Starting phenix.real_space_refine on Tue Mar 3 20:06:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ran_24378/03_2026/7ran_24378.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ran_24378/03_2026/7ran_24378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ran_24378/03_2026/7ran_24378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ran_24378/03_2026/7ran_24378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ran_24378/03_2026/7ran_24378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ran_24378/03_2026/7ran_24378.map" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5425 2.51 5 N 1449 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8523 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2023 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1837 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2556 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 376 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'3IQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.69, per 1000 atoms: 0.20 Number of scatterers: 8523 At special positions: 0 Unit cell: (103.104, 106.513, 125.259, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1594 8.00 N 1449 7.00 C 5425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 313.6 milliseconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 14 sheets defined 37.1% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 79 through 102 removed outlier: 3.603A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 138 removed outlier: 4.250A pdb=" N MET A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 148 through 179 removed outlier: 3.618A pdb=" N ASN A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 186 Processing helix chain 'A' and resid 190 through 208 removed outlier: 3.929A pdb=" N LEU A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.320A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 213 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 217 " --> pdb=" O PHE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.600A pdb=" N VAL A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 266 removed outlier: 3.692A pdb=" N VAL A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 314 through 349 removed outlier: 3.719A pdb=" N CYS A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 4.007A pdb=" N ILE A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 383 removed outlier: 3.863A pdb=" N ASN A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Proline residue: A 377 - end of helix removed outlier: 3.636A pdb=" N TYR A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 397 Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.606A pdb=" N LYS B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.810A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.537A pdb=" N ALA B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.683A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.569A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.567A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.688A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.999A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.666A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.834A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 10 through 24 removed outlier: 3.840A pdb=" N LYS D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.883A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 70 through 76 removed outlier: 6.455A pdb=" N LEU B 34 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE B 84 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B 36 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.964A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.004A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.500A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.572A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP C 170 " --> pdb=" O GLN C 175 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C 175 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 191 removed outlier: 3.675A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.669A pdb=" N ALA C 242 " --> pdb=" O CYS C 233 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.652A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 33 through 35 removed outlier: 3.570A pdb=" N ARG E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB3, first strand: chain 'E' and resid 49 through 51 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.561A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 148 402 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2771 1.35 - 1.46: 2106 1.46 - 1.58: 3741 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 8698 Sorted by residual: bond pdb=" N ILE A 85 " pdb=" CA ILE A 85 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.52e+00 bond pdb=" N ILE A 93 " pdb=" CA ILE A 93 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.50e+00 bond pdb=" N ILE A 96 " pdb=" CA ILE A 96 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.14e+00 bond pdb=" N VAL A 150 " pdb=" CA VAL A 150 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.85e+00 bond pdb=" N ILE A 86 " pdb=" CA ILE A 86 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.84e+00 ... (remaining 8693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 11418 1.48 - 2.96: 346 2.96 - 4.44: 43 4.44 - 5.92: 12 5.92 - 7.40: 5 Bond angle restraints: 11824 Sorted by residual: angle pdb=" C ARG C 129 " pdb=" N GLU C 130 " pdb=" CA GLU C 130 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 angle pdb=" N GLU C 130 " pdb=" CA GLU C 130 " pdb=" CB GLU C 130 " ideal model delta sigma weight residual 110.49 116.36 -5.87 1.69e+00 3.50e-01 1.20e+01 angle pdb=" CA GLU C 130 " pdb=" CB GLU C 130 " pdb=" CG GLU C 130 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA VAL A 150 " pdb=" C VAL A 150 " pdb=" O VAL A 150 " ideal model delta sigma weight residual 120.95 117.80 3.15 1.04e+00 9.25e-01 9.16e+00 angle pdb=" N ASN A 343 " pdb=" CA ASN A 343 " pdb=" C ASN A 343 " ideal model delta sigma weight residual 111.07 107.87 3.20 1.07e+00 8.73e-01 8.97e+00 ... (remaining 11819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4742 17.82 - 35.64: 329 35.64 - 53.46: 57 53.46 - 71.28: 8 71.28 - 89.09: 3 Dihedral angle restraints: 5139 sinusoidal: 1893 harmonic: 3246 Sorted by residual: dihedral pdb=" CB CYS A 148 " pdb=" SG CYS A 148 " pdb=" SG CYS A 227 " pdb=" CB CYS A 227 " ideal model delta sinusoidal sigma weight residual -86.00 -175.09 89.09 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CA PRO A 209 " pdb=" C PRO A 209 " pdb=" N ILE A 210 " pdb=" CA ILE A 210 " ideal model delta harmonic sigma weight residual -180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 5136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1030 0.046 - 0.093: 244 0.093 - 0.139: 80 0.139 - 0.186: 11 0.186 - 0.232: 6 Chirality restraints: 1371 Sorted by residual: chirality pdb=" CA GLU C 130 " pdb=" N GLU C 130 " pdb=" C GLU C 130 " pdb=" CB GLU C 130 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA THR A 88 " pdb=" N THR A 88 " pdb=" C THR A 88 " pdb=" CB THR A 88 " both_signs ideal model delta sigma weight residual False 2.53 2.73 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB THR C 181 " pdb=" CA THR C 181 " pdb=" OG1 THR C 181 " pdb=" CG2 THR C 181 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1368 not shown) Planarity restraints: 1501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 208 " -0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO A 209 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 128 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 129 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 342 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C THR A 342 " -0.023 2.00e-02 2.50e+03 pdb=" O THR A 342 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A 343 " 0.008 2.00e-02 2.50e+03 ... (remaining 1498 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 75 2.65 - 3.21: 7636 3.21 - 3.78: 11833 3.78 - 4.34: 15572 4.34 - 4.90: 27288 Nonbonded interactions: 62404 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.091 3.040 nonbonded pdb=" OD1 ASN A 110 " pdb=" OH TYR A 387 " model vdw 2.150 3.040 nonbonded pdb=" OG SER E 192 " pdb=" OG1 THR E 203 " model vdw 2.215 3.040 nonbonded pdb=" OG SER C 281 " pdb=" O HIS D 44 " model vdw 2.317 3.040 nonbonded pdb=" O GLY E 9 " pdb=" NH1 ARG E 18 " model vdw 2.319 3.120 ... (remaining 62399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.520 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.003 0.035 8701 Z= 0.204 Angle : 0.627 7.395 11830 Z= 0.383 Chirality : 0.046 0.232 1371 Planarity : 0.004 0.088 1501 Dihedral : 12.453 79.829 3032 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.61 (0.25), residues: 1100 helix: 2.65 (0.26), residues: 380 sheet: -0.07 (0.32), residues: 259 loop : -1.29 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 31 TYR 0.011 0.001 TYR E 59 PHE 0.019 0.001 PHE A 240 TRP 0.013 0.001 TRP C 339 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8698) covalent geometry : angle 0.62499 (11824) SS BOND : bond 0.00527 ( 3) SS BOND : angle 2.05090 ( 6) hydrogen bonds : bond 0.15245 ( 402) hydrogen bonds : angle 4.95875 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.358 Fit side-chains REVERT: A 208 MET cc_start: 0.5954 (tpp) cc_final: 0.5544 (ttp) REVERT: B 166 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7732 (tm-30) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0881 time to fit residues: 18.0023 Evaluate side-chains 118 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 179 ASN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120775 restraints weight = 12453.408| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.40 r_work: 0.3246 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8701 Z= 0.134 Angle : 0.538 6.697 11830 Z= 0.290 Chirality : 0.042 0.148 1371 Planarity : 0.004 0.066 1501 Dihedral : 4.150 34.119 1216 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.12 % Allowed : 8.49 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.73 (0.25), residues: 1100 helix: 2.61 (0.26), residues: 384 sheet: 0.09 (0.32), residues: 271 loop : -1.20 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 168 TYR 0.010 0.001 TYR E 59 PHE 0.012 0.001 PHE A 240 TRP 0.010 0.001 TRP C 339 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8698) covalent geometry : angle 0.53742 (11824) SS BOND : bond 0.00697 ( 3) SS BOND : angle 0.95851 ( 6) hydrogen bonds : bond 0.05564 ( 402) hydrogen bonds : angle 4.04342 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.338 Fit side-chains REVERT: A 179 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7091 (p0) REVERT: B 82 HIS cc_start: 0.8231 (m-70) cc_final: 0.7958 (m-70) REVERT: B 166 GLU cc_start: 0.8697 (mm-30) cc_final: 0.7811 (tm-30) outliers start: 10 outliers final: 4 residues processed: 124 average time/residue: 0.0795 time to fit residues: 14.3530 Evaluate side-chains 109 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 75 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.150534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121805 restraints weight = 12401.185| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.45 r_work: 0.3254 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8701 Z= 0.118 Angle : 0.512 6.483 11830 Z= 0.277 Chirality : 0.041 0.149 1371 Planarity : 0.003 0.055 1501 Dihedral : 4.025 32.792 1216 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.45 % Allowed : 11.28 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1100 helix: 2.64 (0.26), residues: 386 sheet: 0.21 (0.32), residues: 271 loop : -1.20 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 168 TYR 0.009 0.001 TYR E 59 PHE 0.011 0.001 PHE C 241 TRP 0.008 0.001 TRP A 141 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8698) covalent geometry : angle 0.51174 (11824) SS BOND : bond 0.00589 ( 3) SS BOND : angle 0.81317 ( 6) hydrogen bonds : bond 0.05032 ( 402) hydrogen bonds : angle 3.86851 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.329 Fit side-chains REVERT: E 208 GLU cc_start: 0.8193 (pp20) cc_final: 0.7522 (pp20) outliers start: 13 outliers final: 6 residues processed: 111 average time/residue: 0.0865 time to fit residues: 13.7634 Evaluate side-chains 113 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121485 restraints weight = 12397.634| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.49 r_work: 0.3136 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8701 Z= 0.134 Angle : 0.529 6.428 11830 Z= 0.284 Chirality : 0.041 0.144 1371 Planarity : 0.004 0.053 1501 Dihedral : 4.094 33.821 1216 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.01 % Allowed : 11.96 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.79 (0.25), residues: 1100 helix: 2.55 (0.26), residues: 386 sheet: 0.27 (0.32), residues: 271 loop : -1.20 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 168 TYR 0.009 0.001 TYR E 59 PHE 0.013 0.001 PHE C 241 TRP 0.011 0.001 TRP A 141 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8698) covalent geometry : angle 0.52821 (11824) SS BOND : bond 0.00670 ( 3) SS BOND : angle 0.95592 ( 6) hydrogen bonds : bond 0.05374 ( 402) hydrogen bonds : angle 3.89518 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.324 Fit side-chains REVERT: A 120 ASP cc_start: 0.7820 (t0) cc_final: 0.7561 (t70) REVERT: A 208 MET cc_start: 0.5963 (tpt) cc_final: 0.5461 (ttp) REVERT: E 208 GLU cc_start: 0.8201 (pp20) cc_final: 0.7540 (pp20) outliers start: 18 outliers final: 9 residues processed: 112 average time/residue: 0.0861 time to fit residues: 13.9462 Evaluate side-chains 108 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.117459 restraints weight = 12458.791| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.54 r_work: 0.3106 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8701 Z= 0.162 Angle : 0.569 7.175 11830 Z= 0.307 Chirality : 0.043 0.157 1371 Planarity : 0.004 0.052 1501 Dihedral : 4.294 36.042 1216 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.68 % Allowed : 14.41 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.61 (0.25), residues: 1100 helix: 2.35 (0.26), residues: 386 sheet: 0.14 (0.32), residues: 277 loop : -1.23 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.009 0.001 TYR E 178 PHE 0.015 0.001 PHE C 241 TRP 0.012 0.001 TRP A 141 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8698) covalent geometry : angle 0.56899 (11824) SS BOND : bond 0.00740 ( 3) SS BOND : angle 1.13944 ( 6) hydrogen bonds : bond 0.06016 ( 402) hydrogen bonds : angle 4.01114 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.333 Fit side-chains REVERT: E 208 GLU cc_start: 0.8192 (pp20) cc_final: 0.7599 (pp20) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.0819 time to fit residues: 12.6748 Evaluate side-chains 109 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118973 restraints weight = 12272.398| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.50 r_work: 0.3129 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8701 Z= 0.136 Angle : 0.533 6.724 11830 Z= 0.288 Chirality : 0.042 0.143 1371 Planarity : 0.003 0.049 1501 Dihedral : 4.177 34.671 1216 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.45 % Allowed : 15.20 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1100 helix: 2.39 (0.26), residues: 386 sheet: 0.17 (0.32), residues: 276 loop : -1.21 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.008 0.001 TYR E 178 PHE 0.013 0.001 PHE C 241 TRP 0.012 0.001 TRP A 141 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8698) covalent geometry : angle 0.53270 (11824) SS BOND : bond 0.00640 ( 3) SS BOND : angle 0.95362 ( 6) hydrogen bonds : bond 0.05384 ( 402) hydrogen bonds : angle 3.91105 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.326 Fit side-chains REVERT: A 120 ASP cc_start: 0.7788 (t0) cc_final: 0.7457 (t0) REVERT: C 61 MET cc_start: 0.8392 (ppp) cc_final: 0.8167 (ptm) REVERT: E 208 GLU cc_start: 0.8212 (pp20) cc_final: 0.7563 (pp20) outliers start: 13 outliers final: 12 residues processed: 110 average time/residue: 0.0891 time to fit residues: 13.8597 Evaluate side-chains 109 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119512 restraints weight = 12307.929| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.49 r_work: 0.3125 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8701 Z= 0.137 Angle : 0.546 8.694 11830 Z= 0.291 Chirality : 0.042 0.150 1371 Planarity : 0.003 0.048 1501 Dihedral : 4.151 34.399 1216 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.79 % Allowed : 15.87 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1100 helix: 2.41 (0.26), residues: 386 sheet: 0.25 (0.32), residues: 269 loop : -1.27 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.009 0.001 TYR E 178 PHE 0.014 0.001 PHE E 68 TRP 0.012 0.001 TRP A 141 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8698) covalent geometry : angle 0.54561 (11824) SS BOND : bond 0.00651 ( 3) SS BOND : angle 0.96873 ( 6) hydrogen bonds : bond 0.05365 ( 402) hydrogen bonds : angle 3.88659 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.316 Fit side-chains REVERT: A 120 ASP cc_start: 0.7775 (t0) cc_final: 0.7466 (t0) REVERT: C 61 MET cc_start: 0.8377 (ppp) cc_final: 0.8158 (ptm) REVERT: E 208 GLU cc_start: 0.8207 (pp20) cc_final: 0.7583 (pp20) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.0638 time to fit residues: 10.2923 Evaluate side-chains 111 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 87 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120242 restraints weight = 12155.508| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.48 r_work: 0.3133 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8701 Z= 0.130 Angle : 0.534 7.254 11830 Z= 0.285 Chirality : 0.041 0.146 1371 Planarity : 0.003 0.047 1501 Dihedral : 4.091 33.691 1216 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.01 % Allowed : 16.31 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.72 (0.25), residues: 1100 helix: 2.47 (0.26), residues: 383 sheet: 0.29 (0.33), residues: 269 loop : -1.21 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 31 TYR 0.009 0.001 TYR E 178 PHE 0.013 0.001 PHE C 241 TRP 0.010 0.001 TRP A 141 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8698) covalent geometry : angle 0.53377 (11824) SS BOND : bond 0.00614 ( 3) SS BOND : angle 0.93862 ( 6) hydrogen bonds : bond 0.05123 ( 402) hydrogen bonds : angle 3.84373 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.313 Fit side-chains REVERT: A 120 ASP cc_start: 0.7776 (t0) cc_final: 0.7452 (t0) REVERT: A 164 MET cc_start: 0.8879 (mmm) cc_final: 0.8536 (mmm) REVERT: C 61 MET cc_start: 0.8366 (ppp) cc_final: 0.8151 (ptm) REVERT: E 208 GLU cc_start: 0.8218 (pp20) cc_final: 0.7599 (pp20) outliers start: 18 outliers final: 14 residues processed: 117 average time/residue: 0.0823 time to fit residues: 13.7771 Evaluate side-chains 115 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 166 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 0.0980 chunk 1 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121650 restraints weight = 12303.398| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.48 r_work: 0.3167 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8701 Z= 0.112 Angle : 0.514 7.703 11830 Z= 0.274 Chirality : 0.041 0.153 1371 Planarity : 0.003 0.046 1501 Dihedral : 3.945 31.880 1216 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.79 % Allowed : 16.76 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.88 (0.26), residues: 1100 helix: 2.60 (0.26), residues: 383 sheet: 0.39 (0.33), residues: 269 loop : -1.14 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.008 0.001 TYR E 178 PHE 0.011 0.001 PHE E 68 TRP 0.009 0.001 TRP A 141 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8698) covalent geometry : angle 0.51387 (11824) SS BOND : bond 0.00512 ( 3) SS BOND : angle 0.77733 ( 6) hydrogen bonds : bond 0.04517 ( 402) hydrogen bonds : angle 3.72350 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.319 Fit side-chains REVERT: A 120 ASP cc_start: 0.7751 (t0) cc_final: 0.7448 (t0) REVERT: A 164 MET cc_start: 0.8883 (mmm) cc_final: 0.8562 (mmm) REVERT: C 61 MET cc_start: 0.8314 (ppp) cc_final: 0.8112 (ptm) REVERT: D 38 MET cc_start: 0.6856 (ptm) cc_final: 0.6472 (ptp) REVERT: E 208 GLU cc_start: 0.8206 (pp20) cc_final: 0.7577 (pp20) outliers start: 16 outliers final: 14 residues processed: 118 average time/residue: 0.0886 time to fit residues: 14.8490 Evaluate side-chains 121 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 74 optimal weight: 0.0870 chunk 100 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121564 restraints weight = 12231.039| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.55 r_work: 0.3147 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8701 Z= 0.117 Angle : 0.523 7.630 11830 Z= 0.278 Chirality : 0.041 0.164 1371 Planarity : 0.003 0.046 1501 Dihedral : 3.948 32.168 1216 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.68 % Allowed : 17.09 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.88 (0.26), residues: 1100 helix: 2.59 (0.26), residues: 384 sheet: 0.39 (0.33), residues: 270 loop : -1.14 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 31 TYR 0.009 0.001 TYR E 178 PHE 0.016 0.001 PHE E 68 TRP 0.009 0.001 TRP A 141 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8698) covalent geometry : angle 0.52292 (11824) SS BOND : bond 0.00562 ( 3) SS BOND : angle 0.85194 ( 6) hydrogen bonds : bond 0.04668 ( 402) hydrogen bonds : angle 3.72960 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.224 Fit side-chains REVERT: A 120 ASP cc_start: 0.7760 (t0) cc_final: 0.7458 (t0) REVERT: A 164 MET cc_start: 0.8876 (mmm) cc_final: 0.8553 (mmm) REVERT: A 208 MET cc_start: 0.5889 (tpt) cc_final: 0.5300 (ttp) REVERT: B 77 ASP cc_start: 0.8129 (t0) cc_final: 0.7776 (m-30) REVERT: C 61 MET cc_start: 0.8346 (ppp) cc_final: 0.8137 (ptm) REVERT: D 38 MET cc_start: 0.6848 (ptm) cc_final: 0.6461 (ptp) REVERT: E 208 GLU cc_start: 0.8195 (pp20) cc_final: 0.7557 (pp20) outliers start: 15 outliers final: 14 residues processed: 119 average time/residue: 0.0870 time to fit residues: 14.5920 Evaluate side-chains 122 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 82 optimal weight: 0.0040 chunk 31 optimal weight: 4.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.150587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121119 restraints weight = 12338.521| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.51 r_work: 0.3162 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8701 Z= 0.117 Angle : 0.535 12.139 11830 Z= 0.281 Chirality : 0.041 0.167 1371 Planarity : 0.003 0.046 1501 Dihedral : 3.933 32.096 1216 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.56 % Allowed : 17.77 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.88 (0.26), residues: 1100 helix: 2.59 (0.26), residues: 385 sheet: 0.39 (0.33), residues: 270 loop : -1.14 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 31 TYR 0.009 0.001 TYR E 178 PHE 0.015 0.001 PHE E 68 TRP 0.014 0.001 TRP A 141 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8698) covalent geometry : angle 0.53474 (11824) SS BOND : bond 0.00548 ( 3) SS BOND : angle 0.82331 ( 6) hydrogen bonds : bond 0.04591 ( 402) hydrogen bonds : angle 3.73745 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1826.29 seconds wall clock time: 31 minutes 57.87 seconds (1917.87 seconds total)