Starting phenix.real_space_refine on Mon Apr 6 09:00:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qhx_53182/04_2026/9qhx_53182_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qhx_53182/04_2026/9qhx_53182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qhx_53182/04_2026/9qhx_53182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qhx_53182/04_2026/9qhx_53182.map" model { file = "/net/cci-nas-00/data/ceres_data/9qhx_53182/04_2026/9qhx_53182_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qhx_53182/04_2026/9qhx_53182_trim.cif" } resolution = 3.47 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= 0.001 sd= 0.051 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 32 5.16 5 C 5440 2.51 5 N 1448 2.21 5 O 1466 1.98 5 H 8540 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16934 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4440 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain: "B" Number of atoms: 4440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4440 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain: "C" Number of atoms: 3995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 3995 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain: "D" Number of atoms: 3995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 3995 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.30, per 1000 atoms: 0.19 Number of scatterers: 16934 At special positions: 0 Unit cell: (84.5, 81.9, 107.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 32 16.00 P 6 15.00 Mg 2 11.99 O 1466 8.00 N 1448 7.00 C 5440 6.00 H 8540 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.55 Conformation dependent library (CDL) restraints added in 630.5 milliseconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 68.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 32 through 46 removed outlier: 3.528A pdb=" N LEU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 65 removed outlier: 3.788A pdb=" N GLN A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 91 removed outlier: 3.744A pdb=" N ILE A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 121 Proline residue: A 100 - end of helix removed outlier: 3.936A pdb=" N LEU A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.710A pdb=" N ASN A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 137 through 166 removed outlier: 3.584A pdb=" N VAL A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE A 158 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 202 Proline residue: A 179 - end of helix removed outlier: 3.724A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 220 removed outlier: 4.322A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.859A pdb=" N THR A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.568A pdb=" N PHE A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 262 through 288 removed outlier: 3.941A pdb=" N TRP A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'B' and resid 32 through 46 removed outlier: 3.527A pdb=" N LEU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 65 removed outlier: 3.789A pdb=" N GLN B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 91 removed outlier: 3.744A pdb=" N ILE B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 121 Proline residue: B 100 - end of helix removed outlier: 3.935A pdb=" N LEU B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.710A pdb=" N ASN B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 137 through 166 removed outlier: 3.583A pdb=" N VAL B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE B 158 " --> pdb=" O HIS B 154 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 202 Proline residue: B 179 - end of helix removed outlier: 3.724A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 220 removed outlier: 4.321A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.858A pdb=" N THR B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 244 through 258 removed outlier: 3.568A pdb=" N PHE B 248 " --> pdb=" O PRO B 244 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 262 through 288 removed outlier: 3.941A pdb=" N TRP B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 288 " --> pdb=" O MET B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'C' and resid 70 through 79 Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.790A pdb=" N ILE C 116 " --> pdb=" O TYR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 removed outlier: 4.609A pdb=" N ASP C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 154 through 169 Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 184 through 202 removed outlier: 3.772A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 4.086A pdb=" N LEU C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 260 removed outlier: 7.408A pdb=" N ASP C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N GLU C 247 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 79 Processing helix chain 'D' and resid 110 through 122 removed outlier: 3.790A pdb=" N ILE D 116 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 removed outlier: 4.609A pdb=" N ASP D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 154 through 169 Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 184 through 202 removed outlier: 3.773A pdb=" N LYS D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 removed outlier: 4.086A pdb=" N LEU D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 260 removed outlier: 7.409A pdb=" N ASP D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N GLU D 247 " --> pdb=" O TYR D 243 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA D 248 " --> pdb=" O GLU D 244 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 37 removed outlier: 3.742A pdb=" N ALA C 34 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL C 43 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL C 11 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG C 49 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA C 9 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 51 " --> pdb=" O HIS C 7 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS C 7 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU C 53 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLN C 5 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA C 9 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 86 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 95 through 98 removed outlier: 3.653A pdb=" N LEU C 175 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG C 60 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N MET C 223 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY C 62 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE C 225 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 64 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA C 222 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER C 233 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP C 224 " --> pdb=" O LYS C 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 34 through 37 removed outlier: 3.742A pdb=" N ALA D 34 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL D 43 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL D 11 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG D 49 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA D 9 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE D 51 " --> pdb=" O HIS D 7 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N HIS D 7 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU D 53 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLN D 5 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA D 9 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG D 86 " --> pdb=" O ALA D 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 95 through 98 removed outlier: 3.653A pdb=" N LEU D 175 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG D 60 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N MET D 223 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY D 62 " --> pdb=" O MET D 223 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE D 225 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 64 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA D 222 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER D 233 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP D 224 " --> pdb=" O LYS D 231 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1452 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: 3.81 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8536 1.03 - 1.23: 6 1.23 - 1.42: 3582 1.42 - 1.62: 4944 1.62 - 1.81: 60 Bond restraints: 17128 Sorted by residual: bond pdb=" CB GLU B 97 " pdb=" CG GLU B 97 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.26e+00 bond pdb=" CB GLU A 97 " pdb=" CG GLU A 97 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.20e+00 bond pdb=" C THR A 167 " pdb=" N PRO A 168 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.38e+00 bond pdb=" C THR B 167 " pdb=" N PRO B 168 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.36e+00 bond pdb=" CA GLU C 244 " pdb=" CB GLU C 244 " ideal model delta sigma weight residual 1.531 1.546 -0.015 1.51e-02 4.39e+03 9.67e-01 ... (remaining 17123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 30066 1.54 - 3.07: 819 3.07 - 4.61: 85 4.61 - 6.14: 26 6.14 - 7.68: 6 Bond angle restraints: 31002 Sorted by residual: angle pdb=" CA GLU B 97 " pdb=" CB GLU B 97 " pdb=" CG GLU B 97 " ideal model delta sigma weight residual 114.10 120.78 -6.68 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA GLU A 97 " pdb=" CB GLU A 97 " pdb=" CG GLU A 97 " ideal model delta sigma weight residual 114.10 120.76 -6.66 2.00e+00 2.50e-01 1.11e+01 angle pdb=" C3' ATP C 502 " pdb=" C4' ATP C 502 " pdb=" C5' ATP C 502 " ideal model delta sigma weight residual 115.19 109.56 5.63 1.76e+00 3.23e-01 1.02e+01 angle pdb=" C3' ATP D 502 " pdb=" C4' ATP D 502 " pdb=" C5' ATP D 502 " ideal model delta sigma weight residual 115.19 109.60 5.59 1.76e+00 3.23e-01 1.01e+01 angle pdb=" CB MET B 219 " pdb=" CG MET B 219 " pdb=" SD MET B 219 " ideal model delta sigma weight residual 112.70 120.38 -7.68 3.00e+00 1.11e-01 6.55e+00 ... (remaining 30997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 6911 16.97 - 33.93: 717 33.93 - 50.90: 228 50.90 - 67.87: 96 67.87 - 84.83: 24 Dihedral angle restraints: 7976 sinusoidal: 4368 harmonic: 3608 Sorted by residual: dihedral pdb=" CA ILE A 85 " pdb=" C ILE A 85 " pdb=" N LEU A 86 " pdb=" CA LEU A 86 " ideal model delta harmonic sigma weight residual -180.00 -162.64 -17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ILE B 85 " pdb=" C ILE B 85 " pdb=" N LEU B 86 " pdb=" CA LEU B 86 " ideal model delta harmonic sigma weight residual -180.00 -162.65 -17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA GLN A 286 " pdb=" C GLN A 286 " pdb=" N TYR A 287 " pdb=" CA TYR A 287 " ideal model delta harmonic sigma weight residual -180.00 -163.26 -16.74 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 7973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1114 0.054 - 0.109: 194 0.109 - 0.163: 26 0.163 - 0.218: 0 0.218 - 0.272: 6 Chirality restraints: 1340 Sorted by residual: chirality pdb=" C4' ATP C 502 " pdb=" C3' ATP C 502 " pdb=" C5' ATP C 502 " pdb=" O4' ATP C 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.77 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C4' ATP D 502 " pdb=" C3' ATP D 502 " pdb=" C5' ATP D 502 " pdb=" O4' ATP D 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.76 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C2' ATP D 502 " pdb=" C1' ATP D 502 " pdb=" C3' ATP D 502 " pdb=" O2' ATP D 502 " both_signs ideal model delta sigma weight residual False -2.68 -2.95 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1337 not shown) Planarity restraints: 2456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 79 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C THR B 79 " 0.039 2.00e-02 2.50e+03 pdb=" O THR B 79 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA B 80 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 79 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C THR A 79 " -0.039 2.00e-02 2.50e+03 pdb=" O THR A 79 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA A 80 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 77 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C GLY A 77 " 0.037 2.00e-02 2.50e+03 pdb=" O GLY A 77 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 78 " -0.012 2.00e-02 2.50e+03 ... (remaining 2453 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.44: 9075 2.44 - 2.98: 39133 2.98 - 3.52: 45545 3.52 - 4.06: 59305 4.06 - 4.60: 89408 Nonbonded interactions: 242466 Sorted by model distance: nonbonded pdb="HD22 ASN B 187 " pdb=" HG1 THR B 273 " model vdw 1.900 2.100 nonbonded pdb="HD22 ASN A 187 " pdb=" HG1 THR A 273 " model vdw 1.901 2.100 nonbonded pdb=" H THR B 76 " pdb=" HG1 THR B 76 " model vdw 1.950 2.100 nonbonded pdb=" H THR A 76 " pdb=" HG1 THR A 76 " model vdw 1.950 2.100 nonbonded pdb=" H THR B 200 " pdb=" HG1 THR B 200 " model vdw 1.960 2.100 ... (remaining 242461 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = 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: 0.790 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: 0.120 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.660 Find NCS groups from input model: 0.090 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 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 : 0.004 0.045 8588 Z= 0.194 Angle : 0.771 7.676 11680 Z= 0.417 Chirality : 0.045 0.272 1340 Planarity : 0.007 0.054 1448 Dihedral : 16.869 84.833 3138 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.23 % Allowed : 12.73 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.24), residues: 1040 helix: -0.44 (0.19), residues: 658 sheet: -1.87 (0.50), residues: 92 loop : -0.82 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 201 TYR 0.011 0.001 TYR B 101 PHE 0.011 0.001 PHE A 177 TRP 0.026 0.002 TRP B 50 HIS 0.006 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 8588) covalent geometry : angle 0.77130 (11680) hydrogen bonds : bond 0.15546 ( 496) hydrogen bonds : angle 6.74431 ( 1452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 PHE cc_start: 0.5516 (OUTLIER) cc_final: 0.4921 (p90) REVERT: A 249 LEU cc_start: 0.7541 (tt) cc_final: 0.7328 (tp) REVERT: B 177 PHE cc_start: 0.5388 (OUTLIER) cc_final: 0.4799 (p90) REVERT: B 249 LEU cc_start: 0.7446 (tt) cc_final: 0.7225 (tp) REVERT: C 188 MET cc_start: 0.7903 (tpt) cc_final: 0.6859 (tpt) REVERT: D 188 MET cc_start: 0.7904 (tpt) cc_final: 0.6888 (tpt) outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.2197 time to fit residues: 24.2792 Evaluate side-chains 69 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain B residue 177 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.193035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.166226 restraints weight = 25450.223| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.95 r_work: 0.3692 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8588 Z= 0.186 Angle : 0.548 5.062 11680 Z= 0.297 Chirality : 0.039 0.138 1340 Planarity : 0.005 0.048 1448 Dihedral : 7.261 78.785 1212 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.03 % Allowed : 10.36 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.25), residues: 1040 helix: -0.05 (0.19), residues: 660 sheet: -2.16 (0.53), residues: 86 loop : -0.70 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 290 TYR 0.013 0.001 TYR B 87 PHE 0.011 0.001 PHE A 195 TRP 0.014 0.001 TRP B 50 HIS 0.006 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 8588) covalent geometry : angle 0.54823 (11680) hydrogen bonds : bond 0.04670 ( 496) hydrogen bonds : angle 4.48315 ( 1452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 PHE cc_start: 0.6059 (OUTLIER) cc_final: 0.5528 (p90) REVERT: A 190 TRP cc_start: 0.8113 (OUTLIER) cc_final: 0.7791 (p-90) REVERT: A 217 PHE cc_start: 0.7251 (t80) cc_final: 0.6998 (t80) REVERT: A 249 LEU cc_start: 0.7537 (tt) cc_final: 0.7292 (tp) REVERT: B 177 PHE cc_start: 0.5957 (OUTLIER) cc_final: 0.5420 (p90) REVERT: B 249 LEU cc_start: 0.7521 (tt) cc_final: 0.7293 (tp) outliers start: 18 outliers final: 12 residues processed: 101 average time/residue: 0.1844 time to fit residues: 26.7997 Evaluate side-chains 92 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN D 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.189766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.160460 restraints weight = 26338.833| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.18 r_work: 0.3620 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8588 Z= 0.213 Angle : 0.584 5.283 11680 Z= 0.316 Chirality : 0.039 0.143 1340 Planarity : 0.004 0.042 1448 Dihedral : 6.720 69.374 1212 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.82 % Allowed : 11.94 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.24), residues: 1040 helix: -0.05 (0.19), residues: 660 sheet: -2.12 (0.53), residues: 86 loop : -1.05 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 201 TYR 0.011 0.002 TYR B 87 PHE 0.024 0.002 PHE B 217 TRP 0.013 0.002 TRP A 50 HIS 0.005 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 8588) covalent geometry : angle 0.58370 (11680) hydrogen bonds : bond 0.04488 ( 496) hydrogen bonds : angle 4.33507 ( 1452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.5475 (p90) REVERT: A 249 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7113 (tp) REVERT: B 55 TRP cc_start: 0.7330 (t-100) cc_final: 0.6939 (t-100) REVERT: B 177 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.5469 (p90) REVERT: B 249 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7111 (tp) REVERT: C 59 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7403 (t0) REVERT: C 188 MET cc_start: 0.8214 (tpt) cc_final: 0.7793 (tpt) REVERT: D 59 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7388 (t0) REVERT: D 188 MET cc_start: 0.8226 (tpt) cc_final: 0.7801 (tpt) outliers start: 25 outliers final: 15 residues processed: 115 average time/residue: 0.1939 time to fit residues: 31.9636 Evaluate side-chains 113 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN D 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.189741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160735 restraints weight = 26171.667| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.16 r_work: 0.3631 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8588 Z= 0.171 Angle : 0.532 4.361 11680 Z= 0.290 Chirality : 0.038 0.139 1340 Planarity : 0.004 0.039 1448 Dihedral : 6.616 67.353 1212 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.59 % Allowed : 12.05 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.25), residues: 1040 helix: -0.02 (0.19), residues: 662 sheet: -2.01 (0.48), residues: 100 loop : -1.16 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 232 TYR 0.010 0.001 TYR B 87 PHE 0.013 0.001 PHE A 218 TRP 0.013 0.001 TRP A 50 HIS 0.004 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8588) covalent geometry : angle 0.53200 (11680) hydrogen bonds : bond 0.04006 ( 496) hydrogen bonds : angle 4.21543 ( 1452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 PHE cc_start: 0.7372 (t80) cc_final: 0.7007 (t80) REVERT: B 249 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7142 (tp) REVERT: C 188 MET cc_start: 0.8122 (tpt) cc_final: 0.7825 (tpt) REVERT: C 200 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6975 (mm-30) REVERT: D 188 MET cc_start: 0.8116 (tpt) cc_final: 0.7819 (tpt) REVERT: D 200 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6978 (mm-30) outliers start: 23 outliers final: 18 residues processed: 115 average time/residue: 0.1833 time to fit residues: 30.2799 Evaluate side-chains 112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN D 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.187753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.160185 restraints weight = 26252.461| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.07 r_work: 0.3600 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8588 Z= 0.231 Angle : 0.580 5.002 11680 Z= 0.320 Chirality : 0.040 0.161 1340 Planarity : 0.004 0.038 1448 Dihedral : 6.742 68.733 1212 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.05 % Allowed : 11.49 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1040 helix: -0.12 (0.19), residues: 660 sheet: -1.46 (0.65), residues: 66 loop : -1.21 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.010 0.001 TYR B 87 PHE 0.014 0.001 PHE B 195 TRP 0.013 0.002 TRP B 50 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 8588) covalent geometry : angle 0.57950 (11680) hydrogen bonds : bond 0.04262 ( 496) hydrogen bonds : angle 4.29372 ( 1452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7557 (mp) REVERT: A 249 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6988 (mt) REVERT: B 90 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7539 (mp) REVERT: B 217 PHE cc_start: 0.7608 (t80) cc_final: 0.7184 (t80) REVERT: B 249 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7121 (mt) REVERT: C 8 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7608 (mm110) REVERT: C 59 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7358 (t0) REVERT: C 188 MET cc_start: 0.8082 (tpt) cc_final: 0.7762 (tpt) REVERT: C 200 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7024 (mm-30) REVERT: D 8 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7623 (mm110) REVERT: D 59 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7352 (t0) REVERT: D 188 MET cc_start: 0.8073 (tpt) cc_final: 0.7753 (tpt) REVERT: D 200 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7263 (mm-30) REVERT: D 254 GLN cc_start: 0.8091 (tt0) cc_final: 0.7743 (tt0) outliers start: 36 outliers final: 24 residues processed: 130 average time/residue: 0.1960 time to fit residues: 36.1894 Evaluate side-chains 128 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN D 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.186262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158603 restraints weight = 25999.081| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.06 r_work: 0.3612 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8588 Z= 0.185 Angle : 0.547 4.785 11680 Z= 0.300 Chirality : 0.039 0.141 1340 Planarity : 0.004 0.037 1448 Dihedral : 6.667 65.314 1212 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.60 % Allowed : 12.73 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.25), residues: 1040 helix: -0.07 (0.20), residues: 660 sheet: -1.61 (0.67), residues: 56 loop : -1.32 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 232 TYR 0.009 0.001 TYR B 87 PHE 0.014 0.001 PHE A 218 TRP 0.014 0.001 TRP B 50 HIS 0.005 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8588) covalent geometry : angle 0.54687 (11680) hydrogen bonds : bond 0.04043 ( 496) hydrogen bonds : angle 4.23816 ( 1452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7575 (mp) REVERT: A 249 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6996 (tp) REVERT: B 90 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7580 (mp) REVERT: B 249 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7167 (tt) REVERT: C 8 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7498 (mm-40) REVERT: C 59 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7453 (t0) REVERT: C 200 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7007 (mm-30) REVERT: D 8 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7486 (mm-40) REVERT: D 59 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7367 (t0) REVERT: D 188 MET cc_start: 0.8096 (tpt) cc_final: 0.7712 (tpt) REVERT: D 200 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7042 (mm-30) outliers start: 32 outliers final: 22 residues processed: 121 average time/residue: 0.1899 time to fit residues: 32.8392 Evaluate side-chains 125 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 94 optimal weight: 0.0980 chunk 50 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.187449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159217 restraints weight = 25574.948| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.08 r_work: 0.3634 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8588 Z= 0.125 Angle : 0.499 4.946 11680 Z= 0.274 Chirality : 0.038 0.140 1340 Planarity : 0.004 0.036 1448 Dihedral : 6.566 63.342 1212 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.82 % Allowed : 13.06 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.25), residues: 1040 helix: 0.16 (0.20), residues: 662 sheet: -2.00 (0.50), residues: 86 loop : -1.26 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 118 TYR 0.008 0.001 TYR A 101 PHE 0.014 0.001 PHE A 218 TRP 0.014 0.001 TRP B 50 HIS 0.005 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8588) covalent geometry : angle 0.49927 (11680) hydrogen bonds : bond 0.03657 ( 496) hydrogen bonds : angle 4.04970 ( 1452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7275 (mtt) cc_final: 0.6506 (mmt) REVERT: A 90 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7530 (mp) REVERT: B 90 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7533 (mp) REVERT: B 249 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7033 (tt) REVERT: C 200 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6993 (mm-30) REVERT: D 59 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7377 (t0) REVERT: D 200 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6998 (mm-30) outliers start: 25 outliers final: 15 residues processed: 121 average time/residue: 0.2265 time to fit residues: 37.9780 Evaluate side-chains 113 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.183110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.154877 restraints weight = 26606.114| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.13 r_work: 0.3572 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8588 Z= 0.252 Angle : 0.598 5.309 11680 Z= 0.329 Chirality : 0.041 0.146 1340 Planarity : 0.005 0.037 1448 Dihedral : 6.839 70.358 1212 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.27 % Allowed : 12.95 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.14 (0.25), residues: 1040 helix: -0.19 (0.20), residues: 658 sheet: -1.77 (0.68), residues: 56 loop : -1.51 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 232 TYR 0.011 0.002 TYR A 87 PHE 0.017 0.002 PHE B 195 TRP 0.012 0.002 TRP B 50 HIS 0.004 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 8588) covalent geometry : angle 0.59795 (11680) hydrogen bonds : bond 0.04308 ( 496) hydrogen bonds : angle 4.30155 ( 1452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7576 (mp) REVERT: A 249 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6814 (mt) REVERT: B 90 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7577 (mp) REVERT: B 249 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7073 (tt) REVERT: C 188 MET cc_start: 0.8164 (tpt) cc_final: 0.7812 (tpt) REVERT: C 200 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7063 (mm-30) REVERT: C 254 GLN cc_start: 0.8085 (tt0) cc_final: 0.7830 (tt0) REVERT: D 59 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7240 (t0) REVERT: D 188 MET cc_start: 0.8170 (tpt) cc_final: 0.7812 (tpt) REVERT: D 200 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7062 (mm-30) REVERT: D 254 GLN cc_start: 0.8079 (tt0) cc_final: 0.7823 (tt0) outliers start: 29 outliers final: 21 residues processed: 129 average time/residue: 0.1890 time to fit residues: 34.7427 Evaluate side-chains 128 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.186810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158467 restraints weight = 26142.985| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.14 r_work: 0.3610 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8588 Z= 0.136 Angle : 0.505 5.499 11680 Z= 0.273 Chirality : 0.038 0.135 1340 Planarity : 0.004 0.036 1448 Dihedral : 6.535 61.139 1212 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.70 % Allowed : 13.51 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.81 (0.25), residues: 1040 helix: 0.06 (0.20), residues: 662 sheet: -1.59 (0.70), residues: 56 loop : -1.40 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.008 0.001 TYR B 87 PHE 0.011 0.001 PHE B 218 TRP 0.015 0.001 TRP B 50 HIS 0.005 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8588) covalent geometry : angle 0.50466 (11680) hydrogen bonds : bond 0.03672 ( 496) hydrogen bonds : angle 4.06793 ( 1452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7248 (mtt) cc_final: 0.6446 (mmt) REVERT: A 90 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7548 (mp) REVERT: B 90 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7554 (mp) REVERT: B 249 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7120 (tt) REVERT: C 8 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7418 (mm-40) REVERT: C 188 MET cc_start: 0.8099 (tpt) cc_final: 0.7686 (tpt) REVERT: C 200 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7033 (mm-30) REVERT: D 8 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7468 (mm-40) REVERT: D 59 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7242 (t0) REVERT: D 188 MET cc_start: 0.8085 (tpt) cc_final: 0.7648 (tpt) REVERT: D 200 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7037 (mm-30) outliers start: 24 outliers final: 20 residues processed: 119 average time/residue: 0.2039 time to fit residues: 34.7577 Evaluate side-chains 119 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.187081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158808 restraints weight = 25996.272| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.12 r_work: 0.3618 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8588 Z= 0.133 Angle : 0.500 5.748 11680 Z= 0.271 Chirality : 0.038 0.136 1340 Planarity : 0.004 0.063 1448 Dihedral : 6.473 63.522 1212 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.70 % Allowed : 13.63 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.26), residues: 1040 helix: 0.21 (0.20), residues: 662 sheet: -1.93 (0.53), residues: 86 loop : -1.43 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 232 TYR 0.008 0.001 TYR A 101 PHE 0.014 0.001 PHE A 218 TRP 0.016 0.001 TRP A 50 HIS 0.005 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8588) covalent geometry : angle 0.50027 (11680) hydrogen bonds : bond 0.03513 ( 496) hydrogen bonds : angle 3.99416 ( 1452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7196 (mtt) cc_final: 0.6437 (mmt) REVERT: A 90 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7548 (mp) REVERT: B 90 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7546 (mp) REVERT: B 249 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6909 (tt) REVERT: C 8 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7414 (mm-40) REVERT: C 200 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7036 (mm-30) REVERT: D 8 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7417 (mm-40) REVERT: D 59 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7254 (t0) REVERT: D 200 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7043 (mm-30) outliers start: 24 outliers final: 19 residues processed: 117 average time/residue: 0.2011 time to fit residues: 33.7082 Evaluate side-chains 116 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.188143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.159654 restraints weight = 26089.822| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.15 r_work: 0.3618 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8588 Z= 0.125 Angle : 0.493 5.958 11680 Z= 0.266 Chirality : 0.038 0.136 1340 Planarity : 0.004 0.036 1448 Dihedral : 6.400 61.556 1212 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.59 % Allowed : 13.40 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.26), residues: 1040 helix: 0.29 (0.20), residues: 662 sheet: -1.94 (0.53), residues: 86 loop : -1.42 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 232 TYR 0.008 0.001 TYR B 101 PHE 0.013 0.001 PHE A 218 TRP 0.016 0.001 TRP B 50 HIS 0.005 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8588) covalent geometry : angle 0.49304 (11680) hydrogen bonds : bond 0.03432 ( 496) hydrogen bonds : angle 3.94612 ( 1452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3421.98 seconds wall clock time: 58 minutes 47.41 seconds (3527.41 seconds total)