Starting phenix.real_space_refine on Thu Feb 5 11:06:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lho_63103/02_2026/9lho_63103.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lho_63103/02_2026/9lho_63103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lho_63103/02_2026/9lho_63103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lho_63103/02_2026/9lho_63103.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lho_63103/02_2026/9lho_63103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lho_63103/02_2026/9lho_63103.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10335 2.51 5 N 2927 2.21 5 O 3280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16638 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2386 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 299} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1326 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 162} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 846 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "C" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2386 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 299} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1326 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 162} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 846 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2386 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 299} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1326 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 162} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 846 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 946 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 946 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 946 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.94, per 1000 atoms: 0.24 Number of scatterers: 16638 At special positions: 0 Unit cell: (142.48, 140.4, 141.44, 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 96 16.00 O 3280 8.00 N 2927 7.00 C 10335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS B 458 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 268 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 66 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 129 " distance=2.04 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 296 " distance=2.02 Simple disulfide: pdb=" SG CYS B 465 " - pdb=" SG CYS B 469 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 94 " distance=2.04 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS D 458 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 268 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 66 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 296 " distance=2.02 Simple disulfide: pdb=" SG CYS D 465 " - pdb=" SG CYS D 469 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 94 " distance=2.04 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 458 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 268 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 66 " distance=2.02 Simple disulfide: pdb=" SG CYS E 87 " - pdb=" SG CYS E 129 " distance=2.03 Simple disulfide: pdb=" SG CYS E 272 " - pdb=" SG CYS E 296 " distance=2.02 Simple disulfide: pdb=" SG CYS F 465 " - pdb=" SG CYS F 469 " distance=2.02 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 94 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 104 " - pdb=" SG CYS I 109 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 104 " - pdb=" SG CYS O 109 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.03 Simple disulfide: pdb=" SG CYS T 104 " - pdb=" SG CYS T 109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 28 " " NAG A 602 " - " ASN A 231 " " NAG B 601 " - " ASN B 403 " " NAG C 601 " - " ASN C 28 " " NAG C 602 " - " ASN C 231 " " NAG D 601 " - " ASN D 403 " " NAG E 601 " - " ASN E 28 " " NAG E 602 " - " ASN E 231 " " NAG F 601 " - " ASN F 403 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 901.0 milliseconds 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 48 sheets defined 17.9% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.549A pdb=" N GLU A 104 " --> pdb=" O GLN A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'B' and resid 359 through 377 Processing helix chain 'B' and resid 395 through 447 Processing helix chain 'B' and resid 467 through 475 removed outlier: 3.838A pdb=" N ALA B 471 " --> pdb=" O ASP B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 removed outlier: 3.690A pdb=" N ARG B 484 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 89 removed outlier: 3.942A pdb=" N VAL H 89 " --> pdb=" O ALA H 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.509A pdb=" N THR C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 removed outlier: 3.554A pdb=" N ASP C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.560A pdb=" N LEU C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'D' and resid 359 through 377 Processing helix chain 'D' and resid 395 through 447 Processing helix chain 'D' and resid 467 through 475 Processing helix chain 'D' and resid 479 through 483 removed outlier: 3.792A pdb=" N LYS D 482 " --> pdb=" O ASP D 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 4.012A pdb=" N THR E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 67 removed outlier: 3.687A pdb=" N ASP E 67 " --> pdb=" O PRO E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 178 through 186 Processing helix chain 'F' and resid 359 through 377 Processing helix chain 'F' and resid 395 through 447 Processing helix chain 'F' and resid 467 through 475 removed outlier: 3.637A pdb=" N ALA F 471 " --> pdb=" O ASP F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 482 removed outlier: 4.099A pdb=" N LYS F 482 " --> pdb=" O ASP F 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 479 through 482' Processing helix chain 'F' and resid 483 through 488 removed outlier: 3.503A pdb=" N ALA F 487 " --> pdb=" O TYR F 483 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 89 removed outlier: 3.929A pdb=" N VAL S 89 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.622A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.510A pdb=" N THR O 91 " --> pdb=" O ALA O 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 91 removed outlier: 3.594A pdb=" N ASP T 90 " --> pdb=" O ARG T 87 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR T 91 " --> pdb=" O ALA T 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.739A pdb=" N GLY A 6 " --> pdb=" O GLY B 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 41 through 42 removed outlier: 5.910A pdb=" N ILE A 41 " --> pdb=" O ASP A 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.112A pdb=" N ILE A 77 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.833A pdb=" N LYS A 91 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TRP A 225 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 170 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ARG A 247 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.833A pdb=" N LYS A 91 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TRP A 225 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL A 170 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 242 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 126 through 130 Processing sheet with id=AB1, first strand: chain 'A' and resid 155 through 161 removed outlier: 3.874A pdb=" N ASP A 232 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 277 through 279 removed outlier: 4.279A pdb=" N CYS A 272 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 273 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 293 " --> pdb=" O TYR A 273 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 451 through 453 removed outlier: 3.667A pdb=" N GLU B 452 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.637A pdb=" N LEU H 11 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP H 41 " --> pdb=" O LEU H 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.559A pdb=" N GLY C 6 " --> pdb=" O GLY D 344 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB9, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AC1, first strand: chain 'C' and resid 41 through 42 removed outlier: 5.736A pdb=" N ILE C 41 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 49 through 50 removed outlier: 6.707A pdb=" N VAL C 49 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 77 " --> pdb=" O ILE C 258 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.797A pdb=" N LYS C 91 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N TRP C 225 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL C 170 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG C 247 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.797A pdb=" N LYS C 91 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N TRP C 225 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL C 170 " --> pdb=" O PRO C 245 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE C 242 " --> pdb=" O LEU C 143 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 126 through 130 Processing sheet with id=AC6, first strand: chain 'C' and resid 155 through 160 Processing sheet with id=AC7, first strand: chain 'C' and resid 277 through 278 Processing sheet with id=AC8, first strand: chain 'D' and resid 451 through 453 removed outlier: 3.645A pdb=" N GLU D 452 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AD1, first strand: chain 'N' and resid 11 through 12 removed outlier: 4.122A pdb=" N LEU N 11 " --> pdb=" O LYS N 109 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.984A pdb=" N GLY E 6 " --> pdb=" O GLY F 344 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AD4, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AD5, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AD6, first strand: chain 'E' and resid 41 through 42 removed outlier: 5.964A pdb=" N ILE E 41 " --> pdb=" O ASP E 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 48 through 50 removed outlier: 6.277A pdb=" N ILE E 77 " --> pdb=" O ILE E 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 108 through 112 removed outlier: 6.963A pdb=" N ARG E 247 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL E 170 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL E 170 " --> pdb=" O PRO E 245 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 108 through 112 removed outlier: 6.963A pdb=" N ARG E 247 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL E 170 " --> pdb=" O ARG E 247 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 126 through 130 Processing sheet with id=AE2, first strand: chain 'E' and resid 155 through 161 removed outlier: 3.817A pdb=" N ASP E 232 " --> pdb=" O ASN E 161 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 277 through 279 removed outlier: 4.187A pdb=" N CYS E 272 " --> pdb=" O ILE E 279 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 451 through 453 Processing sheet with id=AE5, first strand: chain 'S' and resid 11 through 12 removed outlier: 5.577A pdb=" N LEU S 11 " --> pdb=" O GLU S 111 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP S 41 " --> pdb=" O LEU S 53 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.580A pdb=" N GLY I 10 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 3 through 7 removed outlier: 4.023A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER O 25 " --> pdb=" O GLN O 3 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR O 69 " --> pdb=" O GLN O 82 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.611A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL O 50 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 3 through 7 removed outlier: 3.866A pdb=" N GLN T 3 " --> pdb=" O SER T 25 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER T 25 " --> pdb=" O GLN T 3 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET T 83 " --> pdb=" O LEU T 18 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 11 through 12 removed outlier: 7.298A pdb=" N LEU T 34 " --> pdb=" O VAL T 50 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL T 50 " --> pdb=" O LEU T 34 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP T 36 " --> pdb=" O VAL T 48 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1605 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: 2.63 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5545 1.34 - 1.46: 3673 1.46 - 1.58: 7612 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 16968 Sorted by residual: bond pdb=" N THR S 100 " pdb=" CA THR S 100 " ideal model delta sigma weight residual 1.462 1.495 -0.033 9.50e-03 1.11e+04 1.20e+01 bond pdb=" N SER I 106 " pdb=" CA SER I 106 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.26e+00 bond pdb=" N ILE I 108 " pdb=" CA ILE I 108 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.15e-02 7.56e+03 7.17e+00 bond pdb=" N SER S 99 " pdb=" CA SER S 99 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.18e-02 7.18e+03 6.67e+00 bond pdb=" N CYS I 104 " pdb=" CA CYS I 104 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.42e-02 4.96e+03 6.39e+00 ... (remaining 16963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 22499 2.32 - 4.64: 403 4.64 - 6.96: 52 6.96 - 9.28: 7 9.28 - 11.60: 1 Bond angle restraints: 22962 Sorted by residual: angle pdb=" N CYS I 109 " pdb=" CA CYS I 109 " pdb=" C CYS I 109 " ideal model delta sigma weight residual 113.50 105.74 7.76 1.23e+00 6.61e-01 3.98e+01 angle pdb=" N CYS O 109 " pdb=" CA CYS O 109 " pdb=" C CYS O 109 " ideal model delta sigma weight residual 114.56 106.59 7.97 1.27e+00 6.20e-01 3.94e+01 angle pdb=" C THR H 100 " pdb=" N PRO H 101 " pdb=" CA PRO H 101 " ideal model delta sigma weight residual 119.84 113.69 6.15 1.25e+00 6.40e-01 2.42e+01 angle pdb=" C SER H 31 " pdb=" CA SER H 31 " pdb=" CB SER H 31 " ideal model delta sigma weight residual 116.34 109.90 6.44 1.40e+00 5.10e-01 2.12e+01 angle pdb=" CA CYS O 109 " pdb=" C CYS O 109 " pdb=" N TYR O 110 " ideal model delta sigma weight residual 119.26 114.40 4.86 1.14e+00 7.69e-01 1.82e+01 ... (remaining 22957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9088 17.97 - 35.94: 885 35.94 - 53.91: 214 53.91 - 71.88: 29 71.88 - 89.85: 26 Dihedral angle restraints: 10242 sinusoidal: 4164 harmonic: 6078 Sorted by residual: dihedral pdb=" CB CYS O 104 " pdb=" SG CYS O 104 " pdb=" SG CYS O 109 " pdb=" CB CYS O 109 " ideal model delta sinusoidal sigma weight residual -86.00 -150.96 64.96 1 1.00e+01 1.00e-02 5.54e+01 dihedral pdb=" CA ASN C 231 " pdb=" C ASN C 231 " pdb=" N ASP C 232 " pdb=" CA ASP C 232 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA CYS C 129 " pdb=" C CYS C 129 " pdb=" N ARG C 130 " pdb=" CA ARG C 130 " ideal model delta harmonic sigma weight residual -180.00 -157.01 -22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 10239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2033 0.057 - 0.114: 418 0.114 - 0.171: 57 0.171 - 0.228: 3 0.228 - 0.285: 3 Chirality restraints: 2514 Sorted by residual: chirality pdb=" CB ILE E 280 " pdb=" CA ILE E 280 " pdb=" CG1 ILE E 280 " pdb=" CG2 ILE E 280 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CG LEU F 420 " pdb=" CB LEU F 420 " pdb=" CD1 LEU F 420 " pdb=" CD2 LEU F 420 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ASN H 37 " pdb=" N ASN H 37 " pdb=" C ASN H 37 " pdb=" CB ASN H 37 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2511 not shown) Planarity restraints: 3009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 56 " 0.018 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP H 56 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP H 56 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP H 56 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 56 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 56 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 56 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 56 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 56 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 56 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 231 " 0.002 2.00e-02 2.50e+03 2.86e-02 1.03e+01 pdb=" CG ASN C 231 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN C 231 " -0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN C 231 " 0.033 2.00e-02 2.50e+03 pdb=" C1 NAG C 602 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 64 " 0.050 5.00e-02 4.00e+02 7.68e-02 9.45e+00 pdb=" N PRO H 65 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO H 65 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 65 " 0.042 5.00e-02 4.00e+02 ... (remaining 3006 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1179 2.74 - 3.28: 16248 3.28 - 3.82: 29386 3.82 - 4.36: 34379 4.36 - 4.90: 59465 Nonbonded interactions: 140657 Sorted by model distance: nonbonded pdb=" OG1 THR H 69 " pdb=" OG1 THR H 80 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR N 69 " pdb=" OG1 THR N 80 " model vdw 2.207 3.040 nonbonded pdb=" O PHE A 92 " pdb=" CG GLU A 95 " model vdw 2.272 3.440 nonbonded pdb=" OG1 THR S 69 " pdb=" OG1 THR S 80 " model vdw 2.275 3.040 nonbonded pdb=" OE1 GLN S 6 " pdb=" OG1 THR S 108 " model vdw 2.289 3.040 ... (remaining 140652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 602)) selection = (chain 'C' and (resid 3 through 262 or (resid 263 and (name N or name CA or name \ C or name O or name CB )) or resid 264 through 602)) selection = (chain 'E' and (resid 3 through 262 or (resid 263 and (name N or name CA or name \ C or name O or name CB )) or resid 264 through 602)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'N' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'O' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.090 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1007 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 0.072 17004 Z= 0.183 Angle : 0.749 11.601 23043 Z= 0.403 Chirality : 0.047 0.285 2514 Planarity : 0.006 0.077 3000 Dihedral : 15.221 89.849 6297 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.15 % Favored : 93.71 % Rotamer: Outliers : 0.28 % Allowed : 0.78 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.17), residues: 2115 helix: 0.87 (0.29), residues: 288 sheet: -0.53 (0.22), residues: 549 loop : -1.52 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 346 TYR 0.021 0.002 TYR O 103 PHE 0.023 0.002 PHE E 204 TRP 0.056 0.002 TRP H 56 HIS 0.006 0.001 HIS I 111 Details of bonding type rmsd covalent geometry : bond 0.00368 (16968) covalent geometry : angle 0.73497 (22962) SS BOND : bond 0.00504 ( 27) SS BOND : angle 2.37625 ( 54) hydrogen bonds : bond 0.15590 ( 578) hydrogen bonds : angle 7.25789 ( 1605) link_NAG-ASN : bond 0.00507 ( 9) link_NAG-ASN : angle 2.95361 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 404 TRP cc_start: 0.3664 (t60) cc_final: 0.3348 (t60) REVERT: N 38 TYR cc_start: -0.0715 (m-80) cc_final: -0.0980 (m-80) REVERT: F 466 ASP cc_start: 0.3117 (p0) cc_final: 0.1392 (m-30) REVERT: O 83 MET cc_start: -0.0786 (mmp) cc_final: -0.2010 (mmm) outliers start: 5 outliers final: 2 residues processed: 180 average time/residue: 0.1225 time to fit residues: 32.7840 Evaluate side-chains 156 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain I residue 108 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 224 HIS A 259 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN C 287 ASN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN N 44 GLN E 259 GLN F 389 ASN F 463 HIS F 490 ASN O 13 GLN ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 HIS T 80 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.167663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.153692 restraints weight = 27805.125| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.75 r_work: 0.3975 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1390 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17004 Z= 0.161 Angle : 0.640 7.583 23043 Z= 0.338 Chirality : 0.045 0.234 2514 Planarity : 0.005 0.064 3000 Dihedral : 5.782 52.459 2521 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.50 % Allowed : 7.33 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.18), residues: 2115 helix: 1.15 (0.28), residues: 306 sheet: -0.52 (0.22), residues: 570 loop : -1.41 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 474 TYR 0.023 0.002 TYR B 440 PHE 0.017 0.002 PHE E 238 TRP 0.043 0.003 TRP N 56 HIS 0.008 0.002 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00349 (16968) covalent geometry : angle 0.63536 (22962) SS BOND : bond 0.00653 ( 27) SS BOND : angle 1.27688 ( 54) hydrogen bonds : bond 0.03958 ( 578) hydrogen bonds : angle 5.91443 ( 1605) link_NAG-ASN : bond 0.00584 ( 9) link_NAG-ASN : angle 1.65041 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 SER cc_start: 0.6942 (t) cc_final: 0.6733 (m) REVERT: C 21 GLU cc_start: -0.0891 (OUTLIER) cc_final: -0.1251 (pt0) REVERT: D 447 LEU cc_start: 0.3521 (pp) cc_final: 0.3135 (pp) REVERT: E 21 GLU cc_start: -0.0771 (OUTLIER) cc_final: -0.1505 (tt0) REVERT: S 38 TYR cc_start: -0.0231 (m-80) cc_final: -0.0442 (m-80) REVERT: I 32 TYR cc_start: 0.2738 (m-80) cc_final: 0.1899 (m-80) REVERT: O 83 MET cc_start: -0.1028 (mmp) cc_final: -0.1567 (mmm) outliers start: 9 outliers final: 4 residues processed: 154 average time/residue: 0.1211 time to fit residues: 28.6207 Evaluate side-chains 145 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain I residue 108 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 163 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 196 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN E 263 GLN F 450 ASN S 6 GLN I 111 HIS O 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.170556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.156703 restraints weight = 28217.637| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.77 r_work: 0.4009 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1536 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17004 Z= 0.145 Angle : 0.582 6.991 23043 Z= 0.309 Chirality : 0.043 0.169 2514 Planarity : 0.005 0.059 3000 Dihedral : 5.320 47.783 2521 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.06 % Allowed : 10.91 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.18), residues: 2115 helix: 0.91 (0.27), residues: 324 sheet: -0.55 (0.20), residues: 651 loop : -1.51 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 220 TYR 0.020 0.002 TYR B 440 PHE 0.025 0.002 PHE E 238 TRP 0.040 0.002 TRP H 56 HIS 0.007 0.001 HIS E 174 Details of bonding type rmsd covalent geometry : bond 0.00317 (16968) covalent geometry : angle 0.57831 (22962) SS BOND : bond 0.00296 ( 27) SS BOND : angle 1.05113 ( 54) hydrogen bonds : bond 0.03703 ( 578) hydrogen bonds : angle 5.74239 ( 1605) link_NAG-ASN : bond 0.00375 ( 9) link_NAG-ASN : angle 1.42344 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 56 TRP cc_start: 0.2874 (m-90) cc_final: 0.2089 (m-90) REVERT: D 433 ASP cc_start: 0.4180 (m-30) cc_final: 0.3827 (m-30) REVERT: D 447 LEU cc_start: 0.3885 (OUTLIER) cc_final: 0.3010 (pp) REVERT: E 220 ARG cc_start: 0.1824 (mmt90) cc_final: 0.1383 (mmt90) REVERT: E 256 MET cc_start: 0.1075 (ptp) cc_final: 0.0863 (ptm) REVERT: S 100 THR cc_start: -0.3179 (OUTLIER) cc_final: -0.3638 (p) outliers start: 19 outliers final: 10 residues processed: 157 average time/residue: 0.1418 time to fit residues: 34.0991 Evaluate side-chains 150 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain F residue 342 TRP Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain I residue 108 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 104 optimal weight: 0.5980 chunk 157 optimal weight: 0.5980 chunk 139 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN C 202 GLN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.172181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.158377 restraints weight = 28159.005| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.77 r_work: 0.4032 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1583 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17004 Z= 0.120 Angle : 0.540 6.794 23043 Z= 0.288 Chirality : 0.042 0.216 2514 Planarity : 0.004 0.057 3000 Dihedral : 4.865 38.169 2521 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.68 % Allowed : 12.36 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.18), residues: 2115 helix: 1.21 (0.27), residues: 324 sheet: -0.53 (0.20), residues: 657 loop : -1.57 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 474 TYR 0.017 0.002 TYR N 38 PHE 0.022 0.001 PHE E 238 TRP 0.042 0.002 TRP S 56 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00261 (16968) covalent geometry : angle 0.53776 (22962) SS BOND : bond 0.00236 ( 27) SS BOND : angle 0.90593 ( 54) hydrogen bonds : bond 0.03393 ( 578) hydrogen bonds : angle 5.54706 ( 1605) link_NAG-ASN : bond 0.00304 ( 9) link_NAG-ASN : angle 1.31409 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: -0.0520 (OUTLIER) cc_final: -0.1066 (pt0) REVERT: A 155 MET cc_start: -0.1395 (mtt) cc_final: -0.1759 (mtt) REVERT: B 433 ASP cc_start: 0.3961 (m-30) cc_final: 0.3664 (m-30) REVERT: C 21 GLU cc_start: 0.0783 (OUTLIER) cc_final: -0.0140 (mp0) REVERT: C 36 THR cc_start: 0.1355 (OUTLIER) cc_final: -0.0056 (m) REVERT: D 433 ASP cc_start: 0.4030 (m-30) cc_final: 0.3355 (m-30) REVERT: D 447 LEU cc_start: 0.3904 (OUTLIER) cc_final: 0.3051 (pp) REVERT: F 362 THR cc_start: 0.6370 (m) cc_final: 0.6080 (p) REVERT: F 470 MET cc_start: 0.5458 (ppp) cc_final: 0.5210 (ppp) REVERT: S 54 ILE cc_start: -0.0242 (pt) cc_final: -0.2505 (mt) REVERT: S 100 THR cc_start: -0.2917 (OUTLIER) cc_final: -0.3411 (p) outliers start: 30 outliers final: 13 residues processed: 167 average time/residue: 0.1350 time to fit residues: 34.9982 Evaluate side-chains 158 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain F residue 347 HIS Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 198 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 239 ASN B 450 ASN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN O 111 HIS ** T 35 HIS ** 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 = 0.4351 r_free = 0.4351 target = 0.177492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.164049 restraints weight = 28405.628| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.77 r_work: 0.4101 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1788 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17004 Z= 0.151 Angle : 0.626 15.951 23043 Z= 0.328 Chirality : 0.045 0.245 2514 Planarity : 0.005 0.056 3000 Dihedral : 5.044 34.583 2521 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.76 % Favored : 93.19 % Rotamer: Outliers : 2.35 % Allowed : 14.15 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.18), residues: 2115 helix: 1.30 (0.27), residues: 321 sheet: -0.49 (0.20), residues: 696 loop : -1.67 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 346 TYR 0.022 0.002 TYR S 55 PHE 0.023 0.002 PHE E 238 TRP 0.046 0.003 TRP S 56 HIS 0.006 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00333 (16968) covalent geometry : angle 0.62169 (22962) SS BOND : bond 0.00622 ( 27) SS BOND : angle 1.44268 ( 54) hydrogen bonds : bond 0.03616 ( 578) hydrogen bonds : angle 5.85850 ( 1605) link_NAG-ASN : bond 0.00322 ( 9) link_NAG-ASN : angle 1.34182 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: -0.0179 (OUTLIER) cc_final: -0.1175 (mp0) REVERT: A 142 TRP cc_start: 0.3848 (t60) cc_final: 0.3476 (t60) REVERT: A 155 MET cc_start: -0.1290 (OUTLIER) cc_final: -0.1682 (mtt) REVERT: B 388 ASP cc_start: 0.0085 (OUTLIER) cc_final: -0.0409 (m-30) REVERT: B 433 ASP cc_start: 0.4061 (m-30) cc_final: 0.3843 (m-30) REVERT: H 38 TYR cc_start: 0.0129 (m-80) cc_final: -0.0082 (m-80) REVERT: H 56 TRP cc_start: 0.2900 (m-90) cc_final: 0.2298 (m-90) REVERT: D 433 ASP cc_start: 0.4302 (m-30) cc_final: 0.3955 (m-30) REVERT: D 447 LEU cc_start: 0.4038 (OUTLIER) cc_final: 0.3771 (mp) REVERT: E 220 ARG cc_start: 0.2782 (mmt90) cc_final: 0.2337 (tpp80) REVERT: F 407 ASP cc_start: 0.6307 (m-30) cc_final: 0.5992 (m-30) REVERT: F 470 MET cc_start: 0.5349 (ppp) cc_final: 0.5029 (ppp) REVERT: S 54 ILE cc_start: 0.0078 (pt) cc_final: -0.1986 (mp) REVERT: S 100 THR cc_start: -0.2776 (OUTLIER) cc_final: -0.3401 (p) REVERT: O 36 TRP cc_start: -0.0227 (m100) cc_final: -0.1919 (m100) REVERT: O 83 MET cc_start: 0.0898 (mmm) cc_final: -0.1203 (mpp) outliers start: 42 outliers final: 24 residues processed: 173 average time/residue: 0.1407 time to fit residues: 36.9376 Evaluate side-chains 167 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain D residue 347 HIS Chi-restraints excluded: chain D residue 390 GLU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain F residue 342 TRP Chi-restraints excluded: chain F residue 347 HIS Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 147 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN N 44 GLN N 85 GLN ** E 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS F 490 ASN T 35 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.183062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.170084 restraints weight = 28882.894| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.79 r_work: 0.4165 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2001 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17004 Z= 0.184 Angle : 0.687 12.711 23043 Z= 0.365 Chirality : 0.047 0.236 2514 Planarity : 0.005 0.067 3000 Dihedral : 5.335 29.552 2519 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.24 % Allowed : 15.49 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.18), residues: 2115 helix: 0.99 (0.28), residues: 321 sheet: -0.41 (0.21), residues: 660 loop : -1.68 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 220 TYR 0.046 0.002 TYR S 55 PHE 0.027 0.002 PHE E 238 TRP 0.052 0.003 TRP S 56 HIS 0.007 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00402 (16968) covalent geometry : angle 0.68367 (22962) SS BOND : bond 0.00425 ( 27) SS BOND : angle 1.29777 ( 54) hydrogen bonds : bond 0.04148 ( 578) hydrogen bonds : angle 6.20604 ( 1605) link_NAG-ASN : bond 0.00343 ( 9) link_NAG-ASN : angle 1.37932 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 140 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.0386 (OUTLIER) cc_final: -0.0826 (pm20) REVERT: A 142 TRP cc_start: 0.4277 (t60) cc_final: 0.3755 (t60) REVERT: A 155 MET cc_start: -0.1234 (OUTLIER) cc_final: -0.1728 (mtt) REVERT: A 159 TYR cc_start: 0.2139 (t80) cc_final: -0.0362 (t80) REVERT: A 220 ARG cc_start: 0.3675 (mmm-85) cc_final: 0.3409 (tpt170) REVERT: B 388 ASP cc_start: 0.0109 (OUTLIER) cc_final: -0.0288 (m-30) REVERT: H 56 TRP cc_start: 0.3269 (m-90) cc_final: 0.2612 (m-90) REVERT: C 21 GLU cc_start: 0.2296 (OUTLIER) cc_final: 0.0519 (mp0) REVERT: D 335 TRP cc_start: 0.5222 (m100) cc_final: 0.4089 (m100) REVERT: D 423 MET cc_start: 0.6775 (mmm) cc_final: 0.6527 (mmm) REVERT: D 433 ASP cc_start: 0.4401 (m-30) cc_final: 0.4187 (m-30) REVERT: D 447 LEU cc_start: 0.4176 (OUTLIER) cc_final: 0.3792 (mp) REVERT: N 54 ILE cc_start: -0.1125 (OUTLIER) cc_final: -0.3297 (mp) REVERT: E 159 TYR cc_start: 0.1997 (t80) cc_final: -0.0632 (t80) REVERT: E 311 MET cc_start: 0.1251 (ptm) cc_final: 0.1005 (ptm) REVERT: F 335 TRP cc_start: 0.3013 (m100) cc_final: 0.2318 (t-100) REVERT: F 348 GLN cc_start: 0.4977 (OUTLIER) cc_final: 0.4535 (pm20) REVERT: F 369 ILE cc_start: 0.6988 (mt) cc_final: 0.6649 (mt) REVERT: F 470 MET cc_start: 0.4787 (ppp) cc_final: 0.4500 (ppp) REVERT: S 42 TYR cc_start: 0.2130 (m-80) cc_final: 0.1372 (m-80) REVERT: S 54 ILE cc_start: 0.0262 (pt) cc_final: -0.1705 (mp) outliers start: 58 outliers final: 33 residues processed: 186 average time/residue: 0.1369 time to fit residues: 38.9419 Evaluate side-chains 176 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain D residue 347 HIS Chi-restraints excluded: chain D residue 390 GLU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain F residue 342 TRP Chi-restraints excluded: chain F residue 347 HIS Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain O residue 36 TRP Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 110 TYR Chi-restraints excluded: chain O residue 111 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain T residue 36 TRP Chi-restraints excluded: chain T residue 110 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 67 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 115 optimal weight: 0.0970 chunk 117 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 GLN B 490 ASN ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 ASN D 490 ASN E 182 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.184372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.171240 restraints weight = 28841.375| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.82 r_work: 0.4171 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1954 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17004 Z= 0.129 Angle : 0.599 10.473 23043 Z= 0.314 Chirality : 0.044 0.248 2514 Planarity : 0.004 0.052 3000 Dihedral : 4.950 26.155 2519 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.38 % Favored : 93.57 % Rotamer: Outliers : 2.40 % Allowed : 16.89 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.18), residues: 2115 helix: 1.23 (0.28), residues: 321 sheet: -0.26 (0.21), residues: 660 loop : -1.64 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 38 TYR 0.025 0.002 TYR S 55 PHE 0.022 0.001 PHE E 238 TRP 0.030 0.002 TRP C 142 HIS 0.008 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00288 (16968) covalent geometry : angle 0.59668 (22962) SS BOND : bond 0.00320 ( 27) SS BOND : angle 1.06842 ( 54) hydrogen bonds : bond 0.03546 ( 578) hydrogen bonds : angle 5.86932 ( 1605) link_NAG-ASN : bond 0.00179 ( 9) link_NAG-ASN : angle 1.24562 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.0337 (OUTLIER) cc_final: -0.0819 (mp0) REVERT: A 142 TRP cc_start: 0.4092 (t60) cc_final: 0.3628 (t60) REVERT: A 155 MET cc_start: -0.1088 (OUTLIER) cc_final: -0.1397 (mtt) REVERT: A 159 TYR cc_start: 0.2282 (t80) cc_final: -0.0321 (t80) REVERT: B 433 ASP cc_start: 0.4546 (m-30) cc_final: 0.4164 (m-30) REVERT: D 335 TRP cc_start: 0.5140 (m100) cc_final: 0.4145 (m100) REVERT: D 423 MET cc_start: 0.6857 (mmm) cc_final: 0.6622 (mmm) REVERT: N 54 ILE cc_start: -0.1076 (OUTLIER) cc_final: -0.3395 (mp) REVERT: E 159 TYR cc_start: 0.1926 (t80) cc_final: -0.0623 (t80) REVERT: E 220 ARG cc_start: 0.2721 (tpp80) cc_final: 0.2274 (tpp80) REVERT: E 311 MET cc_start: 0.1179 (ptm) cc_final: 0.0755 (ptm) REVERT: F 369 ILE cc_start: 0.6954 (mt) cc_final: 0.6627 (mt) REVERT: S 42 TYR cc_start: 0.2013 (m-80) cc_final: 0.1178 (m-80) REVERT: O 36 TRP cc_start: -0.0391 (OUTLIER) cc_final: -0.0683 (m100) REVERT: O 83 MET cc_start: 0.0975 (mmm) cc_final: -0.0771 (mpp) outliers start: 43 outliers final: 33 residues processed: 171 average time/residue: 0.1468 time to fit residues: 37.8288 Evaluate side-chains 174 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain D residue 347 HIS Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain F residue 342 TRP Chi-restraints excluded: chain F residue 347 HIS Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 110 VAL Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain O residue 36 TRP Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 110 TYR Chi-restraints excluded: chain O residue 111 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain T residue 36 TRP Chi-restraints excluded: chain T residue 110 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 147 optimal weight: 0.0770 chunk 42 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.186312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.173352 restraints weight = 28991.567| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 2.84 r_work: 0.4196 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2004 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17004 Z= 0.133 Angle : 0.601 11.416 23043 Z= 0.315 Chirality : 0.044 0.187 2514 Planarity : 0.004 0.053 3000 Dihedral : 4.900 21.730 2519 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.91 % Allowed : 16.39 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.18), residues: 2115 helix: 1.34 (0.28), residues: 321 sheet: -0.15 (0.21), residues: 648 loop : -1.72 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 220 TYR 0.021 0.002 TYR S 55 PHE 0.025 0.002 PHE E 238 TRP 0.028 0.002 TRP S 56 HIS 0.007 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00296 (16968) covalent geometry : angle 0.59868 (22962) SS BOND : bond 0.00309 ( 27) SS BOND : angle 1.06225 ( 54) hydrogen bonds : bond 0.03523 ( 578) hydrogen bonds : angle 5.87943 ( 1605) link_NAG-ASN : bond 0.00211 ( 9) link_NAG-ASN : angle 1.22702 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.0367 (OUTLIER) cc_final: -0.0736 (mp0) REVERT: A 142 TRP cc_start: 0.4156 (t60) cc_final: 0.3685 (t60) REVERT: A 155 MET cc_start: -0.1030 (OUTLIER) cc_final: -0.1337 (mtt) REVERT: A 159 TYR cc_start: 0.2796 (t80) cc_final: 0.0614 (t80) REVERT: A 220 ARG cc_start: 0.3367 (tpp80) cc_final: 0.2858 (tpp80) REVERT: B 388 ASP cc_start: -0.0418 (OUTLIER) cc_final: -0.0792 (m-30) REVERT: B 450 ASN cc_start: 0.0119 (OUTLIER) cc_final: -0.0502 (m110) REVERT: H 42 TYR cc_start: 0.2079 (m-80) cc_final: 0.1126 (m-80) REVERT: C 36 THR cc_start: 0.1466 (OUTLIER) cc_final: 0.0171 (m) REVERT: C 204 PHE cc_start: 0.0574 (OUTLIER) cc_final: -0.3121 (t80) REVERT: D 335 TRP cc_start: 0.5171 (m100) cc_final: 0.4235 (m100) REVERT: D 423 MET cc_start: 0.6931 (mmm) cc_final: 0.6671 (mmm) REVERT: N 54 ILE cc_start: -0.1003 (OUTLIER) cc_final: -0.3378 (mp) REVERT: E 159 TYR cc_start: 0.2194 (t80) cc_final: -0.0170 (t80) REVERT: E 220 ARG cc_start: 0.2921 (tpp80) cc_final: 0.2273 (tpp80) REVERT: E 311 MET cc_start: 0.1241 (ptm) cc_final: 0.0845 (ptm) REVERT: F 348 GLN cc_start: 0.5041 (OUTLIER) cc_final: 0.4524 (pm20) REVERT: F 389 ASN cc_start: -0.0163 (OUTLIER) cc_final: -0.0966 (t0) REVERT: F 390 GLU cc_start: 0.3538 (OUTLIER) cc_final: 0.2714 (mt-10) REVERT: S 42 TYR cc_start: 0.2074 (m-80) cc_final: 0.1245 (m-80) REVERT: O 36 TRP cc_start: -0.0276 (OUTLIER) cc_final: -0.0567 (m100) REVERT: O 39 GLN cc_start: 0.4781 (tp40) cc_final: 0.4424 (tp40) REVERT: O 83 MET cc_start: 0.1006 (mmm) cc_final: -0.0632 (mpp) outliers start: 52 outliers final: 36 residues processed: 177 average time/residue: 0.1262 time to fit residues: 34.0424 Evaluate side-chains 182 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain D residue 347 HIS Chi-restraints excluded: chain D residue 390 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 342 TRP Chi-restraints excluded: chain F residue 347 HIS Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain F residue 388 ASP Chi-restraints excluded: chain F residue 389 ASN Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 110 VAL Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain O residue 36 TRP Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 110 TYR Chi-restraints excluded: chain O residue 111 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain T residue 36 TRP Chi-restraints excluded: chain T residue 110 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 180 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 224 HIS C 287 ASN D 389 ASN N 35 ASN E 7 HIS ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 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 = 0.4521 r_free = 0.4521 target = 0.194107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.181255 restraints weight = 30107.639| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.81 r_work: 0.4296 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2263 moved from start: 0.7552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17004 Z= 0.203 Angle : 0.763 10.469 23043 Z= 0.403 Chirality : 0.050 0.279 2514 Planarity : 0.006 0.058 3000 Dihedral : 5.733 25.623 2519 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.42 % Favored : 91.54 % Rotamer: Outliers : 3.24 % Allowed : 16.50 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.18), residues: 2115 helix: 0.41 (0.27), residues: 321 sheet: -0.34 (0.21), residues: 642 loop : -1.89 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 80 TYR 0.030 0.003 TYR S 55 PHE 0.046 0.003 PHE E 238 TRP 0.032 0.003 TRP F 335 HIS 0.009 0.002 HIS E 174 Details of bonding type rmsd covalent geometry : bond 0.00457 (16968) covalent geometry : angle 0.76005 (22962) SS BOND : bond 0.00373 ( 27) SS BOND : angle 1.45431 ( 54) hydrogen bonds : bond 0.04501 ( 578) hydrogen bonds : angle 6.78953 ( 1605) link_NAG-ASN : bond 0.00260 ( 9) link_NAG-ASN : angle 1.32665 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 148 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.1230 (OUTLIER) cc_final: -0.1182 (pp20) REVERT: A 142 TRP cc_start: 0.4421 (t60) cc_final: 0.3896 (t60) REVERT: A 155 MET cc_start: -0.1418 (OUTLIER) cc_final: -0.2023 (mtt) REVERT: A 220 ARG cc_start: 0.3745 (tpp80) cc_final: 0.3044 (tpp80) REVERT: B 388 ASP cc_start: 0.0514 (OUTLIER) cc_final: -0.0119 (t70) REVERT: C 21 GLU cc_start: 0.2941 (OUTLIER) cc_final: 0.1980 (pm20) REVERT: C 155 MET cc_start: -0.2614 (ptp) cc_final: -0.3304 (ptp) REVERT: C 224 HIS cc_start: 0.1363 (OUTLIER) cc_final: 0.0769 (m-70) REVERT: D 390 GLU cc_start: 0.4302 (OUTLIER) cc_final: 0.3900 (mt-10) REVERT: N 60 ARG cc_start: 0.5288 (OUTLIER) cc_final: 0.4597 (mtm180) REVERT: E 140 MET cc_start: 0.1467 (mmt) cc_final: 0.0000 (mmt) REVERT: E 220 ARG cc_start: 0.3364 (tpp80) cc_final: 0.2577 (tpp80) REVERT: E 238 PHE cc_start: 0.1517 (OUTLIER) cc_final: 0.0934 (p90) REVERT: F 335 TRP cc_start: 0.2633 (m100) cc_final: 0.2033 (t60) REVERT: F 369 ILE cc_start: 0.7292 (mt) cc_final: 0.6995 (mp) REVERT: F 390 GLU cc_start: 0.3932 (OUTLIER) cc_final: 0.3569 (mt-10) REVERT: F 415 TYR cc_start: 0.5397 (t80) cc_final: 0.4852 (t80) REVERT: S 42 TYR cc_start: 0.2560 (m-80) cc_final: 0.1826 (m-80) REVERT: O 39 GLN cc_start: 0.5068 (tp40) cc_final: 0.4709 (tp40) REVERT: O 83 MET cc_start: 0.1599 (mmm) cc_final: -0.0091 (mpp) outliers start: 58 outliers final: 34 residues processed: 198 average time/residue: 0.1313 time to fit residues: 39.2341 Evaluate side-chains 190 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain D residue 347 HIS Chi-restraints excluded: chain D residue 390 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 388 ASP Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 110 VAL Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain O residue 36 TRP Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 110 TYR Chi-restraints excluded: chain O residue 111 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain T residue 110 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 202 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 0.0060 chunk 51 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 HIS D 389 ASN D 400 ASN E 202 GLN ** F 416 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 = 0.4517 r_free = 0.4517 target = 0.193728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.181096 restraints weight = 29299.297| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.86 r_work: 0.4284 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2140 moved from start: 0.7497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17004 Z= 0.136 Angle : 0.664 14.187 23043 Z= 0.345 Chirality : 0.045 0.359 2514 Planarity : 0.005 0.099 3000 Dihedral : 5.221 23.443 2519 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.68 % Allowed : 17.11 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.18), residues: 2115 helix: 0.77 (0.27), residues: 321 sheet: -0.27 (0.21), residues: 645 loop : -1.85 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 38 TYR 0.021 0.002 TYR S 55 PHE 0.026 0.002 PHE E 238 TRP 0.060 0.003 TRP I 36 HIS 0.007 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00302 (16968) covalent geometry : angle 0.65885 (22962) SS BOND : bond 0.00328 ( 27) SS BOND : angle 1.62080 ( 54) hydrogen bonds : bond 0.03746 ( 578) hydrogen bonds : angle 6.27849 ( 1605) link_NAG-ASN : bond 0.00184 ( 9) link_NAG-ASN : angle 1.28213 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.1040 (OUTLIER) cc_final: -0.0374 (mp0) REVERT: A 142 TRP cc_start: 0.4336 (t60) cc_final: 0.3778 (t60) REVERT: A 155 MET cc_start: -0.0861 (OUTLIER) cc_final: -0.1125 (mtt) REVERT: A 220 ARG cc_start: 0.3104 (tpp80) cc_final: 0.2447 (tpp80) REVERT: B 388 ASP cc_start: -0.0528 (OUTLIER) cc_final: -0.0792 (t70) REVERT: H 42 TYR cc_start: 0.2445 (m-80) cc_final: 0.1482 (m-80) REVERT: C 3 ILE cc_start: 0.4415 (pt) cc_final: 0.4200 (pt) REVERT: C 21 GLU cc_start: 0.2576 (OUTLIER) cc_final: 0.1507 (mp0) REVERT: C 36 THR cc_start: 0.1420 (OUTLIER) cc_final: 0.0004 (m) REVERT: C 155 MET cc_start: -0.2625 (ptp) cc_final: -0.3281 (ptp) REVERT: D 390 GLU cc_start: 0.4179 (OUTLIER) cc_final: 0.3813 (mt-10) REVERT: N 54 ILE cc_start: -0.0767 (OUTLIER) cc_final: -0.2611 (mp) REVERT: N 60 ARG cc_start: 0.5098 (OUTLIER) cc_final: 0.4456 (mtm180) REVERT: E 67 ASP cc_start: -0.1093 (OUTLIER) cc_final: -0.1588 (m-30) REVERT: F 335 TRP cc_start: 0.2666 (m100) cc_final: 0.2027 (t60) REVERT: F 390 GLU cc_start: 0.3929 (OUTLIER) cc_final: 0.3132 (mt-10) REVERT: F 415 TYR cc_start: 0.5279 (t80) cc_final: 0.4813 (t80) REVERT: F 470 MET cc_start: 0.4923 (ppp) cc_final: 0.4548 (ppp) REVERT: S 42 TYR cc_start: 0.2113 (m-80) cc_final: 0.1370 (m-80) REVERT: O 39 GLN cc_start: 0.5144 (tp40) cc_final: 0.4746 (tp40) REVERT: O 83 MET cc_start: 0.1442 (mmm) cc_final: -0.0100 (mpp) outliers start: 48 outliers final: 33 residues processed: 189 average time/residue: 0.1263 time to fit residues: 36.4685 Evaluate side-chains 188 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain D residue 347 HIS Chi-restraints excluded: chain D residue 390 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain O residue 36 TRP Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 110 TYR Chi-restraints excluded: chain O residue 111 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain T residue 110 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 112 optimal weight: 0.0470 chunk 67 optimal weight: 0.4980 chunk 197 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 1.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 GLN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 ASN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.196899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.184528 restraints weight = 29843.519| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 2.87 r_work: 0.4331 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2302 moved from start: 0.8031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17004 Z= 0.188 Angle : 0.753 14.517 23043 Z= 0.393 Chirality : 0.049 0.384 2514 Planarity : 0.006 0.087 3000 Dihedral : 5.540 24.020 2519 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.63 % Allowed : 17.62 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.18), residues: 2115 helix: 0.59 (0.28), residues: 315 sheet: -0.38 (0.22), residues: 600 loop : -1.96 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 67 TYR 0.028 0.003 TYR S 55 PHE 0.040 0.002 PHE E 238 TRP 0.045 0.003 TRP I 36 HIS 0.007 0.002 HIS E 174 Details of bonding type rmsd covalent geometry : bond 0.00425 (16968) covalent geometry : angle 0.74804 (22962) SS BOND : bond 0.00356 ( 27) SS BOND : angle 1.77458 ( 54) hydrogen bonds : bond 0.04149 ( 578) hydrogen bonds : angle 6.65734 ( 1605) link_NAG-ASN : bond 0.00272 ( 9) link_NAG-ASN : angle 1.29965 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3238.58 seconds wall clock time: 56 minutes 50.66 seconds (3410.66 seconds total)