Starting phenix.real_space_refine on Sun Aug 24 16:55:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ci2_16666/08_2025/8ci2_16666_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ci2_16666/08_2025/8ci2_16666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ci2_16666/08_2025/8ci2_16666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ci2_16666/08_2025/8ci2_16666.map" model { file = "/net/cci-nas-00/data/ceres_data/8ci2_16666/08_2025/8ci2_16666_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ci2_16666/08_2025/8ci2_16666_trim.cif" } resolution = 4.4 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= 0.001 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: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 7180 2.51 5 N 1874 2.21 5 O 2151 1.98 5 H 10298 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21547 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3169 Classifications: {'peptide': 206} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 192} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'PHE:plan': 3, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3155 Classifications: {'peptide': 206} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 192} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'PHE:plan': 3, 'TYR:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3172 Classifications: {'peptide': 206} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 192} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 3, 'TYR:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3169 Classifications: {'peptide': 206} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 192} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'PHE:plan': 3, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "E" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3199 Classifications: {'peptide': 206} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 192} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "F" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1801 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "G" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1801 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "I" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1801 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.42, per 1000 atoms: 0.16 Number of scatterers: 21547 At special positions: 0 Unit cell: (93.12, 95.04, 119.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 2151 8.00 N 1874 7.00 C 7180 6.00 H 10298 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 401 " - " ASN A 23 " " NAG A 402 " - " ASN A 67 " " NAG B 401 " - " ASN B 23 " " NAG B 402 " - " ASN B 67 " " NAG C 401 " - " ASN C 23 " " NAG C 402 " - " ASN C 67 " " NAG D 401 " - " ASN D 23 " " NAG D 402 " - " ASN D 67 " " NAG E 401 " - " ASN E 23 " " NAG E 402 " - " ASN E 67 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 524.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 27 sheets defined 4.3% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.757A pdb=" N GLU C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'I' and resid 29 through 33 removed outlier: 3.835A pdb=" N TYR I 33 " --> pdb=" O PHE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 66 removed outlier: 3.631A pdb=" N LYS I 66 " --> pdb=" O SER I 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 63 through 66' Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.557A pdb=" N LEU A 108 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 110 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A 59 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.557A pdb=" N LEU A 108 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 110 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A 59 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.989A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.989A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 194 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.580A pdb=" N LEU B 108 " --> pdb=" O GLN B 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 59 " --> pdb=" O CYS B 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.580A pdb=" N LEU B 108 " --> pdb=" O GLN B 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 59 " --> pdb=" O CYS B 115 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.990A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.990A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.868A pdb=" N ASN C 110 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP C 59 " --> pdb=" O CYS C 115 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 41 removed outlier: 5.169A pdb=" N LEU C 36 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP C 54 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN C 38 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR C 50 " --> pdb=" O MET C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 7.403A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 79 removed outlier: 3.537A pdb=" N TRP D 59 " --> pdb=" O CYS D 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 41 removed outlier: 7.038A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP D 41 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.910A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 115 through 117 Processing sheet with id=AB8, first strand: chain 'E' and resid 115 through 117 removed outlier: 7.700A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.524A pdb=" N MET E 203 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.524A pdb=" N MET E 203 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 5 through 8 removed outlier: 3.608A pdb=" N VAL F 6 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA F 24 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 60 through 61 removed outlier: 6.030A pdb=" N PHE F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG F 39 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE F 52 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET F 35 " --> pdb=" O ILE F 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 19 through 22 Processing sheet with id=AC6, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.852A pdb=" N PHE G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG G 39 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR G 112 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.852A pdb=" N PHE G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG G 39 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 5 through 8 removed outlier: 3.885A pdb=" N SER I 22 " --> pdb=" O SER I 8 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP I 74 " --> pdb=" O THR I 79 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.607A pdb=" N PHE I 48 " --> pdb=" O ARG I 39 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG I 39 " --> pdb=" O PHE I 48 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET I 35 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE I 38 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR I 96 " --> pdb=" O PHE I 38 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 885 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: 4.11 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10290 1.03 - 1.23: 69 1.23 - 1.42: 5002 1.42 - 1.62: 6425 1.62 - 1.81: 71 Bond restraints: 21857 Sorted by residual: bond pdb=" CB PRO A 135 " pdb=" CG PRO A 135 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.80e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.88e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.27e+00 ... (remaining 21852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.34: 39121 7.34 - 14.68: 2 14.68 - 22.02: 0 22.02 - 29.36: 0 29.36 - 36.70: 3 Bond angle restraints: 39126 Sorted by residual: angle pdb=" CB PHE C 134 " pdb=" CA PHE C 134 " pdb=" HA PHE C 134 " ideal model delta sigma weight residual 109.00 72.30 36.70 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C PHE C 134 " pdb=" CA PHE C 134 " pdb=" HA PHE C 134 " ideal model delta sigma weight residual 109.00 74.41 34.59 3.00e+00 1.11e-01 1.33e+02 angle pdb=" N PHE C 134 " pdb=" CA PHE C 134 " pdb=" HA PHE C 134 " ideal model delta sigma weight residual 110.00 76.86 33.14 3.00e+00 1.11e-01 1.22e+02 angle pdb=" CA PRO A 135 " pdb=" N PRO A 135 " pdb=" CD PRO A 135 " ideal model delta sigma weight residual 112.00 101.23 10.77 1.40e+00 5.10e-01 5.92e+01 angle pdb=" CA LYS A 45 " pdb=" CB LYS A 45 " pdb=" CG LYS A 45 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 ... (remaining 39121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.70: 10019 25.70 - 51.39: 642 51.39 - 77.09: 88 77.09 - 102.78: 12 102.78 - 128.48: 2 Dihedral angle restraints: 10763 sinusoidal: 5773 harmonic: 4990 Sorted by residual: dihedral pdb=" CA TYR A 167 " pdb=" C TYR A 167 " pdb=" N ILE A 168 " pdb=" CA ILE A 168 " ideal model delta harmonic sigma weight residual 180.00 152.54 27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual 93.00 47.18 45.82 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" CA TYR B 167 " pdb=" C TYR B 167 " pdb=" N ILE B 168 " pdb=" CA ILE B 168 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 10760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1504 0.067 - 0.134: 208 0.134 - 0.201: 6 0.201 - 0.268: 0 0.268 - 0.335: 2 Chirality restraints: 1720 Sorted by residual: chirality pdb=" CA PHE C 134 " pdb=" N PHE C 134 " pdb=" C PHE C 134 " pdb=" CB PHE C 134 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 67 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 23 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 1717 not shown) Planarity restraints: 3327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 134 " -0.090 5.00e-02 4.00e+02 1.28e-01 2.64e+01 pdb=" N PRO A 135 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 134 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO C 135 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 135 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 135 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 45 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C LYS A 45 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS A 45 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN A 46 " 0.013 2.00e-02 2.50e+03 ... (remaining 3324 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1757 2.21 - 2.81: 42255 2.81 - 3.41: 48373 3.41 - 4.00: 68116 4.00 - 4.60: 102456 Nonbonded interactions: 262957 Sorted by model distance: nonbonded pdb="HH21 ARG I 73 " pdb=" OD1 ASN I 75 " model vdw 1.617 2.450 nonbonded pdb=" O CYS G 23 " pdb=" HG1 THR G 79 " model vdw 1.623 2.450 nonbonded pdb=" HZ1 LYS C 144 " pdb=" OD2 ASP C 196 " model vdw 1.680 2.450 nonbonded pdb=" OD1 ASP C 196 " pdb=" H VAL C 197 " model vdw 1.703 2.450 nonbonded pdb=" OE1 GLU C 70 " pdb=" H GLU C 70 " model vdw 1.708 2.450 ... (remaining 262952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 193 or (resid 194 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 195 through 402)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 184 or (resid 185 through 192 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 193 through \ 402)) selection = (chain 'D' and (resid 1 through 193 or (resid 194 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 195 through 402)) selection = (chain 'E' and (resid 1 through 184 or (resid 185 through 192 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 193 or (res \ id 194 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 195 through 402)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.260 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 : 0.005 0.130 11579 Z= 0.212 Angle : 0.651 13.339 15797 Z= 0.317 Chirality : 0.045 0.335 1720 Planarity : 0.005 0.128 2003 Dihedral : 16.540 128.480 4403 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.89 % Favored : 85.11 % Rotamer: Outliers : 0.00 % Allowed : 17.70 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.01 (0.21), residues: 1377 helix: 0.64 (0.78), residues: 45 sheet: -0.22 (0.23), residues: 505 loop : -3.58 (0.17), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 182 TYR 0.011 0.001 TYR E 14 PHE 0.010 0.001 PHE G 48 TRP 0.008 0.001 TRP E 59 HIS 0.003 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00486 (11559) covalent geometry : angle 0.61776 (15742) SS BOND : bond 0.00376 ( 5) SS BOND : angle 0.57903 ( 10) hydrogen bonds : bond 0.12006 ( 278) hydrogen bonds : angle 6.07993 ( 885) link_BETA1-4 : bond 0.01912 ( 5) link_BETA1-4 : angle 5.74230 ( 15) link_NAG-ASN : bond 0.00150 ( 10) link_NAG-ASN : angle 2.51521 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ARG cc_start: 0.8055 (mtm180) cc_final: 0.6624 (mtm110) REVERT: B 124 LYS cc_start: 0.8039 (ttmt) cc_final: 0.7716 (ttmt) REVERT: C 10 LEU cc_start: 0.8711 (tp) cc_final: 0.8510 (tp) REVERT: D 53 ILE cc_start: 0.8335 (mt) cc_final: 0.8082 (mt) REVERT: E 159 MET cc_start: 0.8538 (ttp) cc_final: 0.8004 (tmm) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2407 time to fit residues: 84.0656 Evaluate side-chains 145 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.062879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.049719 restraints weight = 168533.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.051791 restraints weight = 76947.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.053204 restraints weight = 46863.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.054205 restraints weight = 33417.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.054880 restraints weight = 26041.752| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11579 Z= 0.145 Angle : 0.589 7.036 15797 Z= 0.294 Chirality : 0.043 0.349 1720 Planarity : 0.005 0.070 2003 Dihedral : 9.470 113.090 1939 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.06 (0.21), residues: 1377 helix: 0.17 (0.78), residues: 45 sheet: -0.30 (0.23), residues: 505 loop : -3.54 (0.17), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 205 TYR 0.017 0.001 TYR A 167 PHE 0.016 0.001 PHE G 69 TRP 0.010 0.001 TRP B 173 HIS 0.006 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00327 (11559) covalent geometry : angle 0.57564 (15742) SS BOND : bond 0.00210 ( 5) SS BOND : angle 0.91117 ( 10) hydrogen bonds : bond 0.03660 ( 278) hydrogen bonds : angle 5.37387 ( 885) link_BETA1-4 : bond 0.00874 ( 5) link_BETA1-4 : angle 2.42195 ( 15) link_NAG-ASN : bond 0.00119 ( 10) link_NAG-ASN : angle 2.37338 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.9553 (t0) cc_final: 0.9179 (t0) REVERT: A 81 ASP cc_start: 0.8348 (t70) cc_final: 0.7859 (t0) REVERT: A 98 ARG cc_start: 0.9041 (mtm180) cc_final: 0.8379 (mtm110) REVERT: A 172 GLU cc_start: 0.9085 (tp30) cc_final: 0.8722 (tp30) REVERT: B 12 LYS cc_start: 0.9373 (mmmt) cc_final: 0.8844 (mmmm) REVERT: B 15 ASN cc_start: 0.9647 (t0) cc_final: 0.9427 (t0) REVERT: B 32 PHE cc_start: 0.9245 (t80) cc_final: 0.8946 (t80) REVERT: B 56 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8510 (tm-30) REVERT: B 96 ASP cc_start: 0.9082 (t0) cc_final: 0.8506 (t70) REVERT: B 106 ASN cc_start: 0.9504 (m-40) cc_final: 0.8953 (t0) REVERT: C 32 PHE cc_start: 0.8975 (t80) cc_final: 0.8672 (t80) REVERT: C 96 ASP cc_start: 0.8691 (t70) cc_final: 0.8403 (t0) REVERT: C 98 ARG cc_start: 0.9287 (ptt-90) cc_final: 0.9010 (ptt-90) REVERT: C 203 MET cc_start: 0.7987 (pmm) cc_final: 0.7665 (pmm) REVERT: D 46 ASN cc_start: 0.9145 (t0) cc_final: 0.8866 (t0) REVERT: E 39 ILE cc_start: 0.9527 (tt) cc_final: 0.9326 (mm) REVERT: E 159 MET cc_start: 0.8819 (ttp) cc_final: 0.8470 (tmm) REVERT: E 167 TYR cc_start: 0.8300 (t80) cc_final: 0.7705 (t80) REVERT: E 203 MET cc_start: 0.9308 (pmm) cc_final: 0.9002 (pmm) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2524 time to fit residues: 67.1139 Evaluate side-chains 147 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.060520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.047647 restraints weight = 172230.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.049615 restraints weight = 80021.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.050993 restraints weight = 49171.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.051850 restraints weight = 35328.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.052499 restraints weight = 28182.293| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11579 Z= 0.248 Angle : 0.632 7.194 15797 Z= 0.315 Chirality : 0.043 0.354 1720 Planarity : 0.005 0.055 2003 Dihedral : 9.718 115.050 1939 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.60 % Favored : 85.40 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.21 (0.20), residues: 1377 helix: 0.03 (0.79), residues: 45 sheet: -0.28 (0.25), residues: 422 loop : -3.45 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 205 TYR 0.011 0.001 TYR I 110 PHE 0.011 0.001 PHE A 99 TRP 0.010 0.001 TRP C 173 HIS 0.006 0.002 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00515 (11559) covalent geometry : angle 0.61669 (15742) SS BOND : bond 0.00165 ( 5) SS BOND : angle 0.95827 ( 10) hydrogen bonds : bond 0.03487 ( 278) hydrogen bonds : angle 5.33232 ( 885) link_BETA1-4 : bond 0.00651 ( 5) link_BETA1-4 : angle 2.20956 ( 15) link_NAG-ASN : bond 0.00223 ( 10) link_NAG-ASN : angle 2.77706 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.9585 (t0) cc_final: 0.9304 (t0) REVERT: A 98 ARG cc_start: 0.9204 (mtm180) cc_final: 0.8996 (mpp80) REVERT: A 172 GLU cc_start: 0.9058 (tp30) cc_final: 0.8695 (tp30) REVERT: B 12 LYS cc_start: 0.9363 (mmmt) cc_final: 0.9016 (mmmm) REVERT: B 32 PHE cc_start: 0.9357 (t80) cc_final: 0.8991 (t80) REVERT: B 39 ILE cc_start: 0.9574 (pt) cc_final: 0.9330 (pt) REVERT: B 56 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8526 (tm-30) REVERT: B 106 ASN cc_start: 0.9508 (m-40) cc_final: 0.9168 (m-40) REVERT: C 98 ARG cc_start: 0.9164 (ptt-90) cc_final: 0.8924 (ptt-90) REVERT: C 124 LYS cc_start: 0.9308 (mtmm) cc_final: 0.9058 (mtmm) REVERT: C 128 TYR cc_start: 0.9018 (t80) cc_final: 0.8704 (t80) REVERT: C 203 MET cc_start: 0.8229 (pmm) cc_final: 0.7924 (pmm) REVERT: D 46 ASN cc_start: 0.9195 (t0) cc_final: 0.8907 (t0) REVERT: D 52 ASN cc_start: 0.9379 (t0) cc_final: 0.9159 (t0) REVERT: D 124 LYS cc_start: 0.9486 (ttmt) cc_final: 0.9179 (ttmt) REVERT: E 159 MET cc_start: 0.8877 (ttp) cc_final: 0.8463 (tmm) REVERT: E 167 TYR cc_start: 0.8370 (t80) cc_final: 0.8101 (t80) REVERT: F 66 LYS cc_start: 0.9508 (ttpp) cc_final: 0.9111 (tppt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2557 time to fit residues: 53.9315 Evaluate side-chains 130 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 39 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.060360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.047311 restraints weight = 171103.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.049258 restraints weight = 80256.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.050643 restraints weight = 49896.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.051560 restraints weight = 35841.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.052206 restraints weight = 28446.271| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11579 Z= 0.164 Angle : 0.576 6.954 15797 Z= 0.284 Chirality : 0.042 0.356 1720 Planarity : 0.004 0.073 2003 Dihedral : 9.449 106.606 1939 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.80 % Favored : 86.20 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.13 (0.21), residues: 1377 helix: 0.08 (0.79), residues: 45 sheet: -0.23 (0.24), residues: 472 loop : -3.56 (0.17), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 205 TYR 0.011 0.001 TYR A 117 PHE 0.018 0.001 PHE B 99 TRP 0.008 0.001 TRP B 85 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00357 (11559) covalent geometry : angle 0.56091 (15742) SS BOND : bond 0.00157 ( 5) SS BOND : angle 0.89344 ( 10) hydrogen bonds : bond 0.03056 ( 278) hydrogen bonds : angle 5.13271 ( 885) link_BETA1-4 : bond 0.00679 ( 5) link_BETA1-4 : angle 2.00822 ( 15) link_NAG-ASN : bond 0.00146 ( 10) link_NAG-ASN : angle 2.65601 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.9593 (t0) cc_final: 0.9310 (t0) REVERT: A 172 GLU cc_start: 0.9073 (tp30) cc_final: 0.8701 (tp30) REVERT: B 12 LYS cc_start: 0.9267 (mmmt) cc_final: 0.8824 (mmmm) REVERT: B 32 PHE cc_start: 0.9359 (t80) cc_final: 0.8905 (t80) REVERT: B 39 ILE cc_start: 0.9553 (pt) cc_final: 0.9347 (pt) REVERT: B 56 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8427 (tm-30) REVERT: B 106 ASN cc_start: 0.9501 (m-40) cc_final: 0.9182 (m-40) REVERT: B 124 LYS cc_start: 0.9312 (ttmt) cc_final: 0.8990 (ttmm) REVERT: C 98 ARG cc_start: 0.9181 (ptt-90) cc_final: 0.8927 (ptt-90) REVERT: C 124 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8874 (mtmm) REVERT: C 128 TYR cc_start: 0.9022 (t80) cc_final: 0.8776 (t80) REVERT: C 203 MET cc_start: 0.8184 (pmm) cc_final: 0.7899 (pmm) REVERT: D 46 ASN cc_start: 0.9192 (t0) cc_final: 0.8893 (t0) REVERT: E 128 TYR cc_start: 0.9201 (t80) cc_final: 0.8823 (t80) REVERT: E 159 MET cc_start: 0.8886 (ttp) cc_final: 0.8509 (tmm) REVERT: F 66 LYS cc_start: 0.9508 (ttpp) cc_final: 0.9110 (tppt) REVERT: G 109 ASP cc_start: 0.9427 (m-30) cc_final: 0.8766 (p0) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2531 time to fit residues: 51.2502 Evaluate side-chains 120 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 19 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 ASN I 75 ASN I 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.047287 restraints weight = 172403.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.049230 restraints weight = 79780.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.050532 restraints weight = 49035.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.051443 restraints weight = 35318.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.052092 restraints weight = 27951.746| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11579 Z= 0.160 Angle : 0.570 8.051 15797 Z= 0.281 Chirality : 0.042 0.356 1720 Planarity : 0.004 0.078 2003 Dihedral : 9.193 97.579 1939 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.31 % Favored : 85.69 % Rotamer: Outliers : 0.09 % Allowed : 1.22 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.10 (0.21), residues: 1377 helix: 0.16 (0.79), residues: 45 sheet: -0.11 (0.25), residues: 453 loop : -3.54 (0.17), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 68 TYR 0.009 0.001 TYR A 167 PHE 0.028 0.001 PHE B 32 TRP 0.009 0.001 TRP B 85 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00343 (11559) covalent geometry : angle 0.55510 (15742) SS BOND : bond 0.00116 ( 5) SS BOND : angle 1.16674 ( 10) hydrogen bonds : bond 0.02882 ( 278) hydrogen bonds : angle 4.98561 ( 885) link_BETA1-4 : bond 0.00623 ( 5) link_BETA1-4 : angle 1.92265 ( 15) link_NAG-ASN : bond 0.00155 ( 10) link_NAG-ASN : angle 2.63626 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.9601 (t0) cc_final: 0.9329 (t0) REVERT: A 81 ASP cc_start: 0.8274 (t0) cc_final: 0.7936 (t0) REVERT: A 83 GLN cc_start: 0.8697 (mp10) cc_final: 0.8483 (mp10) REVERT: A 172 GLU cc_start: 0.9097 (tp30) cc_final: 0.8752 (tp30) REVERT: B 12 LYS cc_start: 0.9289 (mmmt) cc_final: 0.8705 (mmmm) REVERT: B 56 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8757 (tm-30) REVERT: B 57 MET cc_start: 0.8426 (mmp) cc_final: 0.8008 (mmm) REVERT: B 106 ASN cc_start: 0.9480 (m-40) cc_final: 0.9138 (m-40) REVERT: B 124 LYS cc_start: 0.9308 (ttmt) cc_final: 0.8969 (ttmm) REVERT: C 124 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8938 (mtmm) REVERT: C 128 TYR cc_start: 0.9044 (t80) cc_final: 0.8811 (t80) REVERT: C 203 MET cc_start: 0.8338 (pmm) cc_final: 0.8048 (pmm) REVERT: D 46 ASN cc_start: 0.9199 (t0) cc_final: 0.8897 (t0) REVERT: D 124 LYS cc_start: 0.9482 (ttmt) cc_final: 0.9148 (ttmt) REVERT: E 128 TYR cc_start: 0.9191 (t80) cc_final: 0.8793 (t80) REVERT: E 159 MET cc_start: 0.8847 (ttp) cc_final: 0.8480 (tmm) REVERT: E 167 TYR cc_start: 0.8156 (t80) cc_final: 0.7912 (t80) REVERT: G 109 ASP cc_start: 0.9406 (m-30) cc_final: 0.8683 (p0) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.2314 time to fit residues: 47.7906 Evaluate side-chains 116 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 170 ASN D 13 ASN E 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.046361 restraints weight = 175706.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.048270 restraints weight = 82026.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.049593 restraints weight = 50704.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.050445 restraints weight = 36261.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.051063 restraints weight = 28866.510| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11579 Z= 0.219 Angle : 0.620 8.893 15797 Z= 0.304 Chirality : 0.042 0.357 1720 Planarity : 0.004 0.057 2003 Dihedral : 8.291 56.400 1939 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.32 % Favored : 84.68 % Rotamer: Outliers : 0.09 % Allowed : 0.61 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.27 (0.20), residues: 1377 helix: -0.17 (0.76), residues: 45 sheet: -0.45 (0.25), residues: 428 loop : -3.42 (0.17), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 205 TYR 0.011 0.001 TYR D 7 PHE 0.010 0.001 PHE D 123 TRP 0.011 0.001 TRP B 85 HIS 0.005 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00457 (11559) covalent geometry : angle 0.60483 (15742) SS BOND : bond 0.00145 ( 5) SS BOND : angle 1.15687 ( 10) hydrogen bonds : bond 0.03069 ( 278) hydrogen bonds : angle 5.07308 ( 885) link_BETA1-4 : bond 0.00656 ( 5) link_BETA1-4 : angle 2.02286 ( 15) link_NAG-ASN : bond 0.00235 ( 10) link_NAG-ASN : angle 2.84697 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.9618 (t0) cc_final: 0.9362 (t0) REVERT: A 41 ASP cc_start: 0.8748 (p0) cc_final: 0.8528 (p0) REVERT: A 83 GLN cc_start: 0.8699 (mp10) cc_final: 0.8443 (mp10) REVERT: A 172 GLU cc_start: 0.9122 (tp30) cc_final: 0.8775 (tp30) REVERT: B 12 LYS cc_start: 0.9312 (mmmt) cc_final: 0.8906 (mmmm) REVERT: B 56 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8585 (tm-30) REVERT: B 106 ASN cc_start: 0.9430 (m-40) cc_final: 0.9126 (m-40) REVERT: B 124 LYS cc_start: 0.9293 (ttmt) cc_final: 0.8966 (ttmm) REVERT: C 124 LYS cc_start: 0.9255 (mtmm) cc_final: 0.9048 (mtmm) REVERT: C 128 TYR cc_start: 0.9047 (t80) cc_final: 0.8820 (t80) REVERT: C 139 GLN cc_start: 0.8564 (mt0) cc_final: 0.8234 (mp10) REVERT: C 203 MET cc_start: 0.8306 (pmm) cc_final: 0.7463 (pmm) REVERT: D 12 LYS cc_start: 0.9202 (mmmt) cc_final: 0.8965 (mmmm) REVERT: D 46 ASN cc_start: 0.9193 (t0) cc_final: 0.8886 (t0) REVERT: D 124 LYS cc_start: 0.9474 (ttmt) cc_final: 0.9132 (ttmt) REVERT: E 15 ASN cc_start: 0.9445 (t0) cc_final: 0.9223 (t0) REVERT: E 128 TYR cc_start: 0.9150 (t80) cc_final: 0.8775 (t80) REVERT: E 159 MET cc_start: 0.8857 (ttp) cc_final: 0.8459 (tmm) REVERT: G 109 ASP cc_start: 0.9361 (m-30) cc_final: 0.8688 (p0) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.2352 time to fit residues: 43.0618 Evaluate side-chains 106 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 123 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN F 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.058678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.046281 restraints weight = 180158.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.048120 restraints weight = 83218.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.049420 restraints weight = 51794.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.050369 restraints weight = 37010.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.050996 restraints weight = 29033.402| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11579 Z= 0.220 Angle : 0.629 8.004 15797 Z= 0.309 Chirality : 0.043 0.358 1720 Planarity : 0.004 0.058 2003 Dihedral : 7.933 57.469 1939 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.69 % Favored : 84.31 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.37 (0.20), residues: 1377 helix: -0.25 (0.76), residues: 45 sheet: -0.57 (0.25), residues: 425 loop : -3.45 (0.17), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 182 TYR 0.015 0.002 TYR D 7 PHE 0.018 0.002 PHE B 99 TRP 0.016 0.001 TRP B 85 HIS 0.005 0.002 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00462 (11559) covalent geometry : angle 0.61242 (15742) SS BOND : bond 0.00154 ( 5) SS BOND : angle 1.04406 ( 10) hydrogen bonds : bond 0.03028 ( 278) hydrogen bonds : angle 5.06333 ( 885) link_BETA1-4 : bond 0.00613 ( 5) link_BETA1-4 : angle 2.08925 ( 15) link_NAG-ASN : bond 0.00259 ( 10) link_NAG-ASN : angle 2.94815 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.9630 (t0) cc_final: 0.9372 (t0) REVERT: A 39 ILE cc_start: 0.9397 (tp) cc_final: 0.9132 (tp) REVERT: A 41 ASP cc_start: 0.8878 (p0) cc_final: 0.8674 (p0) REVERT: A 83 GLN cc_start: 0.8769 (mp10) cc_final: 0.8480 (mp10) REVERT: A 172 GLU cc_start: 0.9154 (tp30) cc_final: 0.8807 (tp30) REVERT: B 12 LYS cc_start: 0.9358 (mmmt) cc_final: 0.8954 (mmtm) REVERT: B 56 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8683 (tm-30) REVERT: B 106 ASN cc_start: 0.9403 (m-40) cc_final: 0.9120 (m-40) REVERT: B 124 LYS cc_start: 0.9290 (ttmt) cc_final: 0.8966 (ttmm) REVERT: C 128 TYR cc_start: 0.9068 (t80) cc_final: 0.8863 (t80) REVERT: C 139 GLN cc_start: 0.8585 (mt0) cc_final: 0.8207 (mp10) REVERT: C 203 MET cc_start: 0.8245 (pmm) cc_final: 0.7352 (pmm) REVERT: D 12 LYS cc_start: 0.9157 (mmmt) cc_final: 0.8917 (mmmm) REVERT: D 46 ASN cc_start: 0.9212 (t0) cc_final: 0.8914 (t0) REVERT: D 124 LYS cc_start: 0.9465 (ttmt) cc_final: 0.9114 (ttmt) REVERT: E 15 ASN cc_start: 0.9443 (t0) cc_final: 0.9217 (t0) REVERT: E 128 TYR cc_start: 0.9144 (t80) cc_final: 0.8783 (t80) REVERT: E 159 MET cc_start: 0.8868 (ttp) cc_final: 0.8619 (tmm) REVERT: F 45 GLU cc_start: 0.8491 (pm20) cc_final: 0.8206 (pm20) REVERT: G 109 ASP cc_start: 0.9316 (m-30) cc_final: 0.8678 (p0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2639 time to fit residues: 49.0744 Evaluate side-chains 103 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 92 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 126 optimal weight: 0.0670 chunk 84 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** E 110 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 = 0.2962 r_free = 0.2962 target = 0.058826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.046417 restraints weight = 177966.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.048340 restraints weight = 82169.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.049675 restraints weight = 50314.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.050608 restraints weight = 35889.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.051300 restraints weight = 28047.771| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11579 Z= 0.135 Angle : 0.588 9.598 15797 Z= 0.287 Chirality : 0.044 0.362 1720 Planarity : 0.004 0.073 2003 Dihedral : 7.609 58.768 1939 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.96 % Favored : 85.04 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.24 (0.21), residues: 1377 helix: -0.09 (0.76), residues: 45 sheet: -0.49 (0.24), residues: 475 loop : -3.51 (0.18), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 204 TYR 0.014 0.001 TYR D 7 PHE 0.009 0.001 PHE A 123 TRP 0.013 0.001 TRP B 85 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00300 (11559) covalent geometry : angle 0.56558 (15742) SS BOND : bond 0.00194 ( 5) SS BOND : angle 0.97707 ( 10) hydrogen bonds : bond 0.02775 ( 278) hydrogen bonds : angle 4.86812 ( 885) link_BETA1-4 : bond 0.00653 ( 5) link_BETA1-4 : angle 1.91925 ( 15) link_NAG-ASN : bond 0.00269 ( 10) link_NAG-ASN : angle 3.47319 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.9594 (t0) cc_final: 0.9311 (t0) REVERT: A 83 GLN cc_start: 0.8747 (mp10) cc_final: 0.8458 (mp10) REVERT: A 172 GLU cc_start: 0.9166 (tp30) cc_final: 0.8813 (tp30) REVERT: B 12 LYS cc_start: 0.9334 (mmmt) cc_final: 0.8795 (mmmm) REVERT: B 56 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8538 (tm-30) REVERT: B 106 ASN cc_start: 0.9389 (m-40) cc_final: 0.9080 (m-40) REVERT: B 124 LYS cc_start: 0.9291 (ttmt) cc_final: 0.8964 (ttmm) REVERT: C 128 TYR cc_start: 0.9094 (t80) cc_final: 0.8879 (t80) REVERT: C 203 MET cc_start: 0.8195 (pmm) cc_final: 0.7883 (pmm) REVERT: D 12 LYS cc_start: 0.9126 (mmmt) cc_final: 0.8875 (mmmm) REVERT: D 46 ASN cc_start: 0.9187 (t0) cc_final: 0.8892 (t0) REVERT: D 124 LYS cc_start: 0.9461 (ttmt) cc_final: 0.9123 (ttmt) REVERT: E 15 ASN cc_start: 0.9425 (t0) cc_final: 0.9204 (t0) REVERT: E 128 TYR cc_start: 0.9168 (t80) cc_final: 0.8814 (t80) REVERT: E 159 MET cc_start: 0.8798 (ttp) cc_final: 0.8446 (tmm) REVERT: G 109 ASP cc_start: 0.9313 (m-30) cc_final: 0.8663 (p0) REVERT: I 2 GLN cc_start: 0.9267 (mt0) cc_final: 0.9020 (mm-40) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2201 time to fit residues: 38.9590 Evaluate side-chains 108 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 56 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 0.0770 chunk 84 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** E 110 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 = 0.2958 r_free = 0.2958 target = 0.058684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.046126 restraints weight = 173160.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.048054 restraints weight = 80318.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.049375 restraints weight = 49494.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.050283 restraints weight = 35383.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.050881 restraints weight = 27898.981| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11579 Z= 0.179 Angle : 0.598 8.654 15797 Z= 0.293 Chirality : 0.043 0.364 1720 Planarity : 0.004 0.062 2003 Dihedral : 7.524 58.782 1939 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.05 % Favored : 83.95 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.26 (0.21), residues: 1377 helix: -0.14 (0.76), residues: 45 sheet: -0.47 (0.24), residues: 469 loop : -3.52 (0.18), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 205 TYR 0.010 0.001 TYR D 7 PHE 0.023 0.001 PHE D 99 TRP 0.013 0.001 TRP B 85 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00382 (11559) covalent geometry : angle 0.57650 (15742) SS BOND : bond 0.00356 ( 5) SS BOND : angle 1.81464 ( 10) hydrogen bonds : bond 0.02841 ( 278) hydrogen bonds : angle 4.92923 ( 885) link_BETA1-4 : bond 0.00476 ( 5) link_BETA1-4 : angle 1.84834 ( 15) link_NAG-ASN : bond 0.00344 ( 10) link_NAG-ASN : angle 3.29727 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.9611 (t0) cc_final: 0.9348 (t0) REVERT: A 83 GLN cc_start: 0.8767 (mp10) cc_final: 0.8449 (mp10) REVERT: A 172 GLU cc_start: 0.9176 (tp30) cc_final: 0.8821 (tp30) REVERT: B 12 LYS cc_start: 0.9356 (mmmt) cc_final: 0.8822 (mmmm) REVERT: B 56 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8562 (tm-30) REVERT: B 106 ASN cc_start: 0.9372 (m-40) cc_final: 0.9075 (m-40) REVERT: B 124 LYS cc_start: 0.9311 (ttmt) cc_final: 0.8984 (ttmm) REVERT: C 203 MET cc_start: 0.7977 (pmm) cc_final: 0.7740 (pmm) REVERT: D 12 LYS cc_start: 0.9095 (mmmt) cc_final: 0.8857 (mmmm) REVERT: D 46 ASN cc_start: 0.9194 (t0) cc_final: 0.8903 (t0) REVERT: D 124 LYS cc_start: 0.9465 (ttmt) cc_final: 0.9125 (ttmt) REVERT: E 15 ASN cc_start: 0.9406 (t0) cc_final: 0.9166 (t0) REVERT: E 128 TYR cc_start: 0.9143 (t80) cc_final: 0.8818 (t80) REVERT: E 159 MET cc_start: 0.8774 (ttp) cc_final: 0.8520 (tmm) REVERT: G 109 ASP cc_start: 0.9291 (m-30) cc_final: 0.8664 (p0) REVERT: I 2 GLN cc_start: 0.9256 (mt0) cc_final: 0.8995 (mm-40) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2443 time to fit residues: 42.5428 Evaluate side-chains 102 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** E 110 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 = 0.2969 r_free = 0.2969 target = 0.059160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.046507 restraints weight = 175339.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.048461 restraints weight = 81054.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.049786 restraints weight = 49700.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.050675 restraints weight = 35597.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.051311 restraints weight = 28251.470| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11579 Z= 0.126 Angle : 0.573 7.988 15797 Z= 0.281 Chirality : 0.043 0.367 1720 Planarity : 0.004 0.059 2003 Dihedral : 7.308 59.472 1939 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.89 % Favored : 85.11 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.22 (0.21), residues: 1377 helix: -0.05 (0.76), residues: 45 sheet: -0.53 (0.24), residues: 475 loop : -3.46 (0.18), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 185 TYR 0.012 0.001 TYR D 7 PHE 0.010 0.001 PHE B 99 TRP 0.013 0.001 TRP E 85 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00283 (11559) covalent geometry : angle 0.55371 (15742) SS BOND : bond 0.00278 ( 5) SS BOND : angle 1.67124 ( 10) hydrogen bonds : bond 0.02744 ( 278) hydrogen bonds : angle 4.75731 ( 885) link_BETA1-4 : bond 0.00577 ( 5) link_BETA1-4 : angle 1.79784 ( 15) link_NAG-ASN : bond 0.00282 ( 10) link_NAG-ASN : angle 3.07865 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue ILE 129 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue VAL 138 is missing expected H atoms. Skipping. Residue TYR 187 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.9596 (t0) cc_final: 0.9317 (t0) REVERT: A 41 ASP cc_start: 0.8772 (p0) cc_final: 0.8551 (p0) REVERT: A 172 GLU cc_start: 0.9173 (tp30) cc_final: 0.8822 (tp30) REVERT: B 12 LYS cc_start: 0.9352 (mmmt) cc_final: 0.8954 (mmtp) REVERT: B 56 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8572 (tm-30) REVERT: B 106 ASN cc_start: 0.9373 (m-40) cc_final: 0.9080 (m-40) REVERT: B 124 LYS cc_start: 0.9311 (ttmt) cc_final: 0.8978 (ttmm) REVERT: C 203 MET cc_start: 0.7949 (pmm) cc_final: 0.7719 (pmm) REVERT: D 12 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8884 (mmmm) REVERT: D 46 ASN cc_start: 0.9181 (t0) cc_final: 0.8905 (t0) REVERT: D 124 LYS cc_start: 0.9464 (ttmt) cc_final: 0.9153 (ttmt) REVERT: E 15 ASN cc_start: 0.9411 (t0) cc_final: 0.9174 (t0) REVERT: E 128 TYR cc_start: 0.9146 (t80) cc_final: 0.8841 (t80) REVERT: E 159 MET cc_start: 0.8750 (ttp) cc_final: 0.8538 (tmm) REVERT: G 109 ASP cc_start: 0.9293 (m-30) cc_final: 0.8619 (p0) REVERT: I 2 GLN cc_start: 0.9267 (mt0) cc_final: 0.8979 (mm-40) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2106 time to fit residues: 37.0691 Evaluate side-chains 103 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 97 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN E 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.046622 restraints weight = 176959.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.048553 restraints weight = 81643.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.049819 restraints weight = 49940.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.050739 restraints weight = 36018.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.051402 restraints weight = 28437.741| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11579 Z= 0.156 Angle : 0.573 7.854 15797 Z= 0.282 Chirality : 0.043 0.368 1720 Planarity : 0.004 0.054 2003 Dihedral : 7.264 59.285 1939 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.69 % Favored : 84.31 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.22 (0.21), residues: 1377 helix: -0.15 (0.76), residues: 45 sheet: -0.49 (0.24), residues: 469 loop : -3.47 (0.18), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 98 TYR 0.019 0.001 TYR C 128 PHE 0.025 0.001 PHE D 99 TRP 0.014 0.001 TRP E 85 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00338 (11559) covalent geometry : angle 0.55502 (15742) SS BOND : bond 0.00252 ( 5) SS BOND : angle 1.47601 ( 10) hydrogen bonds : bond 0.02742 ( 278) hydrogen bonds : angle 4.78946 ( 885) link_BETA1-4 : bond 0.00507 ( 5) link_BETA1-4 : angle 1.67678 ( 15) link_NAG-ASN : bond 0.00282 ( 10) link_NAG-ASN : angle 3.01447 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2594.41 seconds wall clock time: 45 minutes 15.37 seconds (2715.37 seconds total)