Starting phenix.real_space_refine on Thu Jul 2 20:30:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kc2_22805/07_2026/7kc2_22805.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kc2_22805/07_2026/7kc2_22805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kc2_22805/07_2026/7kc2_22805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kc2_22805/07_2026/7kc2_22805.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kc2_22805/07_2026/7kc2_22805.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kc2_22805/07_2026/7kc2_22805.cif" model { file = "/net/cci-nas-00/data/ceres_data/7kc2_22805/07_2026/7kc2_22805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kc2_22805/07_2026/7kc2_22805.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 8 5.49 5 S 56 5.16 5 C 6428 2.51 5 N 1732 2.21 5 O 1960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10192 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2501 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 715 SG CYS A 97 28.453 49.930 34.890 1.00 44.12 S ATOM 734 SG CYS A 100 32.114 50.441 34.141 1.00 36.60 S ATOM 761 SG CYS A 103 31.274 49.062 37.415 1.00 37.10 S ATOM 819 SG CYS A 111 30.350 52.684 36.643 1.00 41.20 S ATOM 316 SG CYS A 43 35.889 60.403 55.039 1.00 46.99 S ATOM 1126 SG CYS A 153 34.886 57.151 53.195 1.00 35.09 S Restraints were copied for chains: B, C, D Time building chain proxies: 2.22, per 1000 atoms: 0.22 Number of scatterers: 10192 At special positions: 0 Unit cell: (106.05, 85.05, 80.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 56 16.00 P 8 15.00 O 1960 8.00 N 1732 7.00 C 6428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS D 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS C 277 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 406.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 111 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 100 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 103 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 97 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 153 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 402 " - pdb=" NE2 HIS A 66 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 111 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 100 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 97 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 103 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 153 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 402 " - pdb=" NE2 HIS B 66 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 111 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 100 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 103 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 153 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 402 " - pdb=" NE2 HIS C 66 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 111 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 100 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 97 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 103 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 153 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 402 " - pdb=" NE2 HIS D 66 " Number of angles added : 24 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 22 sheets defined 34.6% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.625A pdb=" N LEU A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.657A pdb=" N LEU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.520A pdb=" N CYS A 111 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 150 through 165 removed outlier: 5.008A pdb=" N ILE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 157 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 193 removed outlier: 4.000A pdb=" N LEU A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 214 removed outlier: 3.767A pdb=" N LEU A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.688A pdb=" N THR A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'B' and resid 43 through 52 removed outlier: 3.625A pdb=" N LEU B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.657A pdb=" N LEU B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.522A pdb=" N CYS B 111 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 150 through 165 removed outlier: 5.008A pdb=" N ILE B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 157 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 4.000A pdb=" N LEU B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.767A pdb=" N LEU B 209 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.688A pdb=" N THR B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.625A pdb=" N LEU C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.657A pdb=" N LEU C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.520A pdb=" N CYS C 111 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 150 through 165 removed outlier: 5.008A pdb=" N ILE C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C 157 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 193 removed outlier: 4.001A pdb=" N LEU C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 removed outlier: 3.767A pdb=" N LEU C 209 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 248 through 256 removed outlier: 3.688A pdb=" N THR C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'C' and resid 297 through 310 Processing helix chain 'C' and resid 324 through 334 Processing helix chain 'D' and resid 43 through 52 removed outlier: 3.623A pdb=" N LEU D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 removed outlier: 3.657A pdb=" N LEU D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.521A pdb=" N CYS D 111 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 150 through 165 removed outlier: 5.008A pdb=" N ILE D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR D 157 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 193 removed outlier: 4.000A pdb=" N LEU D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.767A pdb=" N LEU D 209 " --> pdb=" O GLY D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 236 Processing helix chain 'D' and resid 248 through 256 removed outlier: 3.687A pdb=" N THR D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 324 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.655A pdb=" N GLU A 67 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER A 40 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA A 69 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 34 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.655A pdb=" N GLU A 67 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER A 40 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA A 69 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 34 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR A 341 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 95 removed outlier: 6.503A pdb=" N ASP A 115 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 220 removed outlier: 6.063A pdb=" N VAL A 173 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE A 200 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 175 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A 242 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 279 removed outlier: 3.797A pdb=" N SER D 278 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 278 " --> pdb=" O CYS D 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.656A pdb=" N GLU B 67 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER B 40 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 69 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 34 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.656A pdb=" N GLU B 67 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER B 40 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 69 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 34 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR B 341 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.503A pdb=" N ASP B 115 " --> pdb=" O ASN B 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 217 through 220 removed outlier: 6.064A pdb=" N VAL B 173 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE B 200 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE B 175 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL B 242 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 275 through 279 removed outlier: 3.788A pdb=" N SER C 278 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 278 " --> pdb=" O CYS C 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 24 Processing sheet with id=AB5, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.655A pdb=" N GLU C 67 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER C 40 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 69 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 34 " --> pdb=" O VAL C 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.655A pdb=" N GLU C 67 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER C 40 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 69 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 34 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR C 341 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.503A pdb=" N ASP C 115 " --> pdb=" O ASN C 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 217 through 220 removed outlier: 6.064A pdb=" N VAL C 173 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE C 200 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 175 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL C 242 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AC1, first strand: chain 'D' and resid 87 through 90 removed outlier: 6.656A pdb=" N GLU D 67 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER D 40 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA D 69 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU D 34 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 87 through 90 removed outlier: 6.656A pdb=" N GLU D 67 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER D 40 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA D 69 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU D 34 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR D 341 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 93 through 95 removed outlier: 6.503A pdb=" N ASP D 115 " --> pdb=" O ASN D 94 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 217 through 220 removed outlier: 6.064A pdb=" N VAL D 173 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE D 200 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 175 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL D 242 " --> pdb=" O VAL D 266 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1248 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: 1.55 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3344 1.34 - 1.46: 1983 1.46 - 1.57: 4989 1.57 - 1.69: 16 1.69 - 1.81: 80 Bond restraints: 10412 Sorted by residual: bond pdb=" O3 NAD D 403 " pdb=" PA NAD D 403 " ideal model delta sigma weight residual 1.653 1.599 0.054 2.00e-02 2.50e+03 7.24e+00 bond pdb=" O3 NAD C 403 " pdb=" PA NAD C 403 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" O3 NAD A 403 " pdb=" PA NAD A 403 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 7.00e+00 bond pdb=" O3 NAD B 403 " pdb=" PA NAD B 403 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" C5B NAD B 403 " pdb=" O5B NAD B 403 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 3.98e+00 ... (remaining 10407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 13494 1.34 - 2.68: 574 2.68 - 4.02: 108 4.02 - 5.36: 36 5.36 - 6.70: 12 Bond angle restraints: 14224 Sorted by residual: angle pdb=" CA TYR C 258 " pdb=" CB TYR C 258 " pdb=" CG TYR C 258 " ideal model delta sigma weight residual 113.90 117.84 -3.94 1.80e+00 3.09e-01 4.80e+00 angle pdb=" CA TYR D 258 " pdb=" CB TYR D 258 " pdb=" CG TYR D 258 " ideal model delta sigma weight residual 113.90 117.84 -3.94 1.80e+00 3.09e-01 4.80e+00 angle pdb=" CA TYR A 258 " pdb=" CB TYR A 258 " pdb=" CG TYR A 258 " ideal model delta sigma weight residual 113.90 117.84 -3.94 1.80e+00 3.09e-01 4.80e+00 angle pdb=" CA TYR B 258 " pdb=" CB TYR B 258 " pdb=" CG TYR B 258 " ideal model delta sigma weight residual 113.90 117.84 -3.94 1.80e+00 3.09e-01 4.79e+00 angle pdb=" C2D NAD C 403 " pdb=" C1D NAD C 403 " pdb=" O4D NAD C 403 " ideal model delta sigma weight residual 105.82 99.83 5.99 3.00e+00 1.11e-01 3.99e+00 ... (remaining 14219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.45: 5177 13.45 - 26.90: 479 26.90 - 40.35: 194 40.35 - 53.80: 32 53.80 - 67.25: 32 Dihedral angle restraints: 5914 sinusoidal: 2050 harmonic: 3864 Sorted by residual: dihedral pdb=" CB CYS B 277 " pdb=" SG CYS B 277 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual 93.00 123.35 -30.35 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " pdb=" SG CYS D 277 " pdb=" CB CYS D 277 " ideal model delta sinusoidal sigma weight residual 93.00 123.30 -30.30 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CA VAL C 197 " pdb=" C VAL C 197 " pdb=" N LEU C 198 " pdb=" CA LEU C 198 " ideal model delta harmonic sigma weight residual 180.00 162.77 17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 5911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 990 0.039 - 0.078: 458 0.078 - 0.116: 147 0.116 - 0.155: 21 0.155 - 0.194: 8 Chirality restraints: 1624 Sorted by residual: chirality pdb=" C1D NAD B 403 " pdb=" C2D NAD B 403 " pdb=" N1N NAD B 403 " pdb=" O4D NAD B 403 " both_signs ideal model delta sigma weight residual False 2.41 2.61 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" C1D NAD C 403 " pdb=" C2D NAD C 403 " pdb=" N1N NAD C 403 " pdb=" O4D NAD C 403 " both_signs ideal model delta sigma weight residual False 2.41 2.61 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" C1D NAD D 403 " pdb=" C2D NAD D 403 " pdb=" N1N NAD D 403 " pdb=" O4D NAD D 403 " both_signs ideal model delta sigma weight residual False 2.41 2.61 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 1621 not shown) Planarity restraints: 1820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD C 403 " 0.066 2.00e-02 2.50e+03 4.42e-02 3.91e+01 pdb=" C2N NAD C 403 " -0.089 2.00e-02 2.50e+03 pdb=" C3N NAD C 403 " -0.012 2.00e-02 2.50e+03 pdb=" C4N NAD C 403 " 0.020 2.00e-02 2.50e+03 pdb=" C5N NAD C 403 " 0.013 2.00e-02 2.50e+03 pdb=" C6N NAD C 403 " -0.021 2.00e-02 2.50e+03 pdb=" C7N NAD C 403 " 0.042 2.00e-02 2.50e+03 pdb=" N1N NAD C 403 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 403 " -0.066 2.00e-02 2.50e+03 4.42e-02 3.91e+01 pdb=" C2N NAD A 403 " 0.089 2.00e-02 2.50e+03 pdb=" C3N NAD A 403 " 0.011 2.00e-02 2.50e+03 pdb=" C4N NAD A 403 " -0.020 2.00e-02 2.50e+03 pdb=" C5N NAD A 403 " -0.013 2.00e-02 2.50e+03 pdb=" C6N NAD A 403 " 0.022 2.00e-02 2.50e+03 pdb=" C7N NAD A 403 " -0.042 2.00e-02 2.50e+03 pdb=" N1N NAD A 403 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 403 " 0.066 2.00e-02 2.50e+03 4.41e-02 3.90e+01 pdb=" C2N NAD D 403 " -0.089 2.00e-02 2.50e+03 pdb=" C3N NAD D 403 " -0.011 2.00e-02 2.50e+03 pdb=" C4N NAD D 403 " 0.020 2.00e-02 2.50e+03 pdb=" C5N NAD D 403 " 0.013 2.00e-02 2.50e+03 pdb=" C6N NAD D 403 " -0.021 2.00e-02 2.50e+03 pdb=" C7N NAD D 403 " 0.042 2.00e-02 2.50e+03 pdb=" N1N NAD D 403 " -0.020 2.00e-02 2.50e+03 ... (remaining 1817 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1637 2.75 - 3.29: 9992 3.29 - 3.83: 17537 3.83 - 4.36: 21905 4.36 - 4.90: 37870 Nonbonded interactions: 88941 Sorted by model distance: nonbonded pdb=" OD2 ASP B 201 " pdb=" O3B NAD B 403 " model vdw 2.216 3.040 nonbonded pdb=" OD2 ASP C 201 " pdb=" O3B NAD C 403 " model vdw 2.216 3.040 nonbonded pdb=" OD2 ASP A 201 " pdb=" O3B NAD A 403 " model vdw 2.216 3.040 nonbonded pdb=" OD2 ASP D 201 " pdb=" O3B NAD D 403 " model vdw 2.216 3.040 nonbonded pdb=" O VAL C 231 " pdb=" OG1 THR C 235 " model vdw 2.221 3.040 ... (remaining 88936 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 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: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.670 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.008 0.054 10442 Z= 0.334 Angle : 0.713 6.704 14252 Z= 0.365 Chirality : 0.049 0.194 1624 Planarity : 0.005 0.044 1820 Dihedral : 13.473 67.251 3484 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.21), residues: 1380 helix: -1.61 (0.22), residues: 464 sheet: -2.56 (0.35), residues: 220 loop : -1.60 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 260 TYR 0.027 0.002 TYR D 294 PHE 0.014 0.001 PHE C 221 TRP 0.010 0.002 TRP A 92 HIS 0.006 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.33 (10412) covalent geometry : angle 0.70364 / 0.36 (14224) SS BOND : bond 0.00346 / 0.17 ( 2) SS BOND : angle 0.31073 / 0.16 ( 4) hydrogen bonds : bond 0.19401 / 13.95 ( 404) hydrogen bonds : angle 8.94197 / 6.09 ( 1248) metal coordination : bond 0.01165 / 0.76 ( 28) metal coordination : angle 2.94230 / 1.85 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.377 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.5189 time to fit residues: 52.0826 Evaluate side-chains 73 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 HIS B 51 HIS C 51 HIS D 51 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.156237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.115043 restraints weight = 10505.793| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.43 r_work: 0.3550 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10442 Z= 0.113 Angle : 0.513 6.079 14252 Z= 0.260 Chirality : 0.043 0.139 1624 Planarity : 0.004 0.030 1820 Dihedral : 5.668 53.535 1496 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.40 % Allowed : 9.07 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.21), residues: 1380 helix: -0.32 (0.24), residues: 452 sheet: -2.34 (0.33), residues: 204 loop : -1.34 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 302 TYR 0.014 0.001 TYR A 329 PHE 0.012 0.002 PHE B 221 TRP 0.005 0.001 TRP C 172 HIS 0.002 0.000 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10412) covalent geometry : angle 0.50061 / 0.26 (14224) SS BOND : bond 0.00047 / 0.02 ( 2) SS BOND : angle 0.02646 / 0.01 ( 4) hydrogen bonds : bond 0.03106 / 2.22 ( 404) hydrogen bonds : angle 5.72566 / 3.93 ( 1248) metal coordination : bond 0.00230 / 0.15 ( 28) metal coordination : angle 2.81902 / 1.64 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.343 Fit side-chains REVERT: A 83 LYS cc_start: 0.7270 (mtmm) cc_final: 0.7051 (mttm) REVERT: A 168 MET cc_start: 0.8319 (mtt) cc_final: 0.7951 (mtm) REVERT: B 83 LYS cc_start: 0.7276 (mtmm) cc_final: 0.7062 (mttm) REVERT: B 168 MET cc_start: 0.8319 (mtt) cc_final: 0.7958 (mtm) REVERT: C 83 LYS cc_start: 0.7239 (mtmm) cc_final: 0.7022 (mttm) REVERT: C 168 MET cc_start: 0.8259 (mtt) cc_final: 0.7888 (mtm) REVERT: D 83 LYS cc_start: 0.7236 (mtmm) cc_final: 0.7020 (mttm) outliers start: 4 outliers final: 0 residues processed: 108 average time/residue: 0.3469 time to fit residues: 42.0162 Evaluate side-chains 80 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS D 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.147869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106502 restraints weight = 10560.728| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.35 r_work: 0.3458 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 10442 Z= 0.335 Angle : 0.623 5.513 14252 Z= 0.315 Chirality : 0.048 0.134 1624 Planarity : 0.004 0.034 1820 Dihedral : 5.882 52.072 1496 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.81 % Allowed : 12.50 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.21), residues: 1380 helix: -0.41 (0.24), residues: 452 sheet: -2.29 (0.30), residues: 260 loop : -1.32 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 302 TYR 0.022 0.002 TYR A 258 PHE 0.011 0.002 PHE C 221 TRP 0.012 0.002 TRP C 92 HIS 0.006 0.001 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.33 (10412) covalent geometry : angle 0.61231 / 0.31 (14224) SS BOND : bond 0.00014 / 0.01 ( 2) SS BOND : angle 0.43235 / 0.22 ( 4) hydrogen bonds : bond 0.04158 / 2.99 ( 404) hydrogen bonds : angle 5.92226 / 4.09 ( 1248) metal coordination : bond 0.01074 / 0.70 ( 28) metal coordination : angle 2.87811 / 1.79 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.276 Fit side-chains REVERT: A 303 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7642 (mt-10) REVERT: B 303 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7624 (mt-10) REVERT: D 303 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7628 (mt-10) outliers start: 18 outliers final: 8 residues processed: 108 average time/residue: 0.4510 time to fit residues: 53.4656 Evaluate side-chains 89 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 HIS A 262 ASN B 262 ASN C 51 HIS C 262 ASN D 51 HIS D 262 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108128 restraints weight = 10574.930| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.56 r_work: 0.3363 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10442 Z= 0.118 Angle : 0.489 4.722 14252 Z= 0.247 Chirality : 0.043 0.131 1624 Planarity : 0.003 0.029 1820 Dihedral : 5.477 54.468 1496 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.21 % Allowed : 15.02 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.22), residues: 1380 helix: 0.17 (0.25), residues: 448 sheet: -2.11 (0.29), residues: 256 loop : -1.13 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 298 TYR 0.016 0.001 TYR A 329 PHE 0.011 0.002 PHE B 221 TRP 0.006 0.001 TRP C 50 HIS 0.003 0.000 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10412) covalent geometry : angle 0.47815 / 0.25 (14224) SS BOND : bond 0.00013 / 0.01 ( 2) SS BOND : angle 0.14321 / 0.07 ( 4) hydrogen bonds : bond 0.02905 / 2.07 ( 404) hydrogen bonds : angle 5.28680 / 3.66 ( 1248) metal coordination : bond 0.00250 / 0.16 ( 28) metal coordination : angle 2.52570 / 1.50 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.344 Fit side-chains REVERT: A 168 MET cc_start: 0.8012 (mtt) cc_final: 0.7619 (mtm) REVERT: B 168 MET cc_start: 0.8009 (mtt) cc_final: 0.7614 (mtm) REVERT: C 168 MET cc_start: 0.7989 (mtt) cc_final: 0.7599 (mtm) REVERT: D 168 MET cc_start: 0.7870 (mtt) cc_final: 0.7497 (mtm) outliers start: 12 outliers final: 8 residues processed: 93 average time/residue: 0.3674 time to fit residues: 37.9865 Evaluate side-chains 82 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.152941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.111284 restraints weight = 10506.192| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.46 r_work: 0.3353 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 10442 Z= 0.155 Angle : 0.500 4.665 14252 Z= 0.252 Chirality : 0.044 0.131 1624 Planarity : 0.003 0.027 1820 Dihedral : 5.454 54.016 1496 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.81 % Allowed : 16.53 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.22), residues: 1380 helix: 0.27 (0.25), residues: 448 sheet: -2.04 (0.29), residues: 256 loop : -1.12 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 302 TYR 0.016 0.001 TYR A 329 PHE 0.010 0.002 PHE C 221 TRP 0.004 0.001 TRP C 50 HIS 0.003 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (10412) covalent geometry : angle 0.49167 / 0.25 (14224) SS BOND : bond 0.00003 / 0.00 ( 2) SS BOND : angle 0.21330 / 0.11 ( 4) hydrogen bonds : bond 0.03114 / 2.22 ( 404) hydrogen bonds : angle 5.23618 / 3.62 ( 1248) metal coordination : bond 0.00464 / 0.30 ( 28) metal coordination : angle 2.21593 / 1.33 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.365 Fit side-chains REVERT: A 168 MET cc_start: 0.8054 (mtt) cc_final: 0.7672 (mtm) REVERT: B 168 MET cc_start: 0.8044 (mtt) cc_final: 0.7655 (mtm) REVERT: C 168 MET cc_start: 0.8042 (mtt) cc_final: 0.7663 (mtm) outliers start: 8 outliers final: 8 residues processed: 81 average time/residue: 0.4067 time to fit residues: 36.4406 Evaluate side-chains 78 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 80 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.149720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108092 restraints weight = 10712.953| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.40 r_work: 0.3307 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 10442 Z= 0.259 Angle : 0.560 5.065 14252 Z= 0.284 Chirality : 0.046 0.132 1624 Planarity : 0.003 0.028 1820 Dihedral : 5.650 52.535 1496 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.52 % Allowed : 18.95 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.22), residues: 1380 helix: 0.06 (0.24), residues: 448 sheet: -2.04 (0.30), residues: 260 loop : -1.18 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 302 TYR 0.020 0.002 TYR A 258 PHE 0.010 0.002 PHE B 221 TRP 0.008 0.001 TRP B 92 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.26 (10412) covalent geometry : angle 0.55103 / 0.28 (14224) SS BOND : bond 0.00027 / 0.01 ( 2) SS BOND : angle 0.40279 / 0.20 ( 4) hydrogen bonds : bond 0.03605 / 2.59 ( 404) hydrogen bonds : angle 5.48830 / 3.80 ( 1248) metal coordination : bond 0.00804 / 0.52 ( 28) metal coordination : angle 2.47955 / 1.53 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.485 Fit side-chains outliers start: 25 outliers final: 20 residues processed: 107 average time/residue: 0.3956 time to fit residues: 47.4802 Evaluate side-chains 94 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 99 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.152198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.110568 restraints weight = 10483.417| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.45 r_work: 0.3339 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10442 Z= 0.171 Angle : 0.514 4.731 14252 Z= 0.260 Chirality : 0.044 0.131 1624 Planarity : 0.003 0.027 1820 Dihedral : 5.525 53.314 1496 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.32 % Allowed : 19.46 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.22), residues: 1380 helix: 0.20 (0.24), residues: 448 sheet: -2.05 (0.30), residues: 256 loop : -1.13 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 302 TYR 0.024 0.001 TYR A 329 PHE 0.011 0.002 PHE A 221 TRP 0.008 0.001 TRP B 50 HIS 0.004 0.001 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (10412) covalent geometry : angle 0.50570 / 0.26 (14224) SS BOND : bond 0.00011 / 0.01 ( 2) SS BOND : angle 0.27614 / 0.14 ( 4) hydrogen bonds : bond 0.03178 / 2.27 ( 404) hydrogen bonds : angle 5.30209 / 3.68 ( 1248) metal coordination : bond 0.00482 / 0.32 ( 28) metal coordination : angle 2.32956 / 1.39 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.382 Fit side-chains REVERT: A 168 MET cc_start: 0.8057 (mtt) cc_final: 0.7684 (mtm) REVERT: B 168 MET cc_start: 0.8048 (mtt) cc_final: 0.7673 (mtm) REVERT: C 168 MET cc_start: 0.8030 (mtt) cc_final: 0.7661 (mtm) outliers start: 23 outliers final: 15 residues processed: 100 average time/residue: 0.3733 time to fit residues: 42.0043 Evaluate side-chains 86 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 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 = 0.4052 r_free = 0.4052 target = 0.152818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.111112 restraints weight = 10520.408| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.47 r_work: 0.3341 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10442 Z= 0.158 Angle : 0.513 4.711 14252 Z= 0.259 Chirality : 0.044 0.138 1624 Planarity : 0.003 0.027 1820 Dihedral : 5.492 53.575 1496 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.61 % Allowed : 21.67 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.22), residues: 1380 helix: 0.30 (0.24), residues: 448 sheet: -2.01 (0.30), residues: 256 loop : -1.08 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 302 TYR 0.016 0.001 TYR A 258 PHE 0.010 0.002 PHE B 221 TRP 0.007 0.001 TRP C 50 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (10412) covalent geometry : angle 0.50516 / 0.26 (14224) SS BOND : bond 0.00003 / 0.00 ( 2) SS BOND : angle 0.23870 / 0.12 ( 4) hydrogen bonds : bond 0.03118 / 2.23 ( 404) hydrogen bonds : angle 5.25211 / 3.64 ( 1248) metal coordination : bond 0.00440 / 0.29 ( 28) metal coordination : angle 2.24177 / 1.34 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.392 Fit side-chains REVERT: A 83 LYS cc_start: 0.6873 (mtmm) cc_final: 0.6632 (mttm) REVERT: A 168 MET cc_start: 0.8057 (mtt) cc_final: 0.7693 (mtm) REVERT: B 168 MET cc_start: 0.8059 (mtt) cc_final: 0.7693 (mtm) REVERT: C 168 MET cc_start: 0.8034 (mtt) cc_final: 0.7667 (mtm) outliers start: 16 outliers final: 15 residues processed: 92 average time/residue: 0.4672 time to fit residues: 47.5630 Evaluate side-chains 80 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 86 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 123 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 HIS ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS C 121 HIS D 121 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.156999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.115189 restraints weight = 10451.315| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.50 r_work: 0.3396 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10442 Z= 0.102 Angle : 0.480 5.211 14252 Z= 0.243 Chirality : 0.043 0.136 1624 Planarity : 0.003 0.026 1820 Dihedral : 5.346 54.137 1496 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.11 % Allowed : 23.29 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.22), residues: 1380 helix: 0.61 (0.25), residues: 448 sheet: -1.95 (0.30), residues: 256 loop : -0.98 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 260 TYR 0.013 0.001 TYR A 258 PHE 0.011 0.002 PHE B 210 TRP 0.008 0.001 TRP A 82 HIS 0.002 0.000 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (10412) covalent geometry : angle 0.47245 / 0.24 (14224) SS BOND : bond 0.00032 / 0.02 ( 2) SS BOND : angle 0.11731 / 0.06 ( 4) hydrogen bonds : bond 0.02763 / 1.96 ( 404) hydrogen bonds : angle 5.03131 / 3.48 ( 1248) metal coordination : bond 0.00228 / 0.15 ( 28) metal coordination : angle 2.10140 / 1.23 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.380 Fit side-chains REVERT: A 168 MET cc_start: 0.8137 (mtt) cc_final: 0.7826 (mtm) REVERT: B 75 MET cc_start: 0.7726 (ttp) cc_final: 0.7469 (ttt) REVERT: B 168 MET cc_start: 0.8085 (mtt) cc_final: 0.7735 (mtm) REVERT: C 168 MET cc_start: 0.8106 (mtt) cc_final: 0.7806 (mtm) REVERT: D 168 MET cc_start: 0.7990 (mtt) cc_final: 0.7647 (mtm) outliers start: 11 outliers final: 8 residues processed: 106 average time/residue: 0.3846 time to fit residues: 45.7098 Evaluate side-chains 74 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 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 = 0.4081 r_free = 0.4081 target = 0.156074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.113987 restraints weight = 10415.627| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.51 r_work: 0.3375 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10442 Z= 0.123 Angle : 0.487 5.194 14252 Z= 0.246 Chirality : 0.044 0.140 1624 Planarity : 0.003 0.027 1820 Dihedral : 5.332 53.824 1496 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.81 % Allowed : 23.99 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.22), residues: 1380 helix: 0.57 (0.25), residues: 448 sheet: -1.87 (0.32), residues: 248 loop : -0.88 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.029 0.001 TYR A 329 PHE 0.010 0.002 PHE A 210 TRP 0.006 0.001 TRP B 50 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (10412) covalent geometry : angle 0.48052 / 0.25 (14224) SS BOND : bond 0.00010 / 0.00 ( 2) SS BOND : angle 0.15621 / 0.08 ( 4) hydrogen bonds : bond 0.02914 / 2.07 ( 404) hydrogen bonds : angle 5.05585 / 3.50 ( 1248) metal coordination : bond 0.00328 / 0.22 ( 28) metal coordination : angle 2.06722 / 1.23 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.386 Fit side-chains REVERT: A 168 MET cc_start: 0.8055 (mtt) cc_final: 0.7689 (mtm) REVERT: B 168 MET cc_start: 0.8045 (mtt) cc_final: 0.7689 (mtm) REVERT: C 168 MET cc_start: 0.8018 (mtt) cc_final: 0.7659 (mtm) REVERT: D 168 MET cc_start: 0.7998 (mtt) cc_final: 0.7655 (mtm) REVERT: D 236 ASP cc_start: 0.7877 (t0) cc_final: 0.7597 (t0) outliers start: 8 outliers final: 8 residues processed: 83 average time/residue: 0.3698 time to fit residues: 34.7461 Evaluate side-chains 76 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 93 optimal weight: 0.0470 chunk 134 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 82 optimal weight: 0.0000 overall best weight: 1.1886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 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 = 0.4079 r_free = 0.4079 target = 0.155693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113590 restraints weight = 10547.427| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.51 r_work: 0.3376 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10442 Z= 0.131 Angle : 0.490 5.303 14252 Z= 0.248 Chirality : 0.044 0.137 1624 Planarity : 0.003 0.027 1820 Dihedral : 5.337 53.516 1496 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.81 % Allowed : 24.40 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.22), residues: 1380 helix: 0.89 (0.25), residues: 424 sheet: -1.87 (0.31), residues: 248 loop : -0.84 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.014 0.001 TYR C 258 PHE 0.010 0.002 PHE D 210 TRP 0.007 0.001 TRP B 50 HIS 0.003 0.001 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (10412) covalent geometry : angle 0.48242 / 0.25 (14224) SS BOND : bond 0.00007 / 0.00 ( 2) SS BOND : angle 0.15739 / 0.08 ( 4) hydrogen bonds : bond 0.02949 / 2.09 ( 404) hydrogen bonds : angle 5.07021 / 3.51 ( 1248) metal coordination : bond 0.00358 / 0.24 ( 28) metal coordination : angle 2.09662 / 1.24 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3341.09 seconds wall clock time: 57 minutes 52.80 seconds (3472.80 seconds total)