Starting phenix.real_space_refine on Sat Jun 14 09:19:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tz5_26202/06_2025/7tz5_26202_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tz5_26202/06_2025/7tz5_26202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tz5_26202/06_2025/7tz5_26202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tz5_26202/06_2025/7tz5_26202.map" model { file = "/net/cci-nas-00/data/ceres_data/7tz5_26202/06_2025/7tz5_26202_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tz5_26202/06_2025/7tz5_26202_neut.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 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 72 5.16 5 C 10056 2.51 5 N 2775 2.21 5 O 3120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16023 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 893 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "I" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 893 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "J" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 893 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "L" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 763 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 763 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 763 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3685 Classifications: {'peptide': 483} Incomplete info: {'backbone_only': 2, 'n_c_alpha_c_only': 1, 'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3685 Classifications: {'peptide': 483} Incomplete info: {'backbone_only': 2, 'n_c_alpha_c_only': 1, 'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3685 Classifications: {'peptide': 483} Incomplete info: {'backbone_only': 2, 'n_c_alpha_c_only': 1, 'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 73 Time building chain proxies: 12.37, per 1000 atoms: 0.77 Number of scatterers: 16023 At special positions: 0 Unit cell: (119.402, 112.564, 179.892, 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 72 16.00 O 3120 8.00 N 2775 7.00 C 10056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.04 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.04 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.04 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 2.9 seconds 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3876 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 51 sheets defined 17.2% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 366 through 385 Processing helix chain 'A' and resid 404 through 455 WARNING: missing atoms! Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.543A pdb=" N ASN A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 496 removed outlier: 4.144A pdb=" N LEU A 496 " --> pdb=" O ASP A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 366 through 385 Processing helix chain 'B' and resid 404 through 455 WARNING: missing atoms! Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.536A pdb=" N ASN B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 4.127A pdb=" N LEU B 496 " --> pdb=" O ASP B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 366 through 385 Processing helix chain 'C' and resid 404 through 455 WARNING: missing atoms! Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.539A pdb=" N ASN C 483 " --> pdb=" O GLY C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 496 removed outlier: 4.132A pdb=" N LEU C 496 " --> pdb=" O ASP C 493 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.604A pdb=" N GLN H 3 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL H 5 " --> pdb=" O LYS H 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.556A pdb=" N VAL H 21 " --> pdb=" O MET H 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 50 through 52 removed outlier: 3.568A pdb=" N ARG H 43 " --> pdb=" O GLU H 51 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLY H 108 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE H 115 " --> pdb=" O GLY H 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 50 through 52 removed outlier: 3.568A pdb=" N ARG H 43 " --> pdb=" O GLU H 51 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 100 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.602A pdb=" N GLN I 3 " --> pdb=" O SER I 26 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL I 5 " --> pdb=" O LYS I 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AA7, first strand: chain 'I' and resid 50 through 52 removed outlier: 3.530A pdb=" N ARG I 43 " --> pdb=" O GLU I 51 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY I 108 " --> pdb=" O PHE I 115 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE I 115 " --> pdb=" O GLY I 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 50 through 52 removed outlier: 3.530A pdb=" N ARG I 43 " --> pdb=" O GLU I 51 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA I 100 " --> pdb=" O VAL I 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.607A pdb=" N GLN J 3 " --> pdb=" O SER J 26 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 5 " --> pdb=" O LYS J 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 20 through 21 removed outlier: 3.529A pdb=" N VAL J 21 " --> pdb=" O MET J 89 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 50 through 52 removed outlier: 3.550A pdb=" N ARG J 43 " --> pdb=" O GLU J 51 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY J 108 " --> pdb=" O PHE J 115 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N PHE J 115 " --> pdb=" O GLY J 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 50 through 52 removed outlier: 3.550A pdb=" N ARG J 43 " --> pdb=" O GLU J 51 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA J 100 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL J 124 " --> pdb=" O ALA J 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 20 through 25 Processing sheet with id=AB5, first strand: chain 'L' and resid 51 through 55 removed outlier: 6.483A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 20 through 25 Processing sheet with id=AB7, first strand: chain 'M' and resid 51 through 55 removed outlier: 6.502A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 20 through 25 Processing sheet with id=AB9, first strand: chain 'N' and resid 51 through 55 removed outlier: 6.498A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 360 through 363 removed outlier: 3.890A pdb=" N GLY A 362 " --> pdb=" O HIS A 355 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS A 355 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 11 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 469 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AC3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.210A pdb=" N CYS A 277 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AC7, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.980A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.881A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AD1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AD2, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.489A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 360 through 363 removed outlier: 3.907A pdb=" N GLY B 362 " --> pdb=" O HIS B 355 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS B 355 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 11 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 469 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AD5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AD6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AD7, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.090A pdb=" N ILE B 51 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N CYS B 277 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B 53 " --> pdb=" O CYS B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 58 through 61 Processing sheet with id=AD9, first strand: chain 'B' and resid 100 through 101 removed outlier: 4.985A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 100 through 101 removed outlier: 7.882A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 136 through 140 removed outlier: 3.556A pdb=" N SER B 146 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AE4, first strand: chain 'B' and resid 281 through 283 removed outlier: 4.508A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 360 through 363 removed outlier: 3.904A pdb=" N GLY C 362 " --> pdb=" O HIS C 355 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS C 355 " --> pdb=" O GLY C 362 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 11 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 469 " --> pdb=" O ALA C 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AE7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AE8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AE9, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.128A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.893A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 100 through 101 removed outlier: 4.977A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.881A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.583A pdb=" N SER C 146 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AF6, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.501A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1623 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: 6.01 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5434 1.36 - 1.50: 4784 1.50 - 1.63: 6069 1.63 - 1.77: 36 1.77 - 1.91: 66 Bond restraints: 16389 Sorted by residual: bond pdb=" CB CYS A 305 " pdb=" SG CYS A 305 " ideal model delta sigma weight residual 1.808 1.664 0.144 3.30e-02 9.18e+02 1.91e+01 bond pdb=" CB CYS B 305 " pdb=" SG CYS B 305 " ideal model delta sigma weight residual 1.808 1.665 0.143 3.30e-02 9.18e+02 1.89e+01 bond pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " ideal model delta sigma weight residual 1.808 1.671 0.137 3.30e-02 9.18e+02 1.71e+01 bond pdb=" CB CYS C 305 " pdb=" SG CYS C 305 " ideal model delta sigma weight residual 1.808 1.672 0.136 3.30e-02 9.18e+02 1.70e+01 bond pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " ideal model delta sigma weight residual 1.808 1.913 -0.105 3.30e-02 9.18e+02 1.01e+01 ... (remaining 16384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.13: 22247 6.13 - 12.26: 48 12.26 - 18.40: 7 18.40 - 24.53: 2 24.53 - 30.66: 4 Bond angle restraints: 22308 Sorted by residual: angle pdb=" CA CYS A 305 " pdb=" CB CYS A 305 " pdb=" SG CYS A 305 " ideal model delta sigma weight residual 114.40 145.06 -30.66 2.30e+00 1.89e-01 1.78e+02 angle pdb=" CA CYS C 305 " pdb=" CB CYS C 305 " pdb=" SG CYS C 305 " ideal model delta sigma weight residual 114.40 144.33 -29.93 2.30e+00 1.89e-01 1.69e+02 angle pdb=" CA CYS B 305 " pdb=" CB CYS B 305 " pdb=" SG CYS B 305 " ideal model delta sigma weight residual 114.40 143.99 -29.59 2.30e+00 1.89e-01 1.66e+02 angle pdb=" CA CYS A 277 " pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " ideal model delta sigma weight residual 114.40 139.92 -25.52 2.30e+00 1.89e-01 1.23e+02 angle pdb=" C CYS A 52 " pdb=" CA CYS A 52 " pdb=" CB CYS A 52 " ideal model delta sigma weight residual 109.65 126.76 -17.11 1.71e+00 3.42e-01 1.00e+02 ... (remaining 22303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8903 17.94 - 35.87: 590 35.87 - 53.81: 110 53.81 - 71.74: 41 71.74 - 89.68: 9 Dihedral angle restraints: 9653 sinusoidal: 3548 harmonic: 6105 Sorted by residual: dihedral pdb=" CB CYS B 52 " pdb=" SG CYS B 52 " pdb=" SG CYS B 277 " pdb=" CB CYS B 277 " ideal model delta sinusoidal sigma weight residual -86.00 -16.69 -69.31 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -16.89 -69.11 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CB CYS B 473 " pdb=" SG CYS B 473 " pdb=" SG CYS B 477 " pdb=" CB CYS B 477 " ideal model delta sinusoidal sigma weight residual 93.00 25.42 67.58 1 1.00e+01 1.00e-02 5.94e+01 ... (remaining 9650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2338 0.125 - 0.249: 113 0.249 - 0.374: 5 0.374 - 0.498: 0 0.498 - 0.623: 4 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA CYS B 305 " pdb=" N CYS B 305 " pdb=" C CYS B 305 " pdb=" CB CYS B 305 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.70e+00 chirality pdb=" CA CYS A 305 " pdb=" N CYS A 305 " pdb=" C CYS A 305 " pdb=" CB CYS A 305 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.67e+00 chirality pdb=" CA CYS C 305 " pdb=" N CYS C 305 " pdb=" C CYS C 305 " pdb=" CB CYS C 305 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.29e+00 ... (remaining 2457 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 471 " -0.015 2.00e-02 2.50e+03 1.54e-02 3.56e+00 pdb=" CG HIS C 471 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS C 471 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS C 471 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS C 471 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS C 471 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 471 " -0.015 2.00e-02 2.50e+03 1.54e-02 3.55e+00 pdb=" CG HIS A 471 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS A 471 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS A 471 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 471 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 471 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 471 " -0.015 2.00e-02 2.50e+03 1.51e-02 3.42e+00 pdb=" CG HIS B 471 " 0.032 2.00e-02 2.50e+03 pdb=" ND1 HIS B 471 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS B 471 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 471 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 471 " -0.007 2.00e-02 2.50e+03 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 292 2.63 - 3.20: 14461 3.20 - 3.77: 23490 3.77 - 4.33: 32492 4.33 - 4.90: 54975 Nonbonded interactions: 125710 Sorted by model distance: nonbonded pdb=" NH1 ARG A 492 " pdb=" O ARG B 499 " model vdw 2.067 3.120 nonbonded pdb=" O ARG A 499 " pdb=" NH1 ARG C 492 " model vdw 2.081 3.120 nonbonded pdb=" NH1 ARG B 492 " pdb=" O ARG C 499 " model vdw 2.085 3.120 nonbonded pdb=" OG1 THR N 5 " pdb=" O GLY N 25 " model vdw 2.147 3.040 nonbonded pdb=" NE2 GLN N 17 " pdb=" O LEU N 94 " model vdw 2.152 3.120 ... (remaining 125705 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 9.660 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: 0.910 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 42.210 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.100 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.009 0.144 16407 Z= 0.374 Angle : 1.241 30.662 22344 Z= 0.689 Chirality : 0.066 0.623 2460 Planarity : 0.005 0.032 2922 Dihedral : 13.200 89.677 5723 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.62 % Favored : 88.95 % Rotamer: Outliers : 0.30 % Allowed : 0.61 % Favored : 99.09 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.16), residues: 2118 helix: 0.83 (0.25), residues: 324 sheet: -1.58 (0.22), residues: 489 loop : -2.33 (0.14), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 180 HIS 0.015 0.003 HIS A 471 PHE 0.026 0.003 PHE C 159 TYR 0.021 0.002 TYR L 55 ARG 0.014 0.001 ARG N 75 Details of bonding type rmsd hydrogen bonds : bond 0.24561 ( 556) hydrogen bonds : angle 8.60586 ( 1623) SS BOND : bond 0.00772 ( 18) SS BOND : angle 9.62549 ( 36) covalent geometry : bond 0.00890 (16389) covalent geometry : angle 1.18033 (22308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 225 time to evaluate : 1.959 Fit side-chains REVERT: H 52 TRP cc_start: 0.8600 (t-100) cc_final: 0.8335 (t60) REVERT: L 103 TYR cc_start: 0.8448 (m-80) cc_final: 0.7725 (m-10) REVERT: M 103 TYR cc_start: 0.8416 (m-10) cc_final: 0.8010 (m-10) REVERT: A 307 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7550 (mmm-85) REVERT: B 307 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7594 (mmm-85) outliers start: 5 outliers final: 5 residues processed: 230 average time/residue: 0.2890 time to fit residues: 99.7591 Evaluate side-chains 190 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 185 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9980 chunk 159 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 100 optimal weight: 30.0000 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 112 HIS N 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.154821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118100 restraints weight = 24880.029| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.97 r_work: 0.3254 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16407 Z= 0.158 Angle : 0.689 8.114 22344 Z= 0.371 Chirality : 0.048 0.169 2460 Planarity : 0.005 0.047 2922 Dihedral : 6.084 58.016 2315 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 1.34 % Allowed : 6.51 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.17), residues: 2118 helix: 2.06 (0.27), residues: 345 sheet: -0.96 (0.23), residues: 468 loop : -2.18 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 52 HIS 0.007 0.001 HIS H 112 PHE 0.014 0.002 PHE B 193 TYR 0.016 0.001 TYR A 423 ARG 0.005 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.05488 ( 556) hydrogen bonds : angle 6.00065 ( 1623) SS BOND : bond 0.00784 ( 18) SS BOND : angle 3.79577 ( 36) covalent geometry : bond 0.00348 (16389) covalent geometry : angle 0.67263 (22308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 1.641 Fit side-chains revert: symmetry clash REVERT: L 103 TYR cc_start: 0.8609 (m-80) cc_final: 0.7838 (m-10) REVERT: M 103 TYR cc_start: 0.8584 (m-10) cc_final: 0.8066 (m-10) REVERT: A 307 ARG cc_start: 0.8028 (mtt-85) cc_final: 0.7554 (mmm-85) REVERT: B 144 ASN cc_start: 0.8062 (t0) cc_final: 0.7838 (m-40) REVERT: B 175 ASP cc_start: 0.8156 (m-30) cc_final: 0.7932 (m-30) outliers start: 22 outliers final: 13 residues processed: 228 average time/residue: 0.3010 time to fit residues: 102.1225 Evaluate side-chains 202 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 99 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 169 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 ASN L 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.152815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112201 restraints weight = 25019.366| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.87 r_work: 0.3245 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16407 Z= 0.164 Angle : 0.614 6.038 22344 Z= 0.327 Chirality : 0.046 0.149 2460 Planarity : 0.004 0.038 2922 Dihedral : 5.780 56.771 2315 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.07 % Allowed : 8.76 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2118 helix: 2.88 (0.27), residues: 324 sheet: -0.96 (0.22), residues: 495 loop : -2.11 (0.15), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 52 HIS 0.006 0.001 HIS I 112 PHE 0.011 0.002 PHE C 159 TYR 0.017 0.001 TYR M 55 ARG 0.004 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 556) hydrogen bonds : angle 5.49796 ( 1623) SS BOND : bond 0.00534 ( 18) SS BOND : angle 2.56364 ( 36) covalent geometry : bond 0.00379 (16389) covalent geometry : angle 0.60615 (22308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 19 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8745 (p) REVERT: I 91 LEU cc_start: 0.8230 (mt) cc_final: 0.7944 (mp) REVERT: M 103 TYR cc_start: 0.8525 (m-10) cc_final: 0.7946 (m-10) REVERT: B 144 ASN cc_start: 0.8100 (t0) cc_final: 0.7699 (m-40) REVERT: B 175 ASP cc_start: 0.8211 (m-30) cc_final: 0.7974 (m-30) outliers start: 34 outliers final: 14 residues processed: 231 average time/residue: 0.2737 time to fit residues: 93.4348 Evaluate side-chains 200 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 15 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 44 GLN J 109 ASN L 44 GLN L 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.151775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110019 restraints weight = 25153.579| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.63 r_work: 0.3238 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16407 Z= 0.194 Angle : 0.612 7.380 22344 Z= 0.325 Chirality : 0.046 0.201 2460 Planarity : 0.004 0.039 2922 Dihedral : 5.661 55.989 2315 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.92 % Allowed : 11.02 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 2118 helix: 3.04 (0.28), residues: 324 sheet: -1.09 (0.22), residues: 516 loop : -2.08 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 52 HIS 0.005 0.001 HIS I 112 PHE 0.012 0.002 PHE C 159 TYR 0.017 0.001 TYR M 55 ARG 0.004 0.000 ARG N 75 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 556) hydrogen bonds : angle 5.21157 ( 1623) SS BOND : bond 0.00589 ( 18) SS BOND : angle 2.43702 ( 36) covalent geometry : bond 0.00450 (16389) covalent geometry : angle 0.60440 (22308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 202 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 91 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8042 (mp) REVERT: L 91 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.6942 (tt) REVERT: L 103 TYR cc_start: 0.8739 (m-80) cc_final: 0.8313 (m-10) REVERT: M 91 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.6884 (tt) REVERT: M 103 TYR cc_start: 0.8723 (m-10) cc_final: 0.8117 (m-10) REVERT: N 91 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.6986 (tt) REVERT: A 144 ASN cc_start: 0.8136 (t0) cc_final: 0.7742 (m-40) REVERT: B 144 ASN cc_start: 0.8188 (t0) cc_final: 0.7738 (m-40) REVERT: B 175 ASP cc_start: 0.8428 (m-30) cc_final: 0.8204 (m-30) REVERT: B 423 TYR cc_start: 0.8737 (t80) cc_final: 0.8387 (t80) REVERT: C 38 ASN cc_start: 0.6681 (t0) cc_final: 0.6088 (p0) outliers start: 48 outliers final: 25 residues processed: 240 average time/residue: 0.2911 time to fit residues: 103.9181 Evaluate side-chains 218 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 109 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 chunk 188 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 ASN M 105 GLN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109013 restraints weight = 25470.476| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.66 r_work: 0.3228 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16407 Z= 0.203 Angle : 0.609 6.301 22344 Z= 0.322 Chirality : 0.046 0.152 2460 Planarity : 0.004 0.040 2922 Dihedral : 5.549 55.322 2315 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.23 % Allowed : 11.56 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2118 helix: 3.08 (0.28), residues: 324 sheet: -1.04 (0.22), residues: 498 loop : -2.13 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 52 HIS 0.006 0.001 HIS I 112 PHE 0.012 0.002 PHE C 159 TYR 0.015 0.001 TYR M 55 ARG 0.005 0.000 ARG L 75 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 556) hydrogen bonds : angle 5.13976 ( 1623) SS BOND : bond 0.00614 ( 18) SS BOND : angle 2.46045 ( 36) covalent geometry : bond 0.00473 (16389) covalent geometry : angle 0.60176 (22308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 91 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.6899 (tt) REVERT: M 91 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.6725 (tt) REVERT: M 103 TYR cc_start: 0.8717 (m-10) cc_final: 0.8155 (m-10) REVERT: N 91 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.6924 (tt) REVERT: A 144 ASN cc_start: 0.8169 (t0) cc_final: 0.7764 (m-40) REVERT: B 144 ASN cc_start: 0.8172 (t0) cc_final: 0.7728 (m-40) REVERT: B 175 ASP cc_start: 0.8429 (m-30) cc_final: 0.8193 (m-30) REVERT: C 38 ASN cc_start: 0.6717 (t0) cc_final: 0.6076 (p0) REVERT: C 53 ASP cc_start: 0.7566 (t70) cc_final: 0.7314 (m-30) outliers start: 53 outliers final: 33 residues processed: 238 average time/residue: 0.2741 time to fit residues: 97.5339 Evaluate side-chains 225 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 78 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 109 ASN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN C 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107467 restraints weight = 25170.058| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.80 r_work: 0.3206 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16407 Z= 0.219 Angle : 0.621 7.599 22344 Z= 0.326 Chirality : 0.046 0.152 2460 Planarity : 0.004 0.042 2922 Dihedral : 5.509 55.152 2315 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.35 % Allowed : 11.99 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.18), residues: 2118 helix: 3.04 (0.27), residues: 324 sheet: -1.13 (0.22), residues: 498 loop : -2.18 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 52 HIS 0.005 0.001 HIS J 112 PHE 0.014 0.002 PHE A 448 TYR 0.014 0.001 TYR M 55 ARG 0.006 0.000 ARG N 75 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 556) hydrogen bonds : angle 5.05043 ( 1623) SS BOND : bond 0.00619 ( 18) SS BOND : angle 2.61389 ( 36) covalent geometry : bond 0.00510 (16389) covalent geometry : angle 0.61215 (22308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 2.808 Fit side-chains REVERT: L 91 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.6837 (tt) REVERT: M 91 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6659 (tt) REVERT: M 103 TYR cc_start: 0.8566 (m-10) cc_final: 0.8010 (m-10) REVERT: N 91 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.6842 (tt) REVERT: A 144 ASN cc_start: 0.8075 (t0) cc_final: 0.7743 (m-40) REVERT: A 307 ARG cc_start: 0.7992 (mtt-85) cc_final: 0.7365 (mmm-85) REVERT: B 144 ASN cc_start: 0.8083 (t0) cc_final: 0.7717 (m-40) REVERT: B 175 ASP cc_start: 0.8246 (m-30) cc_final: 0.7986 (m-30) REVERT: B 307 ARG cc_start: 0.7992 (mtt-85) cc_final: 0.7356 (mmm-85) REVERT: C 53 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7261 (m-30) outliers start: 55 outliers final: 39 residues processed: 241 average time/residue: 0.3854 time to fit residues: 140.2509 Evaluate side-chains 235 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 149 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 97 optimal weight: 0.0070 chunk 130 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 ASN A 458 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.147703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105655 restraints weight = 25522.608| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.72 r_work: 0.3182 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 16407 Z= 0.286 Angle : 0.678 7.246 22344 Z= 0.357 Chirality : 0.048 0.161 2460 Planarity : 0.005 0.045 2922 Dihedral : 5.753 56.061 2315 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 3.71 % Allowed : 12.05 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.17), residues: 2118 helix: 2.85 (0.28), residues: 324 sheet: -1.30 (0.22), residues: 495 loop : -2.31 (0.15), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 52 HIS 0.005 0.002 HIS C 183 PHE 0.015 0.002 PHE A 448 TYR 0.015 0.002 TYR J 88 ARG 0.006 0.001 ARG N 75 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 556) hydrogen bonds : angle 5.23093 ( 1623) SS BOND : bond 0.00745 ( 18) SS BOND : angle 2.86290 ( 36) covalent geometry : bond 0.00667 (16389) covalent geometry : angle 0.66847 (22308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 1.909 Fit side-chains REVERT: J 89 MET cc_start: 0.8418 (ttp) cc_final: 0.8063 (ttm) REVERT: L 91 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.6927 (tt) REVERT: L 103 TYR cc_start: 0.8629 (m-80) cc_final: 0.8204 (m-10) REVERT: M 91 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.6692 (tt) REVERT: M 103 TYR cc_start: 0.8636 (m-10) cc_final: 0.8003 (m-10) REVERT: N 91 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.6869 (tt) REVERT: A 144 ASN cc_start: 0.8075 (t0) cc_final: 0.7784 (m-40) REVERT: A 307 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7440 (mmm-85) REVERT: B 18 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.6963 (t70) REVERT: B 144 ASN cc_start: 0.8089 (t0) cc_final: 0.7754 (m-40) REVERT: B 175 ASP cc_start: 0.8248 (m-30) cc_final: 0.7998 (m-30) REVERT: B 307 ARG cc_start: 0.8149 (mtt-85) cc_final: 0.7434 (mmm-85) REVERT: B 390 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: C 53 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7457 (m-30) outliers start: 61 outliers final: 39 residues processed: 235 average time/residue: 0.2790 time to fit residues: 98.1889 Evaluate side-chains 229 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 88 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 0.0040 chunk 103 optimal weight: 2.9990 chunk 129 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 74 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 112 HIS J 109 ASN L 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.153321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.116545 restraints weight = 24977.563| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.01 r_work: 0.3237 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16407 Z= 0.112 Angle : 0.581 11.523 22344 Z= 0.302 Chirality : 0.044 0.151 2460 Planarity : 0.004 0.055 2922 Dihedral : 5.213 54.473 2315 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.80 % Allowed : 13.21 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2118 helix: 3.10 (0.27), residues: 324 sheet: -1.07 (0.22), residues: 504 loop : -2.06 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 52 HIS 0.007 0.001 HIS I 112 PHE 0.013 0.001 PHE A 448 TYR 0.014 0.001 TYR M 55 ARG 0.008 0.001 ARG N 75 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 556) hydrogen bonds : angle 4.80887 ( 1623) SS BOND : bond 0.00491 ( 18) SS BOND : angle 2.14897 ( 36) covalent geometry : bond 0.00251 (16389) covalent geometry : angle 0.57535 (22308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: J 89 MET cc_start: 0.8251 (ttp) cc_final: 0.7894 (ttm) REVERT: L 91 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.6904 (tt) REVERT: L 103 TYR cc_start: 0.8561 (m-80) cc_final: 0.8135 (m-10) REVERT: M 91 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.6701 (tt) REVERT: M 103 TYR cc_start: 0.8566 (m-10) cc_final: 0.7981 (m-10) REVERT: N 91 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.6856 (tt) REVERT: A 144 ASN cc_start: 0.8150 (t0) cc_final: 0.7877 (m-40) REVERT: A 390 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: B 144 ASN cc_start: 0.8121 (t0) cc_final: 0.7843 (m-40) REVERT: B 175 ASP cc_start: 0.8195 (m-30) cc_final: 0.7984 (m-30) REVERT: B 390 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: B 423 TYR cc_start: 0.8585 (t80) cc_final: 0.8269 (t80) outliers start: 46 outliers final: 31 residues processed: 239 average time/residue: 0.2868 time to fit residues: 102.1013 Evaluate side-chains 225 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 131 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 175 optimal weight: 0.0470 chunk 164 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 112 HIS L 17 GLN M 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.154044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118083 restraints weight = 24999.429| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.98 r_work: 0.3258 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16407 Z= 0.110 Angle : 0.564 6.890 22344 Z= 0.293 Chirality : 0.044 0.182 2460 Planarity : 0.004 0.053 2922 Dihedral : 4.913 49.534 2315 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.07 % Allowed : 14.24 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.18), residues: 2118 helix: 3.21 (0.27), residues: 324 sheet: -1.10 (0.22), residues: 513 loop : -1.92 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 52 HIS 0.004 0.001 HIS J 112 PHE 0.014 0.001 PHE C 193 TYR 0.021 0.001 TYR M 55 ARG 0.008 0.000 ARG L 75 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 556) hydrogen bonds : angle 4.60103 ( 1623) SS BOND : bond 0.00403 ( 18) SS BOND : angle 1.84066 ( 36) covalent geometry : bond 0.00250 (16389) covalent geometry : angle 0.55924 (22308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 2.907 Fit side-chains REVERT: J 7 SER cc_start: 0.6995 (p) cc_final: 0.6641 (t) REVERT: J 89 MET cc_start: 0.8213 (ttp) cc_final: 0.7956 (ttm) REVERT: L 91 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.6869 (tt) REVERT: L 103 TYR cc_start: 0.8562 (m-80) cc_final: 0.7662 (m-10) REVERT: M 91 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.6720 (tt) REVERT: M 103 TYR cc_start: 0.8578 (m-10) cc_final: 0.8016 (m-10) REVERT: N 91 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.6917 (tt) REVERT: A 144 ASN cc_start: 0.8147 (t0) cc_final: 0.7880 (m-40) REVERT: A 175 ASP cc_start: 0.8108 (m-30) cc_final: 0.7644 (m-30) REVERT: A 390 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: B 144 ASN cc_start: 0.8104 (t0) cc_final: 0.7832 (m-40) REVERT: B 390 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: B 423 TYR cc_start: 0.8569 (t80) cc_final: 0.8257 (t80) outliers start: 34 outliers final: 23 residues processed: 234 average time/residue: 0.3161 time to fit residues: 113.5561 Evaluate side-chains 228 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 109 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 66 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 109 ASN A 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111906 restraints weight = 25202.360| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.67 r_work: 0.3275 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16407 Z= 0.134 Angle : 0.574 8.598 22344 Z= 0.297 Chirality : 0.044 0.147 2460 Planarity : 0.004 0.053 2922 Dihedral : 4.832 46.870 2314 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.95 % Allowed : 14.67 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 2118 helix: 3.23 (0.27), residues: 324 sheet: -1.06 (0.23), residues: 513 loop : -1.88 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 52 HIS 0.002 0.001 HIS B 183 PHE 0.011 0.001 PHE C 193 TYR 0.022 0.001 TYR M 55 ARG 0.009 0.000 ARG L 75 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 556) hydrogen bonds : angle 4.59730 ( 1623) SS BOND : bond 0.00439 ( 18) SS BOND : angle 1.92471 ( 36) covalent geometry : bond 0.00312 (16389) covalent geometry : angle 0.56876 (22308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 1.904 Fit side-chains REVERT: J 7 SER cc_start: 0.7104 (p) cc_final: 0.6722 (t) REVERT: J 89 MET cc_start: 0.8287 (ttp) cc_final: 0.8017 (ttm) REVERT: L 91 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.6737 (tt) REVERT: L 103 TYR cc_start: 0.8657 (m-80) cc_final: 0.7714 (m-10) REVERT: M 91 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.6606 (tt) REVERT: M 103 TYR cc_start: 0.8670 (m-10) cc_final: 0.8090 (m-10) REVERT: N 91 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.6777 (tt) REVERT: A 144 ASN cc_start: 0.8175 (t0) cc_final: 0.7771 (m-40) REVERT: A 175 ASP cc_start: 0.8331 (m-30) cc_final: 0.7785 (m-30) REVERT: A 390 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: B 144 ASN cc_start: 0.8148 (t0) cc_final: 0.7736 (m-40) REVERT: B 390 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: B 423 TYR cc_start: 0.8650 (t80) cc_final: 0.8272 (t80) REVERT: C 175 ASP cc_start: 0.8333 (m-30) cc_final: 0.7941 (m-30) outliers start: 32 outliers final: 23 residues processed: 231 average time/residue: 0.3410 time to fit residues: 121.6266 Evaluate side-chains 227 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 58 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 146 optimal weight: 0.0570 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 143 optimal weight: 0.2980 chunk 35 optimal weight: 5.9990 chunk 196 optimal weight: 30.0000 overall best weight: 1.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.153618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116684 restraints weight = 25010.051| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.01 r_work: 0.3239 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16407 Z= 0.138 Angle : 0.576 7.397 22344 Z= 0.298 Chirality : 0.044 0.163 2460 Planarity : 0.004 0.051 2922 Dihedral : 4.777 42.994 2314 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.64 % Allowed : 14.91 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2118 helix: 3.16 (0.27), residues: 327 sheet: -1.06 (0.23), residues: 513 loop : -1.86 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 52 HIS 0.002 0.001 HIS A 183 PHE 0.011 0.001 PHE A 448 TYR 0.022 0.001 TYR M 55 ARG 0.009 0.000 ARG L 75 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 556) hydrogen bonds : angle 4.58028 ( 1623) SS BOND : bond 0.00453 ( 18) SS BOND : angle 1.92530 ( 36) covalent geometry : bond 0.00322 (16389) covalent geometry : angle 0.57133 (22308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10477.05 seconds wall clock time: 185 minutes 36.19 seconds (11136.19 seconds total)