: G 163 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7186 (mtm-85) REVERT: G 167 ASP cc_start: 0.7467 (m-30) cc_final: 0.7115 (m-30) REVERT: G 177 ILE cc_start: 0.7657 (mt) cc_final: 0.7401 (mt) REVERT: G 192 SER cc_start: 0.7695 (m) cc_final: 0.7142 (p) REVERT: G 223 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.7813 (p) REVERT: G 248 ARG cc_start: 0.7493 (ttm110) cc_final: 0.7222 (mtp85) REVERT: G 280 ASP cc_start: 0.7609 (t70) cc_final: 0.7236 (t70) REVERT: G 343 VAL cc_start: 0.8451 (p) cc_final: 0.8193 (m) REVERT: G 353 ASN cc_start: 0.7668 (p0) cc_final: 0.7202 (p0) REVERT: G 401 LYS cc_start: 0.8178 (ttpp) cc_final: 0.7944 (ttpp) REVERT: G 405 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7957 (mmtt) REVERT: G 454 ASP cc_start: 0.7445 (m-30) cc_final: 0.7208 (m-30) REVERT: G 464 PHE cc_start: 0.8056 (m-80) cc_final: 0.7770 (m-80) REVERT: H 100 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7836 (p) REVERT: J 71 SER cc_start: 0.8052 (p) cc_final: 0.7793 (m) REVERT: K 50 ILE cc_start: 0.8345 (mm) cc_final: 0.8050 (mm) REVERT: L 79 GLN cc_start: 0.7661 (mm110) cc_final: 0.7152 (mm110) REVERT: L 102 THR cc_start: 0.8276 (t) cc_final: 0.8025 (p) REVERT: M 98 SER cc_start: 0.8280 (p) cc_final: 0.8027 (m) outliers start: 61 outliers final: 45 residues processed: 537 average time/residue: 0.3938 time to fit residues: 311.0953 Evaluate side-chains 548 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 499 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain 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 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain 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 10 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 0.0870 chunk 180 optimal weight: 2.9990 chunk 242 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 201 optimal weight: 0.7980 chunk 232 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 206 GLN F 307 GLN ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104401 restraints weight = 28252.158| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.79 r_work: 0.3158 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20988 Z= 0.180 Angle : 0.567 8.524 28518 Z= 0.303 Chirality : 0.045 0.210 3261 Planarity : 0.004 0.047 3618 Dihedral : 5.997 59.604 3166 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.95 % Allowed : 14.90 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2643 helix: 0.72 (0.25), residues: 423 sheet: -0.21 (0.16), residues: 954 loop : 0.16 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.005 0.001 HIS C 332 PHE 0.019 0.002 PHE J 29 TYR 0.021 0.002 TYR K 51 ARG 0.008 0.001 ARG G 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 6) link_NAG-ASN : angle 2.05860 ( 18) link_BETA1-4 : bond 0.00604 ( 6) link_BETA1-4 : angle 2.51271 ( 18) hydrogen bonds : bond 0.03751 ( 985) hydrogen bonds : angle 5.55170 ( 2604) SS BOND : bond 0.00390 ( 48) SS BOND : angle 1.09194 ( 96) covalent geometry : bond 0.00404 (20928) covalent geometry : angle 0.55857 (28386) *********************** 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 581 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 515 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8351 (m-80) cc_final: 0.8078 (m-80) REVERT: C 81 LEU cc_start: 0.8221 (tp) cc_final: 0.7994 (tp) REVERT: C 82 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7790 (mtt90) REVERT: C 129 ARG cc_start: 0.7540 (mtp180) cc_final: 0.7214 (ttp-170) REVERT: C 133 GLU cc_start: 0.7444 (tp30) cc_final: 0.6972 (tp30) REVERT: C 166 LYS cc_start: 0.7868 (tttt) cc_final: 0.7645 (tttt) REVERT: C 167 ASP cc_start: 0.7445 (m-30) cc_final: 0.7220 (m-30) REVERT: C 175 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7629 (ttp-170) REVERT: C 188 LYS cc_start: 0.7447 (tmmm) cc_final: 0.6893 (tmmm) REVERT: C 189 MET cc_start: 0.7376 (tpp) cc_final: 0.6821 (tpp) REVERT: C 192 SER cc_start: 0.8123 (t) cc_final: 0.7696 (p) REVERT: C 195 GLN cc_start: 0.8001 (mt0) cc_final: 0.7728 (mt0) REVERT: C 226 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7232 (mt-10) REVERT: C 233 ASN cc_start: 0.6659 (m110) cc_final: 0.6426 (m110) REVERT: C 248 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7586 (mtp85) REVERT: C 305 GLU cc_start: 0.7436 (tp30) cc_final: 0.6935 (mp0) REVERT: C 343 VAL cc_start: 0.8461 (p) cc_final: 0.8244 (m) REVERT: C 399 ILE cc_start: 0.7981 (mm) cc_final: 0.7705 (mt) REVERT: E 74 THR cc_start: 0.8094 (m) cc_final: 0.7517 (p) REVERT: F 62 ASP cc_start: 0.7704 (m-30) cc_final: 0.7186 (m-30) REVERT: F 133 GLU cc_start: 0.7440 (tp30) cc_final: 0.6811 (tp30) REVERT: F 175 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7473 (ttp-170) REVERT: F 189 MET cc_start: 0.7263 (mmt) cc_final: 0.6807 (mmt) REVERT: F 197 ASN cc_start: 0.8296 (p0) cc_final: 0.7753 (p0) REVERT: F 206 GLN cc_start: 0.7395 (mt0) cc_final: 0.7128 (mt0) REVERT: F 250 MET cc_start: 0.6899 (mmm) cc_final: 0.6591 (tmm) REVERT: F 294 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7230 (mt-10) REVERT: F 343 VAL cc_start: 0.8386 (p) cc_final: 0.8033 (m) REVERT: F 397 VAL cc_start: 0.7751 (t) cc_final: 0.7416 (m) REVERT: F 401 LYS cc_start: 0.8249 (ttpp) cc_final: 0.8005 (ttpp) REVERT: F 408 SER cc_start: 0.8148 (m) cc_final: 0.7911 (t) REVERT: F 449 VAL cc_start: 0.8417 (p) cc_final: 0.8184 (m) REVERT: G 20 LYS cc_start: 0.8347 (tttt) cc_final: 0.8114 (tttm) REVERT: G 70 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: G 129 ARG cc_start: 0.7418 (ttp-170) cc_final: 0.7164 (ttp-170) REVERT: G 131 GLU cc_start: 0.7636 (tt0) cc_final: 0.7181 (tt0) REVERT: G 156 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7103 (ptt-90) REVERT: G 163 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7231 (mtm-85) REVERT: G 167 ASP cc_start: 0.7475 (m-30) cc_final: 0.7103 (m-30) REVERT: G 177 ILE cc_start: 0.7609 (mt) cc_final: 0.7350 (mt) REVERT: G 192 SER cc_start: 0.7706 (m) cc_final: 0.7199 (p) REVERT: G 197 ASN cc_start: 0.8466 (p0) cc_final: 0.7810 (p0) REVERT: G 223 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7806 (p) REVERT: G 248 ARG cc_start: 0.7483 (ttm110) cc_final: 0.7260 (mtp85) REVERT: G 250 MET cc_start: 0.6748 (mmm) cc_final: 0.6410 (mmm) REVERT: G 280 ASP cc_start: 0.7606 (t70) cc_final: 0.7232 (t70) REVERT: G 343 VAL cc_start: 0.8454 (p) cc_final: 0.8192 (m) REVERT: G 353 ASN cc_start: 0.7693 (p0) cc_final: 0.7241 (p0) REVERT: G 405 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7950 (mmtt) REVERT: G 454 ASP cc_start: 0.7448 (m-30) cc_final: 0.7221 (m-30) REVERT: G 464 PHE cc_start: 0.8052 (m-80) cc_final: 0.7776 (m-80) REVERT: H 100 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7826 (p) REVERT: J 71 SER cc_start: 0.8050 (p) cc_final: 0.7788 (m) REVERT: K 50 ILE cc_start: 0.8354 (mm) cc_final: 0.8055 (mm) REVERT: L 102 THR cc_start: 0.8288 (t) cc_final: 0.8044 (p) outliers start: 66 outliers final: 51 residues processed: 552 average time/residue: 0.3604 time to fit residues: 290.9278 Evaluate side-chains 553 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 498 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 390 CYS 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 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 GLU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 6 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 241 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN L 89 GLN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104259 restraints weight = 28196.187| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.81 r_work: 0.3161 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20988 Z= 0.200 Angle : 0.575 8.609 28518 Z= 0.308 Chirality : 0.045 0.199 3261 Planarity : 0.004 0.041 3618 Dihedral : 5.983 59.090 3166 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.03 % Allowed : 15.35 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2643 helix: 0.68 (0.25), residues: 423 sheet: -0.21 (0.16), residues: 954 loop : 0.13 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 37 HIS 0.005 0.001 HIS C 332 PHE 0.020 0.002 PHE J 29 TYR 0.023 0.002 TYR K 51 ARG 0.007 0.000 ARG C 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 6) link_NAG-ASN : angle 2.61466 ( 18) link_BETA1-4 : bond 0.00468 ( 6) link_BETA1-4 : angle 2.04117 ( 18) hydrogen bonds : bond 0.03798 ( 985) hydrogen bonds : angle 5.56941 ( 2604) SS BOND : bond 0.00405 ( 48) SS BOND : angle 1.06246 ( 96) covalent geometry : bond 0.00453 (20928) covalent geometry : angle 0.56669 (28386) *********************** 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 579 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 511 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8350 (m-80) cc_final: 0.8098 (m-80) REVERT: C 70 GLU cc_start: 0.7137 (tp30) cc_final: 0.6883 (tp30) REVERT: C 81 LEU cc_start: 0.8215 (tp) cc_final: 0.7983 (tp) REVERT: C 82 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7778 (mtt90) REVERT: C 133 GLU cc_start: 0.7436 (tp30) cc_final: 0.6966 (tp30) REVERT: C 166 LYS cc_start: 0.7860 (tttt) cc_final: 0.7631 (tttt) REVERT: C 167 ASP cc_start: 0.7489 (m-30) cc_final: 0.7268 (m-30) REVERT: C 175 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7636 (ttp-170) REVERT: C 189 MET cc_start: 0.7408 (tpp) cc_final: 0.7071 (tpp) REVERT: C 192 SER cc_start: 0.8149 (t) cc_final: 0.7698 (p) REVERT: C 195 GLN cc_start: 0.8001 (mt0) cc_final: 0.7676 (mt0) REVERT: C 226 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7373 (mt-10) REVERT: C 248 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7564 (mtp85) REVERT: C 305 GLU cc_start: 0.7384 (tp30) cc_final: 0.6902 (mp0) REVERT: C 343 VAL cc_start: 0.8437 (p) cc_final: 0.8215 (m) REVERT: C 399 ILE cc_start: 0.7994 (mm) cc_final: 0.7707 (mt) REVERT: E 74 THR cc_start: 0.8092 (m) cc_final: 0.7538 (p) REVERT: F 62 ASP cc_start: 0.7688 (m-30) cc_final: 0.7179 (m-30) REVERT: F 133 GLU cc_start: 0.7446 (tp30) cc_final: 0.6803 (tp30) REVERT: F 163 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7390 (mtm-85) REVERT: F 175 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7293 (ttp-170) REVERT: F 178 ASN cc_start: 0.7980 (t0) cc_final: 0.7651 (t0) REVERT: F 189 MET cc_start: 0.7256 (mmt) cc_final: 0.6764 (mmt) REVERT: F 206 GLN cc_start: 0.7424 (mt0) cc_final: 0.7123 (mt0) REVERT: F 250 MET cc_start: 0.6970 (mmm) cc_final: 0.6686 (tmm) REVERT: F 294 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7255 (mt-10) REVERT: F 343 VAL cc_start: 0.8384 (p) cc_final: 0.8050 (m) REVERT: F 397 VAL cc_start: 0.7741 (t) cc_final: 0.7422 (m) REVERT: F 401 LYS cc_start: 0.8253 (ttpp) cc_final: 0.8009 (ttpp) REVERT: F 408 SER cc_start: 0.8187 (m) cc_final: 0.7959 (t) REVERT: F 412 ASN cc_start: 0.8163 (p0) cc_final: 0.7844 (p0) REVERT: F 413 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7994 (mm-40) REVERT: F 449 VAL cc_start: 0.8429 (p) cc_final: 0.8191 (m) REVERT: G 20 LYS cc_start: 0.8341 (tttt) cc_final: 0.8115 (tttm) REVERT: G 70 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: G 131 GLU cc_start: 0.7634 (tt0) cc_final: 0.7191 (tt0) REVERT: G 156 ARG cc_start: 0.7447 (ptm-80) cc_final: 0.7023 (ptt-90) REVERT: G 163 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7077 (mtm-85) REVERT: G 167 ASP cc_start: 0.7498 (m-30) cc_final: 0.7100 (m-30) REVERT: G 177 ILE cc_start: 0.7610 (mt) cc_final: 0.7332 (mt) REVERT: G 178 ASN cc_start: 0.7929 (t0) cc_final: 0.7716 (t0) REVERT: G 192 SER cc_start: 0.7717 (m) cc_final: 0.7222 (p) REVERT: G 197 ASN cc_start: 0.8481 (p0) cc_final: 0.7814 (p0) REVERT: G 223 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.7815 (p) REVERT: G 248 ARG cc_start: 0.7491 (ttm110) cc_final: 0.7203 (mtp85) REVERT: G 280 ASP cc_start: 0.7607 (t70) cc_final: 0.7238 (t70) REVERT: G 329 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7542 (ttm-80) REVERT: G 343 VAL cc_start: 0.8445 (p) cc_final: 0.8204 (m) REVERT: G 353 ASN cc_start: 0.7656 (p0) cc_final: 0.7214 (p0) REVERT: G 405 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7958 (mmtt) REVERT: G 454 ASP cc_start: 0.7472 (m-30) cc_final: 0.7254 (m-30) REVERT: G 464 PHE cc_start: 0.8052 (m-80) cc_final: 0.7764 (m-80) REVERT: H 100 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7864 (p) REVERT: J 71 SER cc_start: 0.8054 (p) cc_final: 0.7791 (m) REVERT: K 50 ILE cc_start: 0.8366 (mm) cc_final: 0.8036 (mm) REVERT: L 102 THR cc_start: 0.8320 (t) cc_final: 0.7992 (p) outliers start: 68 outliers final: 53 residues processed: 550 average time/residue: 0.3694 time to fit residues: 298.3086 Evaluate side-chains 562 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 506 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 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 F residue 390 CYS Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain F residue 430 VAL 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 162 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain 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 L residue 53 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 101 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 163 optimal weight: 0.0870 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 240 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 139 ASN G 422 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104949 restraints weight = 28265.919| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.81 r_work: 0.3173 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20988 Z= 0.160 Angle : 0.548 8.285 28518 Z= 0.293 Chirality : 0.044 0.200 3261 Planarity : 0.004 0.037 3618 Dihedral : 5.865 59.294 3166 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.72 % Allowed : 16.02 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2643 helix: 0.89 (0.25), residues: 420 sheet: -0.24 (0.17), residues: 927 loop : 0.16 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 50 HIS 0.004 0.001 HIS G 368 PHE 0.016 0.002 PHE J 29 TYR 0.020 0.002 TYR G 269 ARG 0.010 0.000 ARG C 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 6) link_NAG-ASN : angle 2.50417 ( 18) link_BETA1-4 : bond 0.00436 ( 6) link_BETA1-4 : angle 1.96349 ( 18) hydrogen bonds : bond 0.03568 ( 985) hydrogen bonds : angle 5.48679 ( 2604) SS BOND : bond 0.00371 ( 48) SS BOND : angle 0.93522 ( 96) covalent geometry : bond 0.00361 (20928) covalent geometry : angle 0.54117 (28386) *********************** 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 565 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 504 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8351 (m-80) cc_final: 0.8105 (m-80) REVERT: C 70 GLU cc_start: 0.7122 (tp30) cc_final: 0.6868 (tp30) REVERT: C 81 LEU cc_start: 0.8217 (tp) cc_final: 0.7985 (tp) REVERT: C 82 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7740 (mtt90) REVERT: C 129 ARG cc_start: 0.7480 (mtp180) cc_final: 0.7175 (ttp-170) REVERT: C 133 GLU cc_start: 0.7444 (tp30) cc_final: 0.6961 (tp30) REVERT: C 166 LYS cc_start: 0.7845 (tttt) cc_final: 0.7631 (tttt) REVERT: C 167 ASP cc_start: 0.7453 (m-30) cc_final: 0.7220 (m-30) REVERT: C 189 MET cc_start: 0.7385 (tpp) cc_final: 0.7057 (tpp) REVERT: C 192 SER cc_start: 0.8126 (t) cc_final: 0.7662 (p) REVERT: C 248 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7563 (mtp85) REVERT: C 305 GLU cc_start: 0.7381 (tp30) cc_final: 0.6913 (mp0) REVERT: C 343 VAL cc_start: 0.8447 (p) cc_final: 0.8225 (m) REVERT: C 399 ILE cc_start: 0.7973 (mm) cc_final: 0.7684 (mt) REVERT: E 74 THR cc_start: 0.8086 (m) cc_final: 0.7550 (p) REVERT: F 21 GLU cc_start: 0.7165 (tp30) cc_final: 0.6938 (tp30) REVERT: F 62 ASP cc_start: 0.7648 (m-30) cc_final: 0.7134 (m-30) REVERT: F 133 GLU cc_start: 0.7441 (tp30) cc_final: 0.6806 (tp30) REVERT: F 175 ARG cc_start: 0.7694 (ttp-170) cc_final: 0.7319 (ttp-170) REVERT: F 178 ASN cc_start: 0.7960 (t0) cc_final: 0.7612 (t0) REVERT: F 189 MET cc_start: 0.7245 (mmt) cc_final: 0.6756 (mmt) REVERT: F 206 GLN cc_start: 0.7431 (mt0) cc_final: 0.7150 (mt0) REVERT: F 236 THR cc_start: 0.7967 (p) cc_final: 0.7767 (p) REVERT: F 250 MET cc_start: 0.6976 (mmm) cc_final: 0.6681 (tmm) REVERT: F 294 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7266 (mt-10) REVERT: F 343 VAL cc_start: 0.8389 (p) cc_final: 0.8047 (m) REVERT: F 397 VAL cc_start: 0.7757 (t) cc_final: 0.7442 (m) REVERT: F 401 LYS cc_start: 0.8257 (ttpp) cc_final: 0.8004 (ttpp) REVERT: F 408 SER cc_start: 0.8183 (m) cc_final: 0.7896 (p) REVERT: G 20 LYS cc_start: 0.8340 (tttt) cc_final: 0.8113 (tttm) REVERT: G 40 ARG cc_start: 0.7856 (tmm160) cc_final: 0.7515 (ttp-110) REVERT: G 129 ARG cc_start: 0.7436 (ttp-170) cc_final: 0.7110 (ttp-170) REVERT: G 131 GLU cc_start: 0.7634 (tt0) cc_final: 0.7299 (tt0) REVERT: G 156 ARG cc_start: 0.7466 (ptm-80) cc_final: 0.7056 (ptt-90) REVERT: G 163 ARG cc_start: 0.7670 (ttm-80) cc_final: 0.7010 (mtm-85) REVERT: G 167 ASP cc_start: 0.7517 (m-30) cc_final: 0.7086 (m-30) REVERT: G 177 ILE cc_start: 0.7588 (mt) cc_final: 0.7339 (mt) REVERT: G 178 ASN cc_start: 0.7934 (t0) cc_final: 0.7712 (t0) REVERT: G 192 SER cc_start: 0.7693 (m) cc_final: 0.7165 (p) REVERT: G 197 ASN cc_start: 0.8460 (p0) cc_final: 0.7835 (p0) REVERT: G 223 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.7798 (p) REVERT: G 248 ARG cc_start: 0.7494 (ttm110) cc_final: 0.7265 (mtp85) REVERT: G 250 MET cc_start: 0.6765 (mmm) cc_final: 0.6488 (mmm) REVERT: G 280 ASP cc_start: 0.7602 (t70) cc_final: 0.7218 (t70) REVERT: G 343 VAL cc_start: 0.8451 (p) cc_final: 0.8209 (m) REVERT: G 353 ASN cc_start: 0.7648 (p0) cc_final: 0.7213 (p0) REVERT: G 405 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7945 (mmtt) REVERT: G 454 ASP cc_start: 0.7477 (m-30) cc_final: 0.7248 (m-30) REVERT: G 464 PHE cc_start: 0.8044 (m-80) cc_final: 0.7756 (m-80) REVERT: J 28 THR cc_start: 0.8547 (m) cc_final: 0.8077 (p) REVERT: J 71 SER cc_start: 0.8040 (p) cc_final: 0.7777 (m) REVERT: K 50 ILE cc_start: 0.8339 (mm) cc_final: 0.7992 (mm) REVERT: L 102 THR cc_start: 0.8334 (t) cc_final: 0.8021 (p) outliers start: 61 outliers final: 51 residues processed: 539 average time/residue: 0.3629 time to fit residues: 286.7556 Evaluate side-chains 549 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 497 time to evaluate : 2.141 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 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 73 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 GLU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 49 LEU 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 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 44 optimal weight: 0.0870 chunk 65 optimal weight: 5.9990 chunk 232 optimal weight: 0.4980 chunk 175 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 F 195 GLN F 307 GLN F 413 GLN G 139 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103573 restraints weight = 28342.745| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.90 r_work: 0.3148 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20988 Z= 0.221 Angle : 0.587 8.448 28518 Z= 0.314 Chirality : 0.046 0.211 3261 Planarity : 0.004 0.042 3618 Dihedral : 5.976 59.193 3166 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.68 % Allowed : 16.56 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2643 helix: 0.69 (0.25), residues: 420 sheet: -0.28 (0.17), residues: 918 loop : 0.06 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 37 HIS 0.005 0.001 HIS C 332 PHE 0.020 0.002 PHE J 29 TYR 0.025 0.002 TYR K 51 ARG 0.006 0.000 ARG C 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 6) link_NAG-ASN : angle 2.64483 ( 18) link_BETA1-4 : bond 0.00439 ( 6) link_BETA1-4 : angle 2.06069 ( 18) hydrogen bonds : bond 0.03840 ( 985) hydrogen bonds : angle 5.59913 ( 2604) SS BOND : bond 0.00408 ( 48) SS BOND : angle 1.09503 ( 96) covalent geometry : bond 0.00506 (20928) covalent geometry : angle 0.57876 (28386) *********************** 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 564 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 504 time to evaluate : 2.257 Fit side-chains revert: symmetry clash REVERT: C 81 LEU cc_start: 0.8215 (tp) cc_final: 0.7991 (tp) REVERT: C 129 ARG cc_start: 0.7493 (mtp180) cc_final: 0.7216 (ttp-170) REVERT: C 133 GLU cc_start: 0.7462 (tp30) cc_final: 0.6997 (tp30) REVERT: C 166 LYS cc_start: 0.7872 (tttt) cc_final: 0.7658 (tttt) REVERT: C 167 ASP cc_start: 0.7524 (m-30) cc_final: 0.7298 (m-30) REVERT: C 189 MET cc_start: 0.7470 (tpp) cc_final: 0.7153 (tpp) REVERT: C 192 SER cc_start: 0.8169 (t) cc_final: 0.7704 (p) REVERT: C 248 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7590 (mtp85) REVERT: C 305 GLU cc_start: 0.7357 (tp30) cc_final: 0.6890 (mp0) REVERT: C 343 VAL cc_start: 0.8427 (p) cc_final: 0.8209 (m) REVERT: C 399 ILE cc_start: 0.8014 (mm) cc_final: 0.7734 (mt) REVERT: C 450 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8118 (mmtt) REVERT: E 74 THR cc_start: 0.8095 (m) cc_final: 0.7555 (p) REVERT: F 21 GLU cc_start: 0.7235 (tp30) cc_final: 0.6941 (tp30) REVERT: F 62 ASP cc_start: 0.7653 (m-30) cc_final: 0.7163 (m-30) REVERT: F 133 GLU cc_start: 0.7460 (tp30) cc_final: 0.6790 (tp30) REVERT: F 175 ARG cc_start: 0.7756 (ttp-170) cc_final: 0.7360 (ttp-170) REVERT: F 178 ASN cc_start: 0.7985 (t0) cc_final: 0.7646 (t0) REVERT: F 189 MET cc_start: 0.7286 (mmt) cc_final: 0.6790 (mmt) REVERT: F 206 GLN cc_start: 0.7449 (mt0) cc_final: 0.7241 (mt0) REVERT: F 250 MET cc_start: 0.7016 (mmm) cc_final: 0.6683 (tmm) REVERT: F 294 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7258 (mt-10) REVERT: F 343 VAL cc_start: 0.8379 (p) cc_final: 0.8051 (m) REVERT: F 378 LEU cc_start: 0.8122 (mt) cc_final: 0.7921 (mp) REVERT: F 401 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7997 (ttpp) REVERT: F 408 SER cc_start: 0.8218 (m) cc_final: 0.7932 (p) REVERT: G 20 LYS cc_start: 0.8331 (tttt) cc_final: 0.8111 (tttm) REVERT: G 40 ARG cc_start: 0.7857 (tmm160) cc_final: 0.7474 (ttp-110) REVERT: G 129 ARG cc_start: 0.7450 (ttp-170) cc_final: 0.7137 (ttp-170) REVERT: G 131 GLU cc_start: 0.7731 (tt0) cc_final: 0.7394 (tt0) REVERT: G 156 ARG cc_start: 0.7535 (ptm-80) cc_final: 0.7143 (ptt-90) REVERT: G 163 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7127 (mtm-85) REVERT: G 167 ASP cc_start: 0.7569 (m-30) cc_final: 0.7129 (m-30) REVERT: G 177 ILE cc_start: 0.7610 (mt) cc_final: 0.7332 (mt) REVERT: G 178 ASN cc_start: 0.7964 (t0) cc_final: 0.7745 (t0) REVERT: G 192 SER cc_start: 0.7738 (m) cc_final: 0.7253 (p) REVERT: G 197 ASN cc_start: 0.8502 (p0) cc_final: 0.7846 (p0) REVERT: G 223 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.7839 (p) REVERT: G 248 ARG cc_start: 0.7526 (ttm110) cc_final: 0.7289 (mtp85) REVERT: G 280 ASP cc_start: 0.7630 (t70) cc_final: 0.7266 (t70) REVERT: G 343 VAL cc_start: 0.8409 (p) cc_final: 0.8181 (m) REVERT: G 353 ASN cc_start: 0.7677 (p0) cc_final: 0.7256 (p0) REVERT: G 405 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7972 (mmtt) REVERT: G 454 ASP cc_start: 0.7539 (m-30) cc_final: 0.7323 (m-30) REVERT: J 71 SER cc_start: 0.8069 (p) cc_final: 0.7806 (m) REVERT: K 50 ILE cc_start: 0.8392 (mm) cc_final: 0.8055 (mm) REVERT: L 79 GLN cc_start: 0.7718 (mm110) cc_final: 0.7279 (mm110) REVERT: L 102 THR cc_start: 0.8369 (t) cc_final: 0.8064 (p) outliers start: 60 outliers final: 53 residues processed: 536 average time/residue: 0.3738 time to fit residues: 294.5935 Evaluate side-chains 549 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 495 time to evaluate : 2.199 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 GLU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 49 LEU 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 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 170 optimal weight: 0.5980 chunk 198 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 258 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** F 195 GLN F 307 GLN G 139 ASN G 202 ASN G 351 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104639 restraints weight = 28284.133| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.79 r_work: 0.3168 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20988 Z= 0.173 Angle : 0.561 8.050 28518 Z= 0.299 Chirality : 0.045 0.195 3261 Planarity : 0.004 0.042 3618 Dihedral : 5.879 58.357 3166 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.50 % Allowed : 17.09 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.17), residues: 2643 helix: 0.83 (0.25), residues: 420 sheet: -0.29 (0.17), residues: 927 loop : 0.11 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.005 0.001 HIS F 368 PHE 0.015 0.002 PHE J 29 TYR 0.024 0.002 TYR G 269 ARG 0.006 0.000 ARG C 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 6) link_NAG-ASN : angle 2.83473 ( 18) link_BETA1-4 : bond 0.00440 ( 6) link_BETA1-4 : angle 2.06302 ( 18) hydrogen bonds : bond 0.03628 ( 985) hydrogen bonds : angle 5.52537 ( 2604) SS BOND : bond 0.00359 ( 48) SS BOND : angle 0.96652 ( 96) covalent geometry : bond 0.00393 (20928) covalent geometry : angle 0.55257 (28386) ********************** 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 552 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 496 time to evaluate : 2.124 Fit side-chains revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8333 (m-80) cc_final: 0.8102 (m-80) REVERT: C 70 GLU cc_start: 0.7134 (tp30) cc_final: 0.6881 (tp30) REVERT: C 81 LEU cc_start: 0.8219 (tp) cc_final: 0.7985 (tp) REVERT: C 129 ARG cc_start: 0.7467 (mtp180) cc_final: 0.7176 (ttp-170) REVERT: C 133 GLU cc_start: 0.7432 (tp30) cc_final: 0.6958 (tp30) REVERT: C 166 LYS cc_start: 0.7843 (tttt) cc_final: 0.7621 (tttt) REVERT: C 167 ASP cc_start: 0.7449 (m-30) cc_final: 0.7213 (m-30) REVERT: C 189 MET cc_start: 0.7418 (tpp) cc_final: 0.7094 (tpp) REVERT: C 192 SER cc_start: 0.8111 (t) cc_final: 0.7670 (p) REVERT: C 248 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7581 (mtp85) REVERT: C 305 GLU cc_start: 0.7352 (tp30) cc_final: 0.6885 (mp0) REVERT: C 343 VAL cc_start: 0.8418 (p) cc_final: 0.8185 (m) REVERT: C 399 ILE cc_start: 0.7980 (mm) cc_final: 0.7691 (mt) REVERT: E 74 THR cc_start: 0.8094 (m) cc_final: 0.7562 (p) REVERT: F 21 GLU cc_start: 0.7193 (tp30) cc_final: 0.6923 (tp30) REVERT: F 62 ASP cc_start: 0.7627 (m-30) cc_final: 0.7142 (m-30) REVERT: F 133 GLU cc_start: 0.7447 (tp30) cc_final: 0.6749 (tp30) REVERT: F 175 ARG cc_start: 0.7712 (ttp-170) cc_final: 0.7327 (ttp-170) REVERT: F 178 ASN cc_start: 0.7944 (t0) cc_final: 0.7617 (t0) REVERT: F 189 MET cc_start: 0.7256 (mmt) cc_final: 0.6755 (mmt) REVERT: F 250 MET cc_start: 0.6995 (mmm) cc_final: 0.6664 (tmm) REVERT: F 343 VAL cc_start: 0.8356 (p) cc_final: 0.8036 (m) REVERT: F 397 VAL cc_start: 0.7689 (t) cc_final: 0.7380 (m) REVERT: F 401 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7970 (ttpp) REVERT: F 408 SER cc_start: 0.8188 (m) cc_final: 0.7928 (p) REVERT: G 20 LYS cc_start: 0.8313 (tttt) cc_final: 0.8066 (tttm) REVERT: G 40 ARG cc_start: 0.7872 (tmm160) cc_final: 0.7484 (ttp-110) REVERT: G 131 GLU cc_start: 0.7683 (tt0) cc_final: 0.7354 (tt0) REVERT: G 156 ARG cc_start: 0.7476 (ptm-80) cc_final: 0.7073 (ptt-90) REVERT: G 163 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.6982 (mtm-85) REVERT: G 167 ASP cc_start: 0.7540 (m-30) cc_final: 0.7069 (m-30) REVERT: G 177 ILE cc_start: 0.7572 (mt) cc_final: 0.7312 (mt) REVERT: G 178 ASN cc_start: 0.7940 (t0) cc_final: 0.7737 (t0) REVERT: G 192 SER cc_start: 0.7698 (m) cc_final: 0.7199 (p) REVERT: G 197 ASN cc_start: 0.8482 (p0) cc_final: 0.7838 (p0) REVERT: G 223 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.7823 (p) REVERT: G 248 ARG cc_start: 0.7491 (ttm110) cc_final: 0.7216 (mtp85) REVERT: G 250 MET cc_start: 0.6743 (mmm) cc_final: 0.6514 (mmm) REVERT: G 280 ASP cc_start: 0.7618 (t70) cc_final: 0.7265 (t70) REVERT: G 329 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.7434 (ttm110) REVERT: G 343 VAL cc_start: 0.8402 (p) cc_final: 0.8180 (m) REVERT: G 353 ASN cc_start: 0.7623 (p0) cc_final: 0.7198 (p0) REVERT: G 405 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7957 (mmtt) REVERT: G 454 ASP cc_start: 0.7510 (m-30) cc_final: 0.7289 (m-30) REVERT: J 71 SER cc_start: 0.8042 (p) cc_final: 0.7775 (m) REVERT: K 50 ILE cc_start: 0.8346 (mm) cc_final: 0.8041 (mm) REVERT: L 79 GLN cc_start: 0.7701 (mm110) cc_final: 0.7249 (mm-40) REVERT: L 102 THR cc_start: 0.8367 (t) cc_final: 0.8085 (p) outliers start: 56 outliers final: 54 residues processed: 528 average time/residue: 0.3958 time to fit residues: 308.7162 Evaluate side-chains 545 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 490 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 GLU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 49 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 176 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 239 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 307 GLN G 46 ASN G 139 ASN G 351 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103874 restraints weight = 28515.408| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.89 r_work: 0.3154 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20988 Z= 0.194 Angle : 0.573 8.280 28518 Z= 0.306 Chirality : 0.045 0.203 3261 Planarity : 0.004 0.044 3618 Dihedral : 5.902 58.504 3166 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.50 % Allowed : 17.31 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2643 helix: 0.78 (0.25), residues: 420 sheet: -0.31 (0.17), residues: 927 loop : 0.07 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 37 HIS 0.004 0.001 HIS F 368 PHE 0.018 0.002 PHE J 29 TYR 0.025 0.002 TYR G 269 ARG 0.005 0.000 ARG C 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 6) link_NAG-ASN : angle 2.88358 ( 18) link_BETA1-4 : bond 0.00426 ( 6) link_BETA1-4 : angle 1.95890 ( 18) hydrogen bonds : bond 0.03700 ( 985) hydrogen bonds : angle 5.53864 ( 2604) SS BOND : bond 0.00387 ( 48) SS BOND : angle 1.02025 ( 96) covalent geometry : bond 0.00443 (20928) covalent geometry : angle 0.56435 (28386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11672.44 seconds wall clock time: 200 minutes 37.11 seconds (12037.11 seconds total)