Starting phenix.real_space_refine on Wed Mar 4 02:24:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kc2_22805/03_2026/7kc2_22805.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kc2_22805/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7kc2_22805/03_2026/7kc2_22805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kc2_22805/03_2026/7kc2_22805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kc2_22805/03_2026/7kc2_22805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kc2_22805/03_2026/7kc2_22805.map" } 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-5986/lib/python3.9/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: 2.08, per 1000 atoms: 0.20 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: 0.82 Conformation dependent library (CDL) restraints added in 474.0 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: 1.60 Time building geometry restraints manager: 1.13 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 - 14.13: 5324 14.13 - 28.25: 560 28.25 - 42.38: 158 42.38 - 56.50: 40 56.50 - 70.63: 32 Dihedral angle restraints: 6114 sinusoidal: 2250 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 6111 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: 0.540 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.220 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 14.263 70.629 3684 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 covalent geometry : bond 0.00752 (10412) covalent geometry : angle 0.70364 (14224) SS BOND : bond 0.00346 ( 2) SS BOND : angle 0.31073 ( 4) hydrogen bonds : bond 0.19401 ( 404) hydrogen bonds : angle 8.94197 ( 1248) metal coordination : bond 0.01165 ( 28) metal coordination : angle 2.94230 ( 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 : 0.341 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.5352 time to fit residues: 53.4345 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 : 0.363 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.156250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.114969 restraints weight = 10492.284| |-----------------------------------------------------------------------------| 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: 0.3409 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1324 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= 0.114 Angle : 0.513 6.082 14252 Z= 0.260 Chirality : 0.043 0.138 1624 Planarity : 0.004 0.030 1820 Dihedral : 8.699 56.912 1696 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.40 % Allowed : 9.17 % Favored : 90.42 % 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: -1.77 (0.21), residues: 1380 helix: -0.31 (0.24), residues: 452 sheet: -2.31 (0.33), residues: 204 loop : -1.33 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 298 TYR 0.014 0.001 TYR A 329 PHE 0.011 0.002 PHE B 221 TRP 0.005 0.001 TRP C 172 HIS 0.003 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00249 (10412) covalent geometry : angle 0.49964 (14224) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.02882 ( 4) hydrogen bonds : bond 0.03158 ( 404) hydrogen bonds : angle 5.75616 ( 1248) metal coordination : bond 0.00235 ( 28) metal coordination : angle 2.83377 ( 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 106 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.376 Fit side-chains REVERT: A 83 LYS cc_start: 0.7243 (mtmm) cc_final: 0.7026 (mttm) REVERT: A 168 MET cc_start: 0.8295 (mtt) cc_final: 0.7923 (mtm) REVERT: B 83 LYS cc_start: 0.7245 (mtmm) cc_final: 0.7032 (mttm) REVERT: B 168 MET cc_start: 0.8299 (mtt) cc_final: 0.7935 (mtm) REVERT: C 83 LYS cc_start: 0.7216 (mtmm) cc_final: 0.7001 (mttm) REVERT: C 168 MET cc_start: 0.8235 (mtt) cc_final: 0.7860 (mtm) REVERT: D 83 LYS cc_start: 0.7210 (mtmm) cc_final: 0.6997 (mttm) outliers start: 4 outliers final: 0 residues processed: 106 average time/residue: 0.3638 time to fit residues: 42.8945 Evaluate side-chains 79 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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: 6.9990 chunk 63 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.149495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.107956 restraints weight = 10517.749| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.37 r_work: 0.3477 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 10442 Z= 0.274 Angle : 0.579 5.193 14252 Z= 0.295 Chirality : 0.046 0.133 1624 Planarity : 0.004 0.031 1820 Dihedral : 8.869 54.606 1696 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.81 % Allowed : 11.49 % Favored : 86.69 % 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: -1.78 (0.22), residues: 1380 helix: -0.26 (0.24), residues: 452 sheet: -2.26 (0.29), residues: 252 loop : -1.28 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 302 TYR 0.021 0.002 TYR A 258 PHE 0.011 0.002 PHE B 221 TRP 0.009 0.001 TRP B 92 HIS 0.006 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00639 (10412) covalent geometry : angle 0.56871 (14224) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.29956 ( 4) hydrogen bonds : bond 0.03908 ( 404) hydrogen bonds : angle 5.77419 ( 1248) metal coordination : bond 0.00876 ( 28) metal coordination : angle 2.67385 ( 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 : 0.368 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 108 average time/residue: 0.4290 time to fit residues: 51.0992 Evaluate side-chains 91 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 0.0370 chunk 5 optimal weight: 0.0060 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 61 optimal weight: 0.0070 chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN B 51 HIS B 262 ASN C 51 HIS 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 = 0.4170 r_free = 0.4170 target = 0.161625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.120507 restraints weight = 10459.712| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.45 r_work: 0.3578 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10442 Z= 0.086 Angle : 0.471 4.950 14252 Z= 0.239 Chirality : 0.042 0.131 1624 Planarity : 0.003 0.027 1820 Dihedral : 8.296 58.702 1696 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.81 % Allowed : 15.83 % Favored : 83.37 % 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: -1.26 (0.22), residues: 1380 helix: 0.34 (0.25), residues: 448 sheet: -2.17 (0.32), residues: 208 loop : -1.13 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 298 TYR 0.017 0.001 TYR A 329 PHE 0.011 0.002 PHE D 210 TRP 0.005 0.001 TRP A 50 HIS 0.002 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00193 (10412) covalent geometry : angle 0.46081 (14224) SS BOND : bond 0.00027 ( 2) SS BOND : angle 0.03550 ( 4) hydrogen bonds : bond 0.02631 ( 404) hydrogen bonds : angle 5.12129 ( 1248) metal coordination : bond 0.00098 ( 28) metal coordination : angle 2.45943 ( 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 105 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.372 Fit side-chains REVERT: A 83 LYS cc_start: 0.7169 (mtmm) cc_final: 0.6952 (mttm) REVERT: A 168 MET cc_start: 0.8293 (mtt) cc_final: 0.7972 (mtm) REVERT: B 83 LYS cc_start: 0.7180 (mtmm) cc_final: 0.6965 (mttm) REVERT: B 168 MET cc_start: 0.8290 (mtt) cc_final: 0.7971 (mtm) REVERT: C 83 LYS cc_start: 0.7144 (mtmm) cc_final: 0.6909 (mttm) REVERT: C 168 MET cc_start: 0.8284 (mtt) cc_final: 0.7970 (mtm) REVERT: D 83 LYS cc_start: 0.7145 (mtmm) cc_final: 0.6934 (mttm) REVERT: D 168 MET cc_start: 0.8162 (mtt) cc_final: 0.7826 (mtm) outliers start: 8 outliers final: 0 residues processed: 101 average time/residue: 0.4429 time to fit residues: 49.2728 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 : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 9 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 44 optimal weight: 0.0030 chunk 6 optimal weight: 7.9990 chunk 133 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.152287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.110777 restraints weight = 10564.070| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.40 r_work: 0.3341 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 10442 Z= 0.192 Angle : 0.516 4.648 14252 Z= 0.262 Chirality : 0.044 0.132 1624 Planarity : 0.003 0.026 1820 Dihedral : 8.624 56.263 1696 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.92 % Allowed : 17.54 % Favored : 80.54 % 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: -2.07 (0.29), residues: 256 loop : -1.10 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 302 TYR 0.017 0.001 TYR B 258 PHE 0.009 0.002 PHE D 210 TRP 0.005 0.001 TRP D 92 HIS 0.004 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00450 (10412) covalent geometry : angle 0.50819 (14224) SS BOND : bond 0.00005 ( 2) SS BOND : angle 0.25100 ( 4) hydrogen bonds : bond 0.03294 ( 404) hydrogen bonds : angle 5.29421 ( 1248) metal coordination : bond 0.00598 ( 28) metal coordination : angle 2.28221 ( 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 105 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.385 Fit side-chains REVERT: A 83 LYS cc_start: 0.6970 (mtmm) cc_final: 0.6748 (mttm) REVERT: A 168 MET cc_start: 0.8049 (mtt) cc_final: 0.7671 (mtm) REVERT: B 83 LYS cc_start: 0.7007 (mtmm) cc_final: 0.6794 (mttm) REVERT: B 168 MET cc_start: 0.8037 (mtt) cc_final: 0.7661 (mtm) REVERT: C 83 LYS cc_start: 0.7004 (mtmm) cc_final: 0.6793 (mttm) REVERT: C 168 MET cc_start: 0.8037 (mtt) cc_final: 0.7659 (mtm) REVERT: D 83 LYS cc_start: 0.6990 (mtmm) cc_final: 0.6774 (mttm) outliers start: 19 outliers final: 11 residues processed: 97 average time/residue: 0.4585 time to fit residues: 48.9078 Evaluate side-chains 93 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 313 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 58 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 80 optimal weight: 9.9990 chunk 27 optimal weight: 0.0970 chunk 3 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.153513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.111714 restraints weight = 10687.457| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.48 r_work: 0.3525 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10442 Z= 0.148 Angle : 0.496 4.705 14252 Z= 0.250 Chirality : 0.044 0.132 1624 Planarity : 0.003 0.025 1820 Dihedral : 8.535 57.502 1696 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.11 % Allowed : 20.46 % Favored : 78.43 % 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: -1.23 (0.22), residues: 1380 helix: 0.36 (0.25), residues: 448 sheet: -1.99 (0.30), residues: 256 loop : -1.07 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 302 TYR 0.020 0.001 TYR A 329 PHE 0.009 0.002 PHE C 221 TRP 0.005 0.001 TRP C 50 HIS 0.003 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00344 (10412) covalent geometry : angle 0.48746 (14224) SS BOND : bond 0.00001 ( 2) SS BOND : angle 0.21298 ( 4) hydrogen bonds : bond 0.02985 ( 404) hydrogen bonds : angle 5.18278 ( 1248) metal coordination : bond 0.00415 ( 28) metal coordination : angle 2.23753 ( 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 99 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.364 Fit side-chains REVERT: A 83 LYS cc_start: 0.7208 (mtmm) cc_final: 0.6983 (mttm) REVERT: A 168 MET cc_start: 0.8219 (mtt) cc_final: 0.7873 (mtm) REVERT: B 83 LYS cc_start: 0.7219 (mtmm) cc_final: 0.6997 (mttm) REVERT: B 168 MET cc_start: 0.8221 (mtt) cc_final: 0.7878 (mtm) REVERT: C 83 LYS cc_start: 0.7184 (mtmm) cc_final: 0.6962 (mttm) REVERT: C 168 MET cc_start: 0.8204 (mtt) cc_final: 0.7861 (mtm) REVERT: D 83 LYS cc_start: 0.7212 (mtmm) cc_final: 0.6991 (mttm) outliers start: 11 outliers final: 5 residues processed: 95 average time/residue: 0.4103 time to fit residues: 43.3488 Evaluate side-chains 84 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain C residue 325 LEU 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: 0.6980 chunk 127 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 90 optimal weight: 0.0270 chunk 81 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS 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 = 0.4092 r_free = 0.4092 target = 0.156666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.115001 restraints weight = 10421.066| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.48 r_work: 0.3557 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2112 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= 0.103 Angle : 0.473 4.891 14252 Z= 0.239 Chirality : 0.043 0.132 1624 Planarity : 0.003 0.023 1820 Dihedral : 8.295 58.880 1696 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.31 % Allowed : 21.67 % Favored : 77.02 % 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: -0.99 (0.22), residues: 1380 helix: 0.60 (0.25), residues: 448 sheet: -1.93 (0.30), residues: 260 loop : -0.91 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.023 0.001 TYR B 329 PHE 0.011 0.002 PHE D 210 TRP 0.004 0.001 TRP D 50 HIS 0.002 0.000 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00236 (10412) covalent geometry : angle 0.46515 (14224) SS BOND : bond 0.00018 ( 2) SS BOND : angle 0.13166 ( 4) hydrogen bonds : bond 0.02722 ( 404) hydrogen bonds : angle 5.00289 ( 1248) metal coordination : bond 0.00252 ( 28) metal coordination : angle 2.14141 ( 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 97 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.357 Fit side-chains REVERT: A 168 MET cc_start: 0.8325 (mtt) cc_final: 0.8006 (mtm) REVERT: B 168 MET cc_start: 0.8345 (mtt) cc_final: 0.8029 (mtm) REVERT: C 75 MET cc_start: 0.7914 (ttp) cc_final: 0.7663 (ttm) REVERT: C 168 MET cc_start: 0.8307 (mtt) cc_final: 0.7994 (mtm) REVERT: D 168 MET cc_start: 0.8216 (mtt) cc_final: 0.7907 (mtm) outliers start: 13 outliers final: 5 residues processed: 97 average time/residue: 0.4134 time to fit residues: 44.3522 Evaluate side-chains 75 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain C residue 325 LEU 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: 4.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.155614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113648 restraints weight = 10468.351| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.50 r_work: 0.3540 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2156 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= 0.130 Angle : 0.481 4.809 14252 Z= 0.244 Chirality : 0.043 0.132 1624 Planarity : 0.003 0.024 1820 Dihedral : 8.352 58.461 1696 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.92 % Allowed : 22.78 % Favored : 75.30 % 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: -0.97 (0.22), residues: 1380 helix: 0.57 (0.24), residues: 448 sheet: -1.83 (0.31), residues: 256 loop : -0.90 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.015 0.001 TYR D 258 PHE 0.010 0.002 PHE B 210 TRP 0.005 0.001 TRP D 82 HIS 0.003 0.000 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00303 (10412) covalent geometry : angle 0.47417 (14224) SS BOND : bond 0.00002 ( 2) SS BOND : angle 0.16354 ( 4) hydrogen bonds : bond 0.02870 ( 404) hydrogen bonds : angle 5.05267 ( 1248) metal coordination : bond 0.00367 ( 28) metal coordination : angle 2.07659 ( 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 99 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.391 Fit side-chains REVERT: A 75 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7555 (ttt) REVERT: A 168 MET cc_start: 0.8293 (mtt) cc_final: 0.7961 (mtm) REVERT: B 75 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7568 (ttt) REVERT: B 168 MET cc_start: 0.8283 (mtt) cc_final: 0.7958 (mtm) REVERT: C 168 MET cc_start: 0.8274 (mtt) cc_final: 0.7950 (mtm) REVERT: D 75 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7562 (ttt) REVERT: D 168 MET cc_start: 0.8241 (mtt) cc_final: 0.7933 (mtm) outliers start: 19 outliers final: 12 residues processed: 96 average time/residue: 0.3716 time to fit residues: 39.9762 Evaluate side-chains 89 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 83 LYS 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: 3.9990 chunk 98 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 130 optimal weight: 0.0870 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 36 ASN C 78 ASN D 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.150774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108800 restraints weight = 10563.177| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.45 r_work: 0.3488 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 10442 Z= 0.237 Angle : 0.543 4.704 14252 Z= 0.277 Chirality : 0.046 0.137 1624 Planarity : 0.003 0.025 1820 Dihedral : 8.790 56.201 1696 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.92 % Allowed : 22.98 % Favored : 75.10 % 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: -1.19 (0.22), residues: 1380 helix: 0.32 (0.24), residues: 448 sheet: -1.98 (0.31), residues: 256 loop : -0.97 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 302 TYR 0.026 0.002 TYR D 329 PHE 0.010 0.002 PHE C 11 TRP 0.008 0.001 TRP D 92 HIS 0.004 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00557 (10412) covalent geometry : angle 0.53481 (14224) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.35569 ( 4) hydrogen bonds : bond 0.03435 ( 404) hydrogen bonds : angle 5.34054 ( 1248) metal coordination : bond 0.00711 ( 28) metal coordination : angle 2.39815 ( 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 104 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.374 Fit side-chains REVERT: A 75 MET cc_start: 0.8108 (ttm) cc_final: 0.7845 (ttt) REVERT: A 168 MET cc_start: 0.8242 (mtt) cc_final: 0.7892 (mtm) REVERT: B 168 MET cc_start: 0.8237 (mtt) cc_final: 0.7892 (mtm) REVERT: C 168 MET cc_start: 0.8236 (mtt) cc_final: 0.7886 (mtm) REVERT: D 75 MET cc_start: 0.8062 (ttm) cc_final: 0.7801 (ttt) outliers start: 19 outliers final: 14 residues processed: 99 average time/residue: 0.3756 time to fit residues: 41.6151 Evaluate side-chains 85 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 83 LYS 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: 2.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.153202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.111371 restraints weight = 10408.501| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.45 r_work: 0.3350 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2077 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= 0.159 Angle : 0.509 4.891 14252 Z= 0.259 Chirality : 0.044 0.138 1624 Planarity : 0.003 0.026 1820 Dihedral : 8.587 57.946 1696 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.21 % Allowed : 23.79 % Favored : 75.00 % 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: -1.16 (0.22), residues: 1380 helix: 0.41 (0.24), residues: 448 sheet: -2.07 (0.30), residues: 260 loop : -0.94 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 302 TYR 0.016 0.001 TYR C 258 PHE 0.009 0.002 PHE A 221 TRP 0.007 0.001 TRP D 54 HIS 0.003 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00373 (10412) covalent geometry : angle 0.50108 (14224) SS BOND : bond 0.00006 ( 2) SS BOND : angle 0.26184 ( 4) hydrogen bonds : bond 0.03080 ( 404) hydrogen bonds : angle 5.21962 ( 1248) metal coordination : bond 0.00454 ( 28) metal coordination : angle 2.30177 ( 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 98 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.343 Fit side-chains REVERT: A 168 MET cc_start: 0.8057 (mtt) cc_final: 0.7693 (mtm) REVERT: B 168 MET cc_start: 0.8048 (mtt) cc_final: 0.7686 (mtm) REVERT: C 168 MET cc_start: 0.8039 (mtt) cc_final: 0.7678 (mtm) outliers start: 12 outliers final: 11 residues processed: 97 average time/residue: 0.3689 time to fit residues: 40.3058 Evaluate side-chains 86 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 72 VAL 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 83 LYS 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: 0.8980 chunk 134 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.155058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.112946 restraints weight = 10524.364| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.50 r_work: 0.3365 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2151 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= 0.137 Angle : 0.495 5.035 14252 Z= 0.252 Chirality : 0.044 0.136 1624 Planarity : 0.003 0.025 1820 Dihedral : 8.448 58.569 1696 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.21 % Allowed : 24.40 % Favored : 74.40 % 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: -0.92 (0.22), residues: 1380 helix: 0.80 (0.25), residues: 424 sheet: -2.01 (0.30), residues: 260 loop : -0.86 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.033 0.001 TYR A 329 PHE 0.010 0.002 PHE D 210 TRP 0.007 0.001 TRP D 54 HIS 0.003 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00320 (10412) covalent geometry : angle 0.48766 (14224) SS BOND : bond 0.00014 ( 2) SS BOND : angle 0.22781 ( 4) hydrogen bonds : bond 0.02960 ( 404) hydrogen bonds : angle 5.12699 ( 1248) metal coordination : bond 0.00369 ( 28) metal coordination : angle 2.14239 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3311.28 seconds wall clock time: 57 minutes 13.31 seconds (3433.31 seconds total)