Starting phenix.real_space_refine on Mon Jul 28 07:34:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kc2_22805/07_2025/7kc2_22805.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kc2_22805/07_2025/7kc2_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_2025/7kc2_22805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kc2_22805/07_2025/7kc2_22805.map" model { file = "/net/cci-nas-00/data/ceres_data/7kc2_22805/07_2025/7kc2_22805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kc2_22805/07_2025/7kc2_22805.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 8} 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: C, B, D Time building chain proxies: 5.40, per 1000 atoms: 0.53 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 C 277 " - pdb=" SG CYS B 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: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.32 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: 4.87 Time building geometry restraints manager: 3.31 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.420 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.030 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:134.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.002 TRP A 92 HIS 0.006 0.001 HIS B 48 PHE 0.014 0.001 PHE C 221 TYR 0.027 0.002 TYR D 294 ARG 0.002 0.000 ARG D 260 Details of bonding type rmsd hydrogen bonds : bond 0.19401 ( 404) hydrogen bonds : angle 8.94197 ( 1248) metal coordination : bond 0.01165 ( 28) metal coordination : angle 2.94230 ( 24) SS BOND : bond 0.00346 ( 2) SS BOND : angle 0.31073 ( 4) covalent geometry : bond 0.00752 (10412) covalent geometry : angle 0.70364 (14224) *********************** 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 : 1.055 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 1.1348 time to fit residues: 113.7618 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 : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.154721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.113440 restraints weight = 10383.212| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.40 r_work: 0.3530 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1266 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= 0.140 Angle : 0.521 5.886 14252 Z= 0.266 Chirality : 0.044 0.141 1624 Planarity : 0.004 0.032 1820 Dihedral : 8.741 57.336 1696 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.20 % Allowed : 9.88 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1380 helix: -0.38 (0.24), residues: 452 sheet: -2.43 (0.32), residues: 204 loop : -1.37 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 172 HIS 0.003 0.001 HIS A 48 PHE 0.012 0.002 PHE B 221 TYR 0.014 0.001 TYR D 258 ARG 0.002 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.03174 ( 404) hydrogen bonds : angle 5.76895 ( 1248) metal coordination : bond 0.00363 ( 28) metal coordination : angle 2.73913 ( 24) SS BOND : bond 0.00069 ( 2) SS BOND : angle 0.08797 ( 4) covalent geometry : bond 0.00315 (10412) covalent geometry : angle 0.50961 (14224) *********************** 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 101 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 1.194 Fit side-chains REVERT: C 168 MET cc_start: 0.8236 (mtt) cc_final: 0.7864 (mtm) outliers start: 2 outliers final: 0 residues processed: 101 average time/residue: 1.1083 time to fit residues: 124.4470 Evaluate side-chains 87 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 53 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS B 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.147560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104035 restraints weight = 10579.869| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.50 r_work: 0.3306 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 10442 Z= 0.222 Angle : 0.544 5.104 14252 Z= 0.277 Chirality : 0.045 0.131 1624 Planarity : 0.004 0.030 1820 Dihedral : 8.742 55.309 1696 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.92 % Allowed : 12.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.22), residues: 1380 helix: -0.17 (0.24), residues: 452 sheet: -2.26 (0.29), residues: 252 loop : -1.26 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 50 HIS 0.005 0.001 HIS C 48 PHE 0.011 0.002 PHE B 221 TYR 0.019 0.002 TYR A 258 ARG 0.002 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 404) hydrogen bonds : angle 5.64431 ( 1248) metal coordination : bond 0.00680 ( 28) metal coordination : angle 2.52333 ( 24) SS BOND : bond 0.00009 ( 2) SS BOND : angle 0.25993 ( 4) covalent geometry : bond 0.00521 (10412) covalent geometry : angle 0.53498 (14224) *********************** 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 104 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.509 Fit side-chains REVERT: A 168 MET cc_start: 0.7877 (mtt) cc_final: 0.7475 (mtm) REVERT: B 168 MET cc_start: 0.7883 (mtt) cc_final: 0.7481 (mtm) outliers start: 19 outliers final: 8 residues processed: 99 average time/residue: 1.2211 time to fit residues: 132.4658 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 : 1.327 ------------------------------------------------------------------------------- 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 93 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 88 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.108190 restraints weight = 10525.051| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.55 r_work: 0.3364 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1692 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= 0.122 Angle : 0.479 4.696 14252 Z= 0.244 Chirality : 0.043 0.131 1624 Planarity : 0.003 0.027 1820 Dihedral : 8.426 57.436 1696 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.21 % Allowed : 15.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.22), residues: 1380 helix: 0.24 (0.25), residues: 448 sheet: -2.30 (0.31), residues: 208 loop : -1.17 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.003 0.000 HIS B 48 PHE 0.010 0.002 PHE B 221 TYR 0.015 0.001 TYR D 329 ARG 0.001 0.000 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 404) hydrogen bonds : angle 5.21902 ( 1248) metal coordination : bond 0.00317 ( 28) metal coordination : angle 2.31957 ( 24) SS BOND : bond 0.00005 ( 2) SS BOND : angle 0.12733 ( 4) covalent geometry : bond 0.00281 (10412) covalent geometry : angle 0.46983 (14224) *********************** 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 90 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.250 Fit side-chains REVERT: A 83 LYS cc_start: 0.6876 (mtmm) cc_final: 0.6651 (mttm) REVERT: A 168 MET cc_start: 0.7938 (mtt) cc_final: 0.7556 (mtm) REVERT: B 83 LYS cc_start: 0.6894 (mtmm) cc_final: 0.6667 (mttm) REVERT: B 168 MET cc_start: 0.7932 (mtt) cc_final: 0.7552 (mtm) REVERT: C 83 LYS cc_start: 0.6944 (mtmm) cc_final: 0.6734 (mttm) REVERT: C 168 MET cc_start: 0.7965 (mtt) cc_final: 0.7579 (mtm) REVERT: D 83 LYS cc_start: 0.6876 (mtmm) cc_final: 0.6655 (mttm) outliers start: 12 outliers final: 4 residues processed: 87 average time/residue: 1.3645 time to fit residues: 129.7871 Evaluate side-chains 79 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 58 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.152205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.110681 restraints weight = 10443.215| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.39 r_work: 0.3516 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1689 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= 0.184 Angle : 0.510 4.652 14252 Z= 0.259 Chirality : 0.044 0.131 1624 Planarity : 0.003 0.026 1820 Dihedral : 8.617 56.230 1696 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.61 % Allowed : 15.93 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.22), residues: 1380 helix: 0.25 (0.25), residues: 448 sheet: -2.03 (0.29), residues: 256 loop : -1.13 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 50 HIS 0.004 0.001 HIS D 48 PHE 0.010 0.002 PHE B 221 TYR 0.017 0.001 TYR A 258 ARG 0.002 0.000 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 404) hydrogen bonds : angle 5.27994 ( 1248) metal coordination : bond 0.00561 ( 28) metal coordination : angle 2.26267 ( 24) SS BOND : bond 0.00003 ( 2) SS BOND : angle 0.26583 ( 4) covalent geometry : bond 0.00429 (10412) covalent geometry : angle 0.50156 (14224) *********************** 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 90 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 1.783 Fit side-chains REVERT: A 168 MET cc_start: 0.8201 (mtt) cc_final: 0.7851 (mtm) REVERT: B 168 MET cc_start: 0.8192 (mtt) cc_final: 0.7841 (mtm) REVERT: C 168 MET cc_start: 0.8202 (mtt) cc_final: 0.7850 (mtm) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 1.6681 time to fit residues: 157.8001 Evaluate side-chains 78 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 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 23 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.153486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.111920 restraints weight = 10510.746| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.41 r_work: 0.3526 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1784 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= 0.155 Angle : 0.496 4.649 14252 Z= 0.251 Chirality : 0.044 0.132 1624 Planarity : 0.003 0.025 1820 Dihedral : 8.563 57.028 1696 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.02 % Allowed : 18.45 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1380 helix: 0.30 (0.24), residues: 448 sheet: -1.95 (0.30), residues: 256 loop : -1.10 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 50 HIS 0.003 0.001 HIS A 48 PHE 0.010 0.002 PHE B 221 TYR 0.020 0.001 TYR D 329 ARG 0.001 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 404) hydrogen bonds : angle 5.20680 ( 1248) metal coordination : bond 0.00450 ( 28) metal coordination : angle 2.22204 ( 24) SS BOND : bond 0.00003 ( 2) SS BOND : angle 0.23338 ( 4) covalent geometry : bond 0.00361 (10412) covalent geometry : angle 0.48760 (14224) *********************** 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 102 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.991 Fit side-chains REVERT: A 168 MET cc_start: 0.8195 (mtt) cc_final: 0.7853 (mtm) REVERT: B 168 MET cc_start: 0.8194 (mtt) cc_final: 0.7851 (mtm) REVERT: C 168 MET cc_start: 0.8196 (mtt) cc_final: 0.7853 (mtm) outliers start: 20 outliers final: 12 residues processed: 98 average time/residue: 0.7925 time to fit residues: 87.6040 Evaluate side-chains 88 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 79 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 46 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 57 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.156889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.115215 restraints weight = 10494.990| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.49 r_work: 0.3560 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10442 Z= 0.099 Angle : 0.464 4.793 14252 Z= 0.235 Chirality : 0.043 0.131 1624 Planarity : 0.003 0.024 1820 Dihedral : 8.265 58.492 1696 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.60 % Allowed : 20.56 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.22), residues: 1380 helix: 0.57 (0.25), residues: 448 sheet: -1.81 (0.30), residues: 256 loop : -0.93 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 50 HIS 0.002 0.000 HIS A 48 PHE 0.011 0.002 PHE A 210 TYR 0.025 0.001 TYR B 329 ARG 0.001 0.000 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.02714 ( 404) hydrogen bonds : angle 4.99501 ( 1248) metal coordination : bond 0.00228 ( 28) metal coordination : angle 2.07940 ( 24) SS BOND : bond 0.00002 ( 2) SS BOND : angle 0.12681 ( 4) covalent geometry : bond 0.00226 (10412) covalent geometry : angle 0.45691 (14224) *********************** 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 93 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 1.092 Fit side-chains REVERT: A 83 LYS cc_start: 0.7157 (mtmm) cc_final: 0.6941 (mttm) REVERT: A 168 MET cc_start: 0.8253 (mtt) cc_final: 0.7974 (mtm) REVERT: B 83 LYS cc_start: 0.7180 (mtmm) cc_final: 0.6973 (mttm) REVERT: B 168 MET cc_start: 0.8263 (mtt) cc_final: 0.7990 (mtm) REVERT: C 83 LYS cc_start: 0.7154 (mtmm) cc_final: 0.6947 (mttm) REVERT: C 168 MET cc_start: 0.8292 (mtt) cc_final: 0.8019 (mtm) REVERT: D 83 LYS cc_start: 0.7142 (mtmm) cc_final: 0.6939 (mttm) REVERT: D 168 MET cc_start: 0.8182 (mtt) cc_final: 0.7885 (mtm) outliers start: 6 outliers final: 6 residues processed: 93 average time/residue: 0.7830 time to fit residues: 82.3240 Evaluate side-chains 82 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 117 optimal weight: 0.0970 chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 D 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.161601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.120448 restraints weight = 10550.730| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.47 r_work: 0.3407 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10442 Z= 0.098 Angle : 0.465 5.019 14252 Z= 0.235 Chirality : 0.043 0.132 1624 Planarity : 0.003 0.025 1820 Dihedral : 8.200 58.902 1696 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.71 % Allowed : 23.49 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1380 helix: 1.00 (0.25), residues: 424 sheet: -1.84 (0.30), residues: 260 loop : -0.77 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 50 HIS 0.002 0.000 HIS D 44 PHE 0.010 0.002 PHE D 210 TYR 0.013 0.001 TYR A 258 ARG 0.001 0.000 ARG D 260 Details of bonding type rmsd hydrogen bonds : bond 0.02656 ( 404) hydrogen bonds : angle 4.92907 ( 1248) metal coordination : bond 0.00223 ( 28) metal coordination : angle 1.98851 ( 24) SS BOND : bond 0.00005 ( 2) SS BOND : angle 0.11419 ( 4) covalent geometry : bond 0.00225 (10412) covalent geometry : angle 0.45818 (14224) *********************** 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 106 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 1.012 Fit side-chains REVERT: A 168 MET cc_start: 0.8011 (mtt) cc_final: 0.7721 (mtm) REVERT: A 236 ASP cc_start: 0.7966 (t0) cc_final: 0.7630 (t0) REVERT: B 168 MET cc_start: 0.8026 (mtt) cc_final: 0.7739 (mtm) REVERT: B 236 ASP cc_start: 0.7964 (t0) cc_final: 0.7631 (t0) REVERT: C 168 MET cc_start: 0.8101 (mtt) cc_final: 0.7800 (mtm) REVERT: C 236 ASP cc_start: 0.7972 (t0) cc_final: 0.7637 (t0) REVERT: D 168 MET cc_start: 0.7962 (mtt) cc_final: 0.7649 (mtm) REVERT: D 236 ASP cc_start: 0.7964 (t0) cc_final: 0.7625 (t0) outliers start: 7 outliers final: 7 residues processed: 106 average time/residue: 0.7177 time to fit residues: 86.8754 Evaluate side-chains 86 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 72 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 131 optimal weight: 0.1980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.156326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.114489 restraints weight = 10583.020| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.46 r_work: 0.3385 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2146 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= 0.130 Angle : 0.477 4.786 14252 Z= 0.241 Chirality : 0.043 0.134 1624 Planarity : 0.003 0.025 1820 Dihedral : 8.334 58.409 1696 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.91 % Allowed : 24.90 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1380 helix: 1.00 (0.25), residues: 424 sheet: -1.90 (0.31), residues: 252 loop : -0.80 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.003 0.001 HIS D 48 PHE 0.010 0.002 PHE B 221 TYR 0.026 0.001 TYR A 329 ARG 0.001 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.02855 ( 404) hydrogen bonds : angle 5.00680 ( 1248) metal coordination : bond 0.00351 ( 28) metal coordination : angle 2.01922 ( 24) SS BOND : bond 0.00015 ( 2) SS BOND : angle 0.17117 ( 4) covalent geometry : bond 0.00303 (10412) covalent geometry : angle 0.46976 (14224) *********************** 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 98 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 1.082 Fit side-chains REVERT: A 168 MET cc_start: 0.8119 (mtt) cc_final: 0.7767 (mtm) REVERT: A 236 ASP cc_start: 0.7961 (t0) cc_final: 0.7644 (t0) REVERT: B 168 MET cc_start: 0.8182 (mtt) cc_final: 0.7831 (mtm) REVERT: C 168 MET cc_start: 0.8181 (mtt) cc_final: 0.7834 (mtm) REVERT: C 236 ASP cc_start: 0.7963 (t0) cc_final: 0.7643 (t0) REVERT: D 168 MET cc_start: 0.8026 (mtt) cc_final: 0.7694 (mtm) REVERT: D 236 ASP cc_start: 0.7880 (t0) cc_final: 0.7568 (t0) outliers start: 9 outliers final: 8 residues processed: 97 average time/residue: 0.7343 time to fit residues: 80.5086 Evaluate side-chains 92 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.1980 chunk 123 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.151348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109740 restraints weight = 10642.897| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.42 r_work: 0.3324 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10442 Z= 0.233 Angle : 0.547 4.667 14252 Z= 0.279 Chirality : 0.046 0.137 1624 Planarity : 0.003 0.026 1820 Dihedral : 8.807 56.129 1696 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.01 % Allowed : 24.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.22), residues: 1380 helix: 0.37 (0.24), residues: 448 sheet: -1.84 (0.32), residues: 248 loop : -1.01 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 92 HIS 0.005 0.001 HIS D 48 PHE 0.011 0.002 PHE B 11 TYR 0.019 0.002 TYR B 258 ARG 0.002 0.000 ARG B 302 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 404) hydrogen bonds : angle 5.34824 ( 1248) metal coordination : bond 0.00695 ( 28) metal coordination : angle 2.40652 ( 24) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.38231 ( 4) covalent geometry : bond 0.00547 (10412) covalent geometry : angle 0.53886 (14224) ********************** 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 97 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.080 Fit side-chains REVERT: A 168 MET cc_start: 0.8232 (mtt) cc_final: 0.7883 (mtm) REVERT: B 168 MET cc_start: 0.8219 (mtt) cc_final: 0.7871 (mtm) REVERT: C 168 MET cc_start: 0.8231 (mtt) cc_final: 0.7875 (mtm) outliers start: 10 outliers final: 10 residues processed: 97 average time/residue: 0.8060 time to fit residues: 88.0065 Evaluate side-chains 83 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 58 THR 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 58 THR 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 24 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.156240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.114442 restraints weight = 10413.099| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.50 r_work: 0.3545 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2226 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= 0.113 Angle : 0.484 5.165 14252 Z= 0.246 Chirality : 0.044 0.136 1624 Planarity : 0.003 0.025 1820 Dihedral : 8.382 59.375 1696 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.81 % Allowed : 25.81 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1380 helix: 0.89 (0.25), residues: 424 sheet: -2.01 (0.30), residues: 252 loop : -0.84 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 50 HIS 0.002 0.000 HIS B 48 PHE 0.010 0.002 PHE B 221 TYR 0.014 0.001 TYR B 258 ARG 0.001 0.000 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.02868 ( 404) hydrogen bonds : angle 5.05165 ( 1248) metal coordination : bond 0.00276 ( 28) metal coordination : angle 2.15736 ( 24) SS BOND : bond 0.00035 ( 2) SS BOND : angle 0.17998 ( 4) covalent geometry : bond 0.00258 (10412) covalent geometry : angle 0.47653 (14224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7739.25 seconds wall clock time: 138 minutes 49.33 seconds (8329.33 seconds total)