Starting phenix.real_space_refine on Wed May 21 12:42:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ci2_16666/05_2025/8ci2_16666_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ci2_16666/05_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_16666/05_2025/8ci2_16666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ci2_16666/05_2025/8ci2_16666.map" model { file = "/net/cci-nas-00/data/ceres_data/8ci2_16666/05_2025/8ci2_16666_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ci2_16666/05_2025/8ci2_16666_trim.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG: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: {'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG: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: {'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG: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: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} 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: 10.91, per 1000 atoms: 0.51 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: 5.79 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 2.26 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: 7.12 Time building geometry restraints manager: 6.89 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 206 or resi \ d 401 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 \ 206 or resid 401 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 206 or resi \ d 401 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 206 or resid 401 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.360 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 46.060 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.900 ------------------------------------------------------------------------------- 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 : 6.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.001 TRP E 59 HIS 0.003 0.001 HIS B 114 PHE 0.010 0.001 PHE G 48 TYR 0.011 0.001 TYR E 14 ARG 0.003 0.000 ARG D 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 10) link_NAG-ASN : angle 2.51521 ( 30) link_BETA1-4 : bond 0.01912 ( 5) link_BETA1-4 : angle 5.74230 ( 15) hydrogen bonds : bond 0.12006 ( 278) hydrogen bonds : angle 6.07993 ( 885) SS BOND : bond 0.00376 ( 5) SS BOND : angle 0.57903 ( 10) covalent geometry : bond 0.00486 (11559) covalent geometry : angle 0.61776 (15742) *********************** 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 : 1.674 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: A 49 LEU cc_start: 0.7986 (tt) cc_final: 0.7783 (tt) REVERT: A 98 ARG cc_start: 0.8055 (mtm180) cc_final: 0.6623 (mtm110) REVERT: B 124 LYS cc_start: 0.8039 (ttmt) cc_final: 0.7721 (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: 0.8081 (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: 0.6199 time to fit residues: 215.9539 Evaluate side-chains 143 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.061674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.048961 restraints weight = 170138.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.050971 restraints weight = 78204.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.052319 restraints weight = 47611.864| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11579 Z= 0.226 Angle : 0.644 7.033 15797 Z= 0.322 Chirality : 0.043 0.352 1720 Planarity : 0.006 0.083 2003 Dihedral : 9.688 115.996 1939 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.38 % Favored : 85.62 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.20), residues: 1377 helix: -0.21 (0.76), residues: 45 sheet: -0.42 (0.23), residues: 505 loop : -3.58 (0.17), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 173 HIS 0.006 0.001 HIS A 140 PHE 0.015 0.001 PHE G 69 TYR 0.019 0.001 TYR A 167 ARG 0.018 0.001 ARG C 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 10) link_NAG-ASN : angle 2.60783 ( 30) link_BETA1-4 : bond 0.00747 ( 5) link_BETA1-4 : angle 2.55054 ( 15) hydrogen bonds : bond 0.03664 ( 278) hydrogen bonds : angle 5.47782 ( 885) SS BOND : bond 0.00145 ( 5) SS BOND : angle 0.87592 ( 10) covalent geometry : bond 0.00481 (11559) covalent geometry : angle 0.62987 (15742) *********************** 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 183 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.856 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: A 15 ASN cc_start: 0.9542 (t0) cc_final: 0.9219 (t0) REVERT: A 98 ARG cc_start: 0.9073 (mtm180) cc_final: 0.8048 (mtm110) REVERT: A 172 GLU cc_start: 0.9096 (tp30) cc_final: 0.8753 (tp30) REVERT: B 12 LYS cc_start: 0.9394 (mmmt) cc_final: 0.9042 (mmmm) REVERT: B 15 ASN cc_start: 0.9658 (t0) cc_final: 0.9430 (t0) REVERT: B 32 PHE cc_start: 0.9304 (t80) cc_final: 0.8906 (t80) REVERT: B 56 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8536 (tm-30) REVERT: B 96 ASP cc_start: 0.9180 (t0) cc_final: 0.8543 (t70) REVERT: B 99 PHE cc_start: 0.9159 (t80) cc_final: 0.8908 (t80) REVERT: B 106 ASN cc_start: 0.9510 (m-40) cc_final: 0.9174 (m-40) REVERT: C 96 ASP cc_start: 0.8586 (t70) cc_final: 0.8253 (t0) REVERT: C 98 ARG cc_start: 0.9267 (ptt-90) cc_final: 0.9005 (ptt-90) REVERT: D 46 ASN cc_start: 0.9201 (t0) cc_final: 0.8918 (t0) REVERT: D 52 ASN cc_start: 0.9457 (t0) cc_final: 0.9104 (t0) REVERT: E 159 MET cc_start: 0.8832 (ttp) cc_final: 0.8438 (tmm) REVERT: E 167 TYR cc_start: 0.8219 (t80) cc_final: 0.7720 (t80) REVERT: E 203 MET cc_start: 0.9326 (pmm) cc_final: 0.9042 (pmm) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.6193 time to fit residues: 150.6940 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 : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 101 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.061129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.047910 restraints weight = 168970.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.049920 restraints weight = 78975.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.051342 restraints weight = 48619.219| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11579 Z= 0.141 Angle : 0.569 6.795 15797 Z= 0.282 Chirality : 0.043 0.352 1720 Planarity : 0.004 0.063 2003 Dihedral : 9.415 108.500 1939 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.21), residues: 1377 helix: 0.17 (0.80), residues: 45 sheet: -0.29 (0.23), residues: 490 loop : -3.47 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 59 HIS 0.004 0.001 HIS B 114 PHE 0.011 0.001 PHE I 69 TYR 0.011 0.001 TYR C 92 ARG 0.006 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 10) link_NAG-ASN : angle 2.52626 ( 30) link_BETA1-4 : bond 0.00781 ( 5) link_BETA1-4 : angle 2.21226 ( 15) hydrogen bonds : bond 0.03229 ( 278) hydrogen bonds : angle 5.13991 ( 885) SS BOND : bond 0.00193 ( 5) SS BOND : angle 0.92173 ( 10) covalent geometry : bond 0.00309 (11559) covalent geometry : angle 0.55479 (15742) *********************** 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 164 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.682 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: 0.9579 (t0) cc_final: 0.9260 (t0) REVERT: A 172 GLU cc_start: 0.9087 (tp30) cc_final: 0.8719 (tp30) REVERT: B 12 LYS cc_start: 0.9373 (mmmt) cc_final: 0.9031 (mmmm) REVERT: B 15 ASN cc_start: 0.9651 (t0) cc_final: 0.9406 (t0) REVERT: B 32 PHE cc_start: 0.9291 (t80) cc_final: 0.8911 (t80) REVERT: B 39 ILE cc_start: 0.9550 (pt) cc_final: 0.9272 (pt) REVERT: B 56 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8537 (tm-30) REVERT: B 106 ASN cc_start: 0.9523 (m-40) cc_final: 0.9222 (m-40) REVERT: C 32 PHE cc_start: 0.8997 (t80) cc_final: 0.8767 (t80) REVERT: C 203 MET cc_start: 0.8278 (pmm) cc_final: 0.7968 (pmm) REVERT: D 46 ASN cc_start: 0.9181 (t0) cc_final: 0.8890 (t0) REVERT: E 159 MET cc_start: 0.8840 (ttp) cc_final: 0.8469 (tmm) REVERT: E 167 TYR cc_start: 0.8098 (t80) cc_final: 0.7849 (t80) REVERT: F 66 LYS cc_start: 0.9486 (ttpp) cc_final: 0.9085 (tppt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.6091 time to fit residues: 135.3986 Evaluate side-chains 131 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN D 13 ASN I 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.045915 restraints weight = 179690.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.047837 restraints weight = 84208.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.049179 restraints weight = 51813.351| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11579 Z= 0.280 Angle : 0.689 8.811 15797 Z= 0.341 Chirality : 0.044 0.357 1720 Planarity : 0.005 0.059 2003 Dihedral : 9.867 113.703 1939 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.76 % Favored : 84.24 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.20), residues: 1377 helix: -0.40 (0.77), residues: 45 sheet: -0.50 (0.25), residues: 428 loop : -3.53 (0.17), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 148 HIS 0.007 0.002 HIS A 104 PHE 0.021 0.002 PHE B 99 TYR 0.012 0.002 TYR A 167 ARG 0.005 0.001 ARG C 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 10) link_NAG-ASN : angle 3.21551 ( 30) link_BETA1-4 : bond 0.00833 ( 5) link_BETA1-4 : angle 2.12030 ( 15) hydrogen bonds : bond 0.03396 ( 278) hydrogen bonds : angle 5.39382 ( 885) SS BOND : bond 0.00099 ( 5) SS BOND : angle 0.98584 ( 10) covalent geometry : bond 0.00579 (11559) covalent geometry : angle 0.67190 (15742) *********************** 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 137 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.832 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: 0.9631 (t0) cc_final: 0.9387 (t0) REVERT: A 172 GLU cc_start: 0.9099 (tp30) cc_final: 0.8741 (tp30) REVERT: B 12 LYS cc_start: 0.9328 (mmmt) cc_final: 0.8893 (mmmm) REVERT: B 32 PHE cc_start: 0.9433 (t80) cc_final: 0.9053 (t80) REVERT: B 56 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8615 (tm-30) REVERT: B 96 ASP cc_start: 0.9468 (t0) cc_final: 0.9157 (t70) REVERT: B 106 ASN cc_start: 0.9496 (m-40) cc_final: 0.9184 (m-40) REVERT: B 124 LYS cc_start: 0.9096 (ttmt) cc_final: 0.8890 (ttmm) REVERT: C 203 MET cc_start: 0.8314 (pmm) cc_final: 0.8032 (pmm) REVERT: D 12 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8986 (mmmm) REVERT: D 46 ASN cc_start: 0.9217 (t0) cc_final: 0.8914 (t0) REVERT: E 15 ASN cc_start: 0.9412 (t0) cc_final: 0.9208 (t0) REVERT: E 128 TYR cc_start: 0.9258 (t80) cc_final: 0.8916 (t80) REVERT: E 159 MET cc_start: 0.8903 (ttp) cc_final: 0.8597 (tmm) REVERT: G 109 ASP cc_start: 0.9400 (m-30) cc_final: 0.8672 (p0) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.6113 time to fit residues: 114.6519 Evaluate side-chains 111 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 27 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.058828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.046420 restraints weight = 179831.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.048354 restraints weight = 82667.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.049711 restraints weight = 50483.779| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11579 Z= 0.148 Angle : 0.580 7.689 15797 Z= 0.285 Chirality : 0.043 0.356 1720 Planarity : 0.004 0.052 2003 Dihedral : 9.422 104.215 1939 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.21), residues: 1377 helix: -0.25 (0.76), residues: 45 sheet: -0.39 (0.24), residues: 475 loop : -3.60 (0.17), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 85 HIS 0.004 0.001 HIS B 114 PHE 0.009 0.001 PHE F 69 TYR 0.010 0.001 TYR D 7 ARG 0.006 0.000 ARG F 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 10) link_NAG-ASN : angle 2.85080 ( 30) link_BETA1-4 : bond 0.00637 ( 5) link_BETA1-4 : angle 1.85243 ( 15) hydrogen bonds : bond 0.02992 ( 278) hydrogen bonds : angle 5.10137 ( 885) SS BOND : bond 0.00133 ( 5) SS BOND : angle 1.50876 ( 10) covalent geometry : bond 0.00319 (11559) covalent geometry : angle 0.56307 (15742) *********************** 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 138 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.617 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: A 15 ASN cc_start: 0.9626 (t0) cc_final: 0.9367 (t0) REVERT: A 83 GLN cc_start: 0.8753 (mp10) cc_final: 0.8496 (mp10) REVERT: A 172 GLU cc_start: 0.9115 (tp30) cc_final: 0.8774 (tp30) REVERT: B 12 LYS cc_start: 0.9326 (mmmt) cc_final: 0.8932 (mmmm) REVERT: B 32 PHE cc_start: 0.9407 (t80) cc_final: 0.8969 (t80) REVERT: B 56 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8472 (tm-30) REVERT: B 106 ASN cc_start: 0.9488 (m-40) cc_final: 0.9195 (m-40) REVERT: B 124 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8853 (ttmm) REVERT: C 128 TYR cc_start: 0.9111 (t80) cc_final: 0.8605 (t80) REVERT: C 203 MET cc_start: 0.8314 (pmm) cc_final: 0.8033 (pmm) REVERT: D 12 LYS cc_start: 0.9238 (mmmt) cc_final: 0.8954 (mmmm) REVERT: D 46 ASN cc_start: 0.9215 (t0) cc_final: 0.8908 (t0) REVERT: E 15 ASN cc_start: 0.9411 (t0) cc_final: 0.9207 (t0) REVERT: E 128 TYR cc_start: 0.9256 (t80) cc_final: 0.8908 (t80) REVERT: G 109 ASP cc_start: 0.9401 (m-30) cc_final: 0.8705 (p0) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.5846 time to fit residues: 108.9730 Evaluate side-chains 115 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN D 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.059190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.046578 restraints weight = 176025.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.048514 restraints weight = 82216.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.049854 restraints weight = 50668.070| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11579 Z= 0.194 Angle : 0.603 9.888 15797 Z= 0.295 Chirality : 0.043 0.357 1720 Planarity : 0.004 0.050 2003 Dihedral : 8.769 74.543 1939 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.69 % Favored : 84.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.20), residues: 1377 helix: -0.33 (0.76), residues: 45 sheet: -0.46 (0.25), residues: 425 loop : -3.49 (0.17), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 85 HIS 0.004 0.001 HIS A 104 PHE 0.030 0.001 PHE B 32 TYR 0.010 0.001 TYR A 167 ARG 0.003 0.000 ARG C 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 10) link_NAG-ASN : angle 2.84954 ( 30) link_BETA1-4 : bond 0.00583 ( 5) link_BETA1-4 : angle 1.90493 ( 15) hydrogen bonds : bond 0.02999 ( 278) hydrogen bonds : angle 5.08202 ( 885) SS BOND : bond 0.00172 ( 5) SS BOND : angle 1.51571 ( 10) covalent geometry : bond 0.00408 (11559) covalent geometry : angle 0.58699 (15742) *********************** 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 134 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.827 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: A 15 ASN cc_start: 0.9633 (t0) cc_final: 0.9390 (t0) REVERT: A 41 ASP cc_start: 0.8870 (p0) cc_final: 0.8642 (p0) REVERT: A 83 GLN cc_start: 0.8773 (mp10) cc_final: 0.8511 (mp10) REVERT: A 172 GLU cc_start: 0.9143 (tp30) cc_final: 0.8795 (tp30) REVERT: B 12 LYS cc_start: 0.9337 (mmmt) cc_final: 0.8924 (mmmm) REVERT: B 32 PHE cc_start: 0.9456 (t80) cc_final: 0.9232 (t80) REVERT: B 56 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8679 (tm-30) REVERT: B 57 MET cc_start: 0.8171 (mmp) cc_final: 0.7437 (mmp) REVERT: B 106 ASN cc_start: 0.9414 (m-40) cc_final: 0.9094 (m-40) REVERT: B 124 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8882 (ttmm) REVERT: C 128 TYR cc_start: 0.9105 (t80) cc_final: 0.8855 (t80) REVERT: C 203 MET cc_start: 0.8088 (pmm) cc_final: 0.7875 (pmm) REVERT: D 12 LYS cc_start: 0.9219 (mmmt) cc_final: 0.8981 (mmmm) REVERT: D 46 ASN cc_start: 0.9216 (t0) cc_final: 0.8911 (t0) REVERT: D 124 LYS cc_start: 0.9465 (ttmt) cc_final: 0.9124 (ttmt) REVERT: E 128 TYR cc_start: 0.9226 (t80) cc_final: 0.8883 (t80) REVERT: G 109 ASP cc_start: 0.9358 (m-30) cc_final: 0.8697 (p0) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.5823 time to fit residues: 106.2579 Evaluate side-chains 110 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** F 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.058468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.045623 restraints weight = 175541.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.047573 restraints weight = 82925.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.048908 restraints weight = 51474.935| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4812 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= 0.217 Angle : 0.631 8.139 15797 Z= 0.306 Chirality : 0.043 0.357 1720 Planarity : 0.004 0.063 2003 Dihedral : 8.027 57.611 1939 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.27 % Favored : 83.73 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.21), residues: 1377 helix: -0.35 (0.76), residues: 45 sheet: -0.52 (0.24), residues: 475 loop : -3.68 (0.17), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 85 HIS 0.005 0.001 HIS A 104 PHE 0.015 0.001 PHE B 99 TYR 0.011 0.001 TYR E 167 ARG 0.006 0.001 ARG C 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 10) link_NAG-ASN : angle 3.43008 ( 30) link_BETA1-4 : bond 0.00675 ( 5) link_BETA1-4 : angle 2.05833 ( 15) hydrogen bonds : bond 0.02997 ( 278) hydrogen bonds : angle 5.15420 ( 885) SS BOND : bond 0.00426 ( 5) SS BOND : angle 1.48505 ( 10) covalent geometry : bond 0.00453 (11559) covalent geometry : angle 0.60951 (15742) *********************** 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 129 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.624 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: A 15 ASN cc_start: 0.9637 (t0) cc_final: 0.9395 (t0) REVERT: A 142 LYS cc_start: 0.9311 (mtmm) cc_final: 0.8760 (mmtm) REVERT: A 172 GLU cc_start: 0.9164 (tp30) cc_final: 0.8814 (tp30) REVERT: B 12 LYS cc_start: 0.9357 (mmmt) cc_final: 0.8971 (mmtm) REVERT: B 32 PHE cc_start: 0.9276 (t80) cc_final: 0.9019 (t80) REVERT: B 56 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8561 (tm-30) REVERT: B 106 ASN cc_start: 0.9379 (m-40) cc_final: 0.9072 (m-40) REVERT: B 124 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8897 (ttmm) REVERT: C 128 TYR cc_start: 0.9118 (t80) cc_final: 0.8698 (t80) REVERT: C 203 MET cc_start: 0.8088 (pmm) cc_final: 0.7846 (pmm) REVERT: D 12 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8975 (mmmm) REVERT: D 46 ASN cc_start: 0.9209 (t0) cc_final: 0.8914 (t0) REVERT: D 124 LYS cc_start: 0.9460 (ttmt) cc_final: 0.9122 (ttmt) REVERT: E 15 ASN cc_start: 0.9449 (t0) cc_final: 0.9237 (t0) REVERT: E 128 TYR cc_start: 0.9211 (t80) cc_final: 0.8882 (t80) REVERT: G 109 ASP cc_start: 0.9324 (m-30) cc_final: 0.8664 (p0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.6468 time to fit residues: 111.8285 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 : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 39 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.059251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.046535 restraints weight = 174215.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.048493 restraints weight = 80937.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.049816 restraints weight = 49914.575| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4849 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= 0.123 Angle : 0.570 7.076 15797 Z= 0.280 Chirality : 0.043 0.354 1720 Planarity : 0.004 0.054 2003 Dihedral : 7.645 59.454 1939 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.18 % Favored : 84.82 % Rotamer: Outliers : 0.09 % Allowed : 0.44 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.21), residues: 1377 helix: -0.29 (0.74), residues: 45 sheet: -0.44 (0.24), residues: 475 loop : -3.57 (0.18), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 85 HIS 0.004 0.001 HIS B 114 PHE 0.007 0.001 PHE D 123 TYR 0.009 0.001 TYR B 167 ARG 0.002 0.000 ARG C 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 10) link_NAG-ASN : angle 3.03225 ( 30) link_BETA1-4 : bond 0.00691 ( 5) link_BETA1-4 : angle 1.99191 ( 15) hydrogen bonds : bond 0.02727 ( 278) hydrogen bonds : angle 4.89757 ( 885) SS BOND : bond 0.00238 ( 5) SS BOND : angle 1.32741 ( 10) covalent geometry : bond 0.00274 (11559) covalent geometry : angle 0.55140 (15742) *********************** 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 131 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.637 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: A 15 ASN cc_start: 0.9609 (t0) cc_final: 0.9344 (t0) REVERT: A 172 GLU cc_start: 0.9165 (tp30) cc_final: 0.8810 (tp30) REVERT: B 12 LYS cc_start: 0.9330 (mmmt) cc_final: 0.8794 (mmmm) REVERT: B 56 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8553 (tm-30) REVERT: B 106 ASN cc_start: 0.9410 (m-40) cc_final: 0.9104 (m-40) REVERT: B 124 LYS cc_start: 0.9277 (ttmt) cc_final: 0.8991 (ttmm) REVERT: C 128 TYR cc_start: 0.9110 (t80) cc_final: 0.8872 (t80) REVERT: D 12 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8945 (mmmm) REVERT: D 46 ASN cc_start: 0.9200 (t0) cc_final: 0.8927 (t0) REVERT: D 99 PHE cc_start: 0.9540 (t80) cc_final: 0.9321 (t80) REVERT: D 124 LYS cc_start: 0.9457 (ttmt) cc_final: 0.9140 (ttmt) REVERT: E 15 ASN cc_start: 0.9441 (t0) cc_final: 0.9172 (t0) REVERT: E 128 TYR cc_start: 0.9222 (t80) cc_final: 0.8897 (t80) REVERT: G 109 ASP cc_start: 0.9328 (m-30) cc_final: 0.8646 (p0) REVERT: I 35 MET cc_start: 0.8669 (pmm) cc_final: 0.8468 (pmm) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.5627 time to fit residues: 101.3457 Evaluate side-chains 109 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** ** E 110 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 = 0.2956 r_free = 0.2956 target = 0.058788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.046127 restraints weight = 173497.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.048080 restraints weight = 80965.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.049433 restraints weight = 49681.806| |-----------------------------------------------------------------------------| r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11579 Z= 0.164 Angle : 0.578 7.106 15797 Z= 0.284 Chirality : 0.043 0.358 1720 Planarity : 0.004 0.048 2003 Dihedral : 7.482 58.793 1939 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.27 % Favored : 83.73 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.21), residues: 1377 helix: -0.22 (0.76), residues: 45 sheet: -0.73 (0.23), residues: 515 loop : -3.51 (0.18), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 85 HIS 0.003 0.001 HIS B 114 PHE 0.013 0.001 PHE B 32 TYR 0.009 0.001 TYR B 167 ARG 0.005 0.000 ARG E 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 10) link_NAG-ASN : angle 2.95844 ( 30) link_BETA1-4 : bond 0.00582 ( 5) link_BETA1-4 : angle 1.89199 ( 15) hydrogen bonds : bond 0.02741 ( 278) hydrogen bonds : angle 4.87679 ( 885) SS BOND : bond 0.00204 ( 5) SS BOND : angle 1.21746 ( 10) covalent geometry : bond 0.00355 (11559) covalent geometry : angle 0.56019 (15742) *********************** 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 126 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.666 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: A 15 ASN cc_start: 0.9614 (t0) cc_final: 0.9362 (t0) REVERT: A 172 GLU cc_start: 0.9170 (tp30) cc_final: 0.8824 (tp30) REVERT: B 12 LYS cc_start: 0.9348 (mmmt) cc_final: 0.8819 (mmmm) REVERT: B 56 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8542 (tm-30) REVERT: B 106 ASN cc_start: 0.9360 (m-40) cc_final: 0.9062 (m-40) REVERT: C 128 TYR cc_start: 0.9121 (t80) cc_final: 0.8886 (t80) REVERT: C 203 MET cc_start: 0.8552 (pmm) cc_final: 0.8336 (pmm) REVERT: D 12 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8935 (mmmm) REVERT: D 46 ASN cc_start: 0.9207 (t0) cc_final: 0.8934 (t0) REVERT: D 99 PHE cc_start: 0.9538 (t80) cc_final: 0.9312 (t80) REVERT: D 124 LYS cc_start: 0.9449 (ttmt) cc_final: 0.9148 (ttmt) REVERT: E 15 ASN cc_start: 0.9430 (t0) cc_final: 0.9184 (t0) REVERT: E 128 TYR cc_start: 0.9202 (t80) cc_final: 0.8895 (t80) REVERT: G 109 ASP cc_start: 0.9298 (m-30) cc_final: 0.8679 (p0) REVERT: I 2 GLN cc_start: 0.9286 (mt0) cc_final: 0.9031 (mm-40) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.6105 time to fit residues: 106.9722 Evaluate side-chains 112 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 46 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** E 110 ASN 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 = 0.058964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.046425 restraints weight = 177525.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.048366 restraints weight = 81962.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.049681 restraints weight = 50277.098| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11579 Z= 0.136 Angle : 0.557 6.772 15797 Z= 0.274 Chirality : 0.043 0.361 1720 Planarity : 0.004 0.046 2003 Dihedral : 7.321 59.061 1939 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.47 % Favored : 84.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.21), residues: 1377 helix: -0.16 (0.76), residues: 45 sheet: -0.69 (0.23), residues: 515 loop : -3.49 (0.19), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 85 HIS 0.004 0.001 HIS B 114 PHE 0.011 0.001 PHE B 32 TYR 0.009 0.001 TYR D 117 ARG 0.004 0.000 ARG B 4 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 10) link_NAG-ASN : angle 2.85998 ( 30) link_BETA1-4 : bond 0.00582 ( 5) link_BETA1-4 : angle 1.79029 ( 15) hydrogen bonds : bond 0.02680 ( 278) hydrogen bonds : angle 4.79742 ( 885) SS BOND : bond 0.00204 ( 5) SS BOND : angle 1.14942 ( 10) covalent geometry : bond 0.00299 (11559) covalent geometry : angle 0.54026 (15742) ********************** 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 131 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.795 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: 0.9607 (t0) cc_final: 0.9345 (t0) REVERT: A 172 GLU cc_start: 0.9176 (tp30) cc_final: 0.8834 (tp30) REVERT: B 12 LYS cc_start: 0.9360 (mmmt) cc_final: 0.8834 (mmmm) REVERT: B 56 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8517 (tm-30) REVERT: B 106 ASN cc_start: 0.9369 (m-40) cc_final: 0.9062 (m-40) REVERT: B 124 LYS cc_start: 0.9292 (ttmt) cc_final: 0.9000 (ttmm) REVERT: C 128 TYR cc_start: 0.9119 (t80) cc_final: 0.8881 (t80) REVERT: D 12 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8948 (mmmm) REVERT: D 46 ASN cc_start: 0.9204 (t0) cc_final: 0.8934 (t0) REVERT: D 99 PHE cc_start: 0.9566 (t80) cc_final: 0.9317 (t80) REVERT: D 124 LYS cc_start: 0.9433 (ttmt) cc_final: 0.9129 (ttmt) REVERT: E 15 ASN cc_start: 0.9423 (t0) cc_final: 0.9173 (t0) REVERT: E 128 TYR cc_start: 0.9186 (t80) cc_final: 0.8882 (t80) REVERT: G 109 ASP cc_start: 0.9297 (m-30) cc_final: 0.8646 (p0) REVERT: I 2 GLN cc_start: 0.9299 (mt0) cc_final: 0.9018 (mm-40) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.5430 time to fit residues: 98.5702 Evaluate side-chains 110 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 0.0060 chunk 116 optimal weight: 5.9990 chunk 82 optimal weight: 0.0020 chunk 100 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 overall best weight: 0.9006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.059857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.047293 restraints weight = 173085.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.049204 restraints weight = 79998.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.050554 restraints weight = 49167.917| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 11579 Z= 0.089 Angle : 0.537 6.325 15797 Z= 0.266 Chirality : 0.043 0.365 1720 Planarity : 0.004 0.048 2003 Dihedral : 6.878 54.794 1939 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.21), residues: 1377 helix: 0.03 (0.74), residues: 45 sheet: -0.33 (0.24), residues: 475 loop : -3.45 (0.18), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 85 HIS 0.004 0.000 HIS B 114 PHE 0.014 0.001 PHE B 32 TYR 0.012 0.001 TYR B 167 ARG 0.004 0.000 ARG E 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 10) link_NAG-ASN : angle 2.53752 ( 30) link_BETA1-4 : bond 0.00714 ( 5) link_BETA1-4 : angle 1.83371 ( 15) hydrogen bonds : bond 0.02471 ( 278) hydrogen bonds : angle 4.52966 ( 885) SS BOND : bond 0.00196 ( 5) SS BOND : angle 1.02779 ( 10) covalent geometry : bond 0.00220 (11559) covalent geometry : angle 0.52233 (15742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5364.72 seconds wall clock time: 93 minutes 52.06 seconds (5632.06 seconds total)