Starting phenix.real_space_refine on Thu Sep 18 10:18:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tz5_26202/09_2025/7tz5_26202_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tz5_26202/09_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_26202/09_2025/7tz5_26202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tz5_26202/09_2025/7tz5_26202.map" model { file = "/net/cci-nas-00/data/ceres_data/7tz5_26202/09_2025/7tz5_26202_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tz5_26202/09_2025/7tz5_26202_neut.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU: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: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU: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: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU: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, 'ASP:plan': 6, 'ARG:plan': 5, 'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 1} 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, 'ASP:plan': 6, 'ARG:plan': 5, 'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 1} 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, 'ASP:plan': 6, 'ARG:plan': 5, 'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 73 Time building chain proxies: 4.24, per 1000 atoms: 0.26 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: 1.22 Conformation dependent library (CDL) restraints added in 658.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.82 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: 2.97 Time building geometry restraints manager: 1.67 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: 0.00 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: 10.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.620 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.100 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- 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 : 15.21 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.001 ARG N 75 TYR 0.021 0.002 TYR L 55 PHE 0.026 0.003 PHE C 159 TRP 0.028 0.003 TRP B 180 HIS 0.015 0.003 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00890 (16389) covalent geometry : angle 1.18033 (22308) SS BOND : bond 0.00772 ( 18) SS BOND : angle 9.62549 ( 36) hydrogen bonds : bond 0.24561 ( 556) hydrogen bonds : angle 8.60586 ( 1623) *********************** 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 : 0.491 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: 0.1249 time to fit residues: 43.0919 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 : 0.587 ------------------------------------------------------------------------------- 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 98 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.153606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116866 restraints weight = 24810.635| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.98 r_work: 0.3230 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16407 Z= 0.183 Angle : 0.708 9.520 22344 Z= 0.380 Chirality : 0.048 0.201 2460 Planarity : 0.005 0.040 2922 Dihedral : 6.136 59.793 2315 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 1.58 % Allowed : 6.33 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.17), residues: 2118 helix: 2.03 (0.27), residues: 345 sheet: -1.00 (0.22), residues: 474 loop : -2.19 (0.15), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.016 0.001 TYR A 423 PHE 0.014 0.002 PHE B 193 TRP 0.013 0.002 TRP I 52 HIS 0.006 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00416 (16389) covalent geometry : angle 0.68958 (22308) SS BOND : bond 0.00956 ( 18) SS BOND : angle 4.07220 ( 36) hydrogen bonds : bond 0.05836 ( 556) hydrogen bonds : angle 6.03654 ( 1623) *********************** 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 235 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 103 TYR cc_start: 0.8637 (m-80) cc_final: 0.7901 (m-10) REVERT: M 103 TYR cc_start: 0.8621 (m-10) cc_final: 0.8088 (m-10) REVERT: B 144 ASN cc_start: 0.8068 (t0) cc_final: 0.7833 (m-40) REVERT: B 175 ASP cc_start: 0.8178 (m-30) cc_final: 0.7959 (m-30) outliers start: 26 outliers final: 15 residues processed: 221 average time/residue: 0.1416 time to fit residues: 46.4625 Evaluate side-chains 202 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 247 SER 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 247 SER 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 4 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 ASN H 112 HIS I 44 GLN L 44 GLN L 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.154801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118505 restraints weight = 25155.482| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.00 r_work: 0.3259 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16407 Z= 0.134 Angle : 0.601 7.407 22344 Z= 0.320 Chirality : 0.045 0.154 2460 Planarity : 0.004 0.040 2922 Dihedral : 5.742 57.717 2315 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.19 % Allowed : 8.16 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.17), residues: 2118 helix: 2.81 (0.26), residues: 324 sheet: -0.91 (0.22), residues: 489 loop : -2.10 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.016 0.001 TYR N 55 PHE 0.012 0.002 PHE A 448 TRP 0.014 0.001 TRP I 52 HIS 0.006 0.001 HIS I 112 Details of bonding type rmsd covalent geometry : bond 0.00302 (16389) covalent geometry : angle 0.59416 (22308) SS BOND : bond 0.00499 ( 18) SS BOND : angle 2.33805 ( 36) hydrogen bonds : bond 0.04384 ( 556) hydrogen bonds : angle 5.50813 ( 1623) *********************** 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 255 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: I 19 VAL cc_start: 0.8968 (t) cc_final: 0.8720 (p) REVERT: I 91 LEU cc_start: 0.8375 (mt) cc_final: 0.8022 (mp) REVERT: M 103 TYR cc_start: 0.8591 (m-10) cc_final: 0.7979 (m-10) REVERT: B 144 ASN cc_start: 0.8136 (t0) cc_final: 0.7822 (m-40) REVERT: B 175 ASP cc_start: 0.8170 (m-30) cc_final: 0.7937 (m-30) REVERT: C 38 ASN cc_start: 0.6713 (t0) cc_final: 0.6217 (p0) outliers start: 36 outliers final: 12 residues processed: 243 average time/residue: 0.1398 time to fit residues: 50.2241 Evaluate side-chains 202 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 50 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 45 optimal weight: 0.0010 chunk 197 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 109 ASN L 105 GLN M 105 GLN B 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.148601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105722 restraints weight = 25405.763| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.80 r_work: 0.3166 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 16407 Z= 0.305 Angle : 0.706 6.763 22344 Z= 0.376 Chirality : 0.049 0.205 2460 Planarity : 0.005 0.042 2922 Dihedral : 6.056 57.554 2315 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 3.35 % Allowed : 10.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.17), residues: 2118 helix: 2.81 (0.27), residues: 324 sheet: -1.19 (0.22), residues: 501 loop : -2.23 (0.15), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 80 TYR 0.018 0.002 TYR M 55 PHE 0.016 0.002 PHE C 159 TRP 0.022 0.002 TRP H 52 HIS 0.007 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00714 (16389) covalent geometry : angle 0.69505 (22308) SS BOND : bond 0.00757 ( 18) SS BOND : angle 3.10235 ( 36) hydrogen bonds : bond 0.04945 ( 556) hydrogen bonds : angle 5.56162 ( 1623) *********************** 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 242 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.666 Fit side-chains REVERT: L 91 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.6943 (tt) REVERT: M 91 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.6868 (tt) REVERT: M 103 TYR cc_start: 0.8608 (m-10) cc_final: 0.7975 (m-10) REVERT: N 91 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.6950 (tt) REVERT: B 144 ASN cc_start: 0.8103 (t0) cc_final: 0.7721 (m-40) REVERT: B 175 ASP cc_start: 0.8261 (m-30) cc_final: 0.8023 (m-30) REVERT: B 307 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7394 (mmm-85) outliers start: 55 outliers final: 29 residues processed: 231 average time/residue: 0.1322 time to fit residues: 45.8276 Evaluate side-chains 209 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 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 89 LEU Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 21 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 214 ILE 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 214 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 155 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 129 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 chunk 176 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 ASN I 112 HIS L 105 GLN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.153776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.117583 restraints weight = 25021.321| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.03 r_work: 0.3250 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16407 Z= 0.112 Angle : 0.571 6.245 22344 Z= 0.302 Chirality : 0.044 0.142 2460 Planarity : 0.004 0.043 2922 Dihedral : 5.448 55.759 2315 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.07 % Allowed : 12.78 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.18), residues: 2118 helix: 3.16 (0.27), residues: 321 sheet: -0.88 (0.22), residues: 489 loop : -2.07 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 75 TYR 0.016 0.001 TYR M 55 PHE 0.012 0.001 PHE C 448 TRP 0.011 0.001 TRP I 52 HIS 0.008 0.001 HIS I 112 Details of bonding type rmsd covalent geometry : bond 0.00248 (16389) covalent geometry : angle 0.56457 (22308) SS BOND : bond 0.00449 ( 18) SS BOND : angle 2.27861 ( 36) hydrogen bonds : bond 0.03750 ( 556) hydrogen bonds : angle 5.10411 ( 1623) *********************** 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 242 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: H 52 TRP cc_start: 0.8644 (t-100) cc_final: 0.8219 (t60) REVERT: J 52 TRP cc_start: 0.8687 (t-100) cc_final: 0.8348 (t60) REVERT: J 89 MET cc_start: 0.7827 (ttp) cc_final: 0.7467 (ttm) REVERT: L 91 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.6932 (tt) REVERT: M 91 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.6892 (tt) REVERT: M 103 TYR cc_start: 0.8586 (m-10) cc_final: 0.8000 (m-10) REVERT: N 91 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.6988 (tt) REVERT: A 144 ASN cc_start: 0.8127 (t0) cc_final: 0.7853 (m-40) REVERT: B 144 ASN cc_start: 0.8153 (t0) cc_final: 0.7819 (m-40) REVERT: B 423 TYR cc_start: 0.8643 (t80) cc_final: 0.8272 (t80) outliers start: 34 outliers final: 17 residues processed: 235 average time/residue: 0.1303 time to fit residues: 45.3214 Evaluate side-chains 212 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 247 SER Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER 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 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 165 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 109 ASN M 17 GLN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.151468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109135 restraints weight = 25241.352| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.67 r_work: 0.3236 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16407 Z= 0.182 Angle : 0.597 6.107 22344 Z= 0.314 Chirality : 0.045 0.160 2460 Planarity : 0.004 0.042 2922 Dihedral : 5.346 53.110 2315 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.43 % Allowed : 12.66 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.18), residues: 2118 helix: 3.17 (0.27), residues: 324 sheet: -1.05 (0.22), residues: 501 loop : -2.07 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 75 TYR 0.020 0.001 TYR M 55 PHE 0.012 0.002 PHE C 159 TRP 0.015 0.002 TRP H 52 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00424 (16389) covalent geometry : angle 0.58920 (22308) SS BOND : bond 0.00602 ( 18) SS BOND : angle 2.51740 ( 36) hydrogen bonds : bond 0.04018 ( 556) hydrogen bonds : angle 4.98551 ( 1623) *********************** 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 232 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: H 52 TRP cc_start: 0.8745 (t-100) cc_final: 0.8274 (t60) REVERT: J 89 MET cc_start: 0.8296 (ttp) cc_final: 0.8060 (ttm) REVERT: L 91 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.6900 (tt) REVERT: M 91 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6667 (tt) REVERT: M 103 TYR cc_start: 0.8703 (m-10) cc_final: 0.8156 (m-10) REVERT: N 91 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.6894 (tt) REVERT: A 144 ASN cc_start: 0.8170 (t0) cc_final: 0.7755 (m-40) REVERT: B 144 ASN cc_start: 0.8142 (t0) cc_final: 0.7710 (m-40) outliers start: 40 outliers final: 28 residues processed: 221 average time/residue: 0.1353 time to fit residues: 44.2736 Evaluate side-chains 215 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 19 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 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 247 SER Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER 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 214 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 408 ASP 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 101 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 63 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 17 GLN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114012 restraints weight = 25046.769| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.06 r_work: 0.3189 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16407 Z= 0.205 Angle : 0.607 6.002 22344 Z= 0.319 Chirality : 0.045 0.150 2460 Planarity : 0.004 0.046 2922 Dihedral : 5.312 53.092 2315 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.68 % Allowed : 12.72 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.18), residues: 2118 helix: 3.07 (0.27), residues: 324 sheet: -1.09 (0.22), residues: 498 loop : -2.10 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 75 TYR 0.020 0.001 TYR M 55 PHE 0.012 0.002 PHE C 159 TRP 0.017 0.002 TRP H 52 HIS 0.004 0.001 HIS J 112 Details of bonding type rmsd covalent geometry : bond 0.00478 (16389) covalent geometry : angle 0.59960 (22308) SS BOND : bond 0.00585 ( 18) SS BOND : angle 2.46103 ( 36) hydrogen bonds : bond 0.04111 ( 556) hydrogen bonds : angle 4.94331 ( 1623) *********************** 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 235 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.570 Fit side-chains REVERT: J 67 TYR cc_start: 0.7983 (m-80) cc_final: 0.7761 (m-80) REVERT: J 89 MET cc_start: 0.8381 (ttp) cc_final: 0.8161 (ttm) REVERT: L 91 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.6983 (tt) REVERT: L 103 TYR cc_start: 0.8639 (m-80) cc_final: 0.8226 (m-10) REVERT: M 91 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.6804 (tt) REVERT: M 103 TYR cc_start: 0.8646 (m-10) cc_final: 0.8117 (m-10) REVERT: N 91 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.6993 (tt) REVERT: A 144 ASN cc_start: 0.8153 (t0) cc_final: 0.7879 (m-40) REVERT: B 144 ASN cc_start: 0.8121 (t0) cc_final: 0.7840 (m-40) REVERT: B 390 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7535 (mp0) outliers start: 44 outliers final: 29 residues processed: 223 average time/residue: 0.1179 time to fit residues: 39.1900 Evaluate side-chains 219 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 I residue 38 THR Chi-restraints excluded: chain J residue 19 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 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 107 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 260 ILE 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 214 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 408 ASP 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 23 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 140 optimal weight: 0.0020 chunk 41 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 ASN M 17 GLN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.152942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116207 restraints weight = 25136.174| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.05 r_work: 0.3226 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2898 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= 0.135 Angle : 0.567 6.429 22344 Z= 0.296 Chirality : 0.044 0.145 2460 Planarity : 0.004 0.052 2922 Dihedral : 5.051 51.175 2315 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.25 % Allowed : 13.82 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.18), residues: 2118 helix: 3.14 (0.27), residues: 324 sheet: -0.97 (0.23), residues: 486 loop : -2.04 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 75 TYR 0.018 0.001 TYR M 55 PHE 0.013 0.001 PHE A 448 TRP 0.015 0.001 TRP I 52 HIS 0.004 0.001 HIS J 112 Details of bonding type rmsd covalent geometry : bond 0.00312 (16389) covalent geometry : angle 0.56179 (22308) SS BOND : bond 0.00460 ( 18) SS BOND : angle 1.91779 ( 36) hydrogen bonds : bond 0.03645 ( 556) hydrogen bonds : angle 4.74198 ( 1623) *********************** 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 236 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.673 Fit side-chains REVERT: H 52 TRP cc_start: 0.8622 (t-100) cc_final: 0.8221 (t60) REVERT: L 91 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.6890 (tt) REVERT: L 103 TYR cc_start: 0.8595 (m-80) cc_final: 0.8170 (m-10) REVERT: M 91 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.6743 (tt) REVERT: M 103 TYR cc_start: 0.8601 (m-10) cc_final: 0.8010 (m-10) REVERT: N 91 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.6947 (tt) REVERT: A 144 ASN cc_start: 0.8156 (t0) cc_final: 0.7881 (m-40) REVERT: A 175 ASP cc_start: 0.8118 (m-30) cc_final: 0.7661 (m-30) REVERT: A 390 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: B 144 ASN cc_start: 0.8124 (t0) cc_final: 0.7841 (m-40) REVERT: B 390 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7518 (mp0) outliers start: 37 outliers final: 25 residues processed: 227 average time/residue: 0.1289 time to fit residues: 44.2888 Evaluate side-chains 224 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 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 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 247 SER 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 242 ILE Chi-restraints excluded: chain B residue 260 ILE 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 214 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 146 optimal weight: 6.9990 chunk 158 optimal weight: 0.5980 chunk 207 optimal weight: 20.0000 chunk 109 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 179 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 17 GLN A 458 ASN B 458 ASN C 458 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.151235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108809 restraints weight = 24987.234| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.80 r_work: 0.3218 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16407 Z= 0.186 Angle : 0.595 6.465 22344 Z= 0.312 Chirality : 0.045 0.160 2460 Planarity : 0.004 0.049 2922 Dihedral : 5.118 49.285 2315 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.43 % Allowed : 14.06 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.18), residues: 2118 helix: 3.10 (0.28), residues: 324 sheet: -1.24 (0.22), residues: 507 loop : -2.01 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 75 TYR 0.018 0.001 TYR M 55 PHE 0.013 0.002 PHE A 448 TRP 0.018 0.002 TRP I 52 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00437 (16389) covalent geometry : angle 0.58855 (22308) SS BOND : bond 0.00584 ( 18) SS BOND : angle 2.27708 ( 36) hydrogen bonds : bond 0.03938 ( 556) hydrogen bonds : angle 4.78996 ( 1623) *********************** 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 229 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.699 Fit side-chains REVERT: H 52 TRP cc_start: 0.8713 (t-100) cc_final: 0.8209 (t60) REVERT: L 91 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.6732 (tt) REVERT: L 103 TYR cc_start: 0.8563 (m-80) cc_final: 0.8105 (m-10) REVERT: M 91 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6587 (tt) REVERT: M 103 TYR cc_start: 0.8552 (m-10) cc_final: 0.7900 (m-10) REVERT: N 91 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.6799 (tt) REVERT: A 144 ASN cc_start: 0.8095 (t0) cc_final: 0.7748 (m-40) REVERT: A 390 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: B 144 ASN cc_start: 0.8070 (t0) cc_final: 0.7716 (m-40) REVERT: B 390 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7447 (mp0) outliers start: 40 outliers final: 25 residues processed: 219 average time/residue: 0.1326 time to fit residues: 43.5557 Evaluate side-chains 216 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 19 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 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 247 SER 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 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 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 45 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.152728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110781 restraints weight = 25098.239| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.66 r_work: 0.3259 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16407 Z= 0.142 Angle : 0.573 7.851 22344 Z= 0.298 Chirality : 0.044 0.155 2460 Planarity : 0.004 0.050 2922 Dihedral : 4.972 47.208 2315 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.25 % Allowed : 14.12 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.18), residues: 2118 helix: 3.04 (0.27), residues: 327 sheet: -1.18 (0.22), residues: 504 loop : -1.96 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 75 TYR 0.017 0.001 TYR M 55 PHE 0.012 0.001 PHE A 448 TRP 0.015 0.001 TRP I 52 HIS 0.004 0.001 HIS J 112 Details of bonding type rmsd covalent geometry : bond 0.00330 (16389) covalent geometry : angle 0.56761 (22308) SS BOND : bond 0.00479 ( 18) SS BOND : angle 2.00818 ( 36) hydrogen bonds : bond 0.03645 ( 556) hydrogen bonds : angle 4.67917 ( 1623) ********************** 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 235 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.704 Fit side-chains REVERT: H 52 TRP cc_start: 0.8715 (t-100) cc_final: 0.8238 (t60) REVERT: L 91 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.6728 (tt) REVERT: L 103 TYR cc_start: 0.8654 (m-80) cc_final: 0.7709 (m-10) REVERT: M 91 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6589 (tt) REVERT: M 103 TYR cc_start: 0.8671 (m-10) cc_final: 0.8062 (m-10) REVERT: N 91 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.6778 (tt) REVERT: A 144 ASN cc_start: 0.8177 (t0) cc_final: 0.7775 (m-40) REVERT: A 175 ASP cc_start: 0.8341 (m-30) cc_final: 0.7816 (m-30) REVERT: A 390 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: B 144 ASN cc_start: 0.8145 (t0) cc_final: 0.7727 (m-40) REVERT: B 390 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7563 (mp0) outliers start: 37 outliers final: 27 residues processed: 225 average time/residue: 0.1403 time to fit residues: 47.5805 Evaluate side-chains 224 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 38 THR 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 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 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 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 166 optimal weight: 0.0070 chunk 37 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.154692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.117998 restraints weight = 24946.625| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.99 r_work: 0.3256 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.002 0.035 16407 Z= 0.110 Angle : 0.560 7.302 22344 Z= 0.290 Chirality : 0.044 0.182 2460 Planarity : 0.004 0.049 2922 Dihedral : 4.823 43.345 2315 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.83 % Allowed : 14.67 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.18), residues: 2118 helix: 3.15 (0.27), residues: 327 sheet: -1.10 (0.22), residues: 504 loop : -1.88 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 75 TYR 0.021 0.001 TYR N 103 PHE 0.012 0.001 PHE A 448 TRP 0.011 0.001 TRP I 52 HIS 0.004 0.001 HIS J 112 Details of bonding type rmsd covalent geometry : bond 0.00249 (16389) covalent geometry : angle 0.55387 (22308) SS BOND : bond 0.00406 ( 18) SS BOND : angle 2.07515 ( 36) hydrogen bonds : bond 0.03387 ( 556) hydrogen bonds : angle 4.59539 ( 1623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4887.70 seconds wall clock time: 84 minutes 21.48 seconds (5061.48 seconds total)