Starting phenix.real_space_refine on Wed Jun 11 03:43:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t8x_25748/06_2025/7t8x_25748_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t8x_25748/06_2025/7t8x_25748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t8x_25748/06_2025/7t8x_25748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t8x_25748/06_2025/7t8x_25748.map" model { file = "/net/cci-nas-00/data/ceres_data/7t8x_25748/06_2025/7t8x_25748_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t8x_25748/06_2025/7t8x_25748_neut.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4680 atoms to isotropic. 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 59 5.16 5 C 5468 2.51 5 N 1442 2.21 5 O 1586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8555 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2148 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1706 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2541 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 403 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1747 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.86, per 1000 atoms: 0.68 Number of scatterers: 8555 At special positions: 0 Unit cell: (90.95, 121.55, 125.8, 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 59 16.00 O 1586 8.00 N 1442 7.00 C 5468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 981.3 milliseconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 36.9% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 21 through 51 Processing helix chain 'A' and resid 59 through 87 Processing helix chain 'A' and resid 91 through 127 removed outlier: 4.366A pdb=" N VAL A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 removed outlier: 4.577A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 167 removed outlier: 3.641A pdb=" N ALA A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) Proline residue: A 157 - end of helix removed outlier: 5.659A pdb=" N GLN A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.713A pdb=" N PHE A 181 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 182 " --> pdb=" O GLN A 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 178 through 182' Processing helix chain 'A' and resid 183 through 212 removed outlier: 4.096A pdb=" N THR A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Proline residue: A 198 - end of helix Processing helix chain 'A' and resid 380 through 413 removed outlier: 3.875A pdb=" N THR A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Proline residue: A 402 - end of helix removed outlier: 3.520A pdb=" N MET A 406 " --> pdb=" O PRO A 402 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 432 removed outlier: 3.870A pdb=" N TRP A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 444 through 452 removed outlier: 3.942A pdb=" N LYS A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 30 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.744A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.730A pdb=" N LYS B 211 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 removed outlier: 3.774A pdb=" N GLU B 217 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 271 through 282 removed outlier: 3.665A pdb=" N PHE B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 4.127A pdb=" N ILE B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 331 through 352 removed outlier: 3.747A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 removed outlier: 3.552A pdb=" N ALA C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 29 through 43 removed outlier: 4.103A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.727A pdb=" N PHE B 190 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 199 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39 removed outlier: 5.970A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.648A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.789A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.564A pdb=" N THR C 102 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY C 115 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.925A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.688A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.607A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS C 250 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.335A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.641A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.634A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.502A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1161 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: 2.36 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1369 1.29 - 1.42: 2342 1.42 - 1.55: 4944 1.55 - 1.68: 1 1.68 - 1.81: 85 Bond restraints: 8741 Sorted by residual: bond pdb=" C LEU A 428 " pdb=" O LEU A 428 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.15e-02 7.56e+03 2.00e+01 bond pdb=" C2 ACH A 501 " pdb=" N1 ACH A 501 " ideal model delta sigma weight residual 1.506 1.421 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C9 ACH A 501 " pdb=" N1 ACH A 501 " ideal model delta sigma weight residual 1.492 1.413 0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C10 ACH A 501 " pdb=" N1 ACH A 501 " ideal model delta sigma weight residual 1.491 1.417 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C8 ACH A 501 " pdb=" N1 ACH A 501 " ideal model delta sigma weight residual 1.490 1.420 0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 8736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 11685 2.32 - 4.64: 178 4.64 - 6.96: 24 6.96 - 9.29: 6 9.29 - 11.61: 1 Bond angle restraints: 11894 Sorted by residual: angle pdb=" C GLU B 8 " pdb=" N ASP B 9 " pdb=" CA ASP B 9 " ideal model delta sigma weight residual 121.70 133.31 -11.61 1.80e+00 3.09e-01 4.16e+01 angle pdb=" N ILE A 424 " pdb=" CA ILE A 424 " pdb=" C ILE A 424 " ideal model delta sigma weight residual 110.62 104.18 6.44 1.02e+00 9.61e-01 3.99e+01 angle pdb=" N LEU A 428 " pdb=" CA LEU A 428 " pdb=" C LEU A 428 " ideal model delta sigma weight residual 111.07 104.72 6.35 1.07e+00 8.73e-01 3.52e+01 angle pdb=" N TYR A 426 " pdb=" CA TYR A 426 " pdb=" C TYR A 426 " ideal model delta sigma weight residual 111.71 105.14 6.57 1.15e+00 7.56e-01 3.26e+01 angle pdb=" C ILE C 37 " pdb=" N ASP C 38 " pdb=" CA ASP C 38 " ideal model delta sigma weight residual 121.20 128.46 -7.26 1.40e+00 5.10e-01 2.69e+01 ... (remaining 11889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4708 17.93 - 35.86: 356 35.86 - 53.79: 50 53.79 - 71.72: 8 71.72 - 89.64: 4 Dihedral angle restraints: 5126 sinusoidal: 1864 harmonic: 3262 Sorted by residual: dihedral pdb=" CA TYR E 190 " pdb=" C TYR E 190 " pdb=" N ARG E 191 " pdb=" CA ARG E 191 " ideal model delta harmonic sigma weight residual 180.00 156.14 23.86 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA PRO A 90 " pdb=" C PRO A 90 " pdb=" N LEU A 91 " pdb=" CA LEU A 91 " ideal model delta harmonic sigma weight residual -180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LYS A 127 " pdb=" C LYS A 127 " pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1125 0.057 - 0.113: 219 0.113 - 0.170: 27 0.170 - 0.226: 8 0.226 - 0.283: 2 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA ASP E 74 " pdb=" N ASP E 74 " pdb=" C ASP E 74 " pdb=" CB ASP E 74 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA LYS B 193 " pdb=" N LYS B 193 " pdb=" C LYS B 193 " pdb=" CB LYS B 193 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ASN B 194 " pdb=" N ASN B 194 " pdb=" C ASN B 194 " pdb=" CB ASN B 194 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1378 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 426 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C TYR A 426 " 0.047 2.00e-02 2.50e+03 pdb=" O TYR A 426 " -0.018 2.00e-02 2.50e+03 pdb=" N TRP A 427 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 426 " -0.025 2.00e-02 2.50e+03 1.75e-02 6.15e+00 pdb=" CG TYR A 426 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 426 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 426 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 426 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 426 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 426 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 426 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 193 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" C ALA A 193 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA A 193 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 194 " -0.014 2.00e-02 2.50e+03 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 83 2.63 - 3.20: 7535 3.20 - 3.77: 12419 3.77 - 4.33: 17219 4.33 - 4.90: 29482 Nonbonded interactions: 66738 Sorted by model distance: nonbonded pdb=" O LYS B 193 " pdb=" OD1 ASN B 194 " model vdw 2.063 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.120 3.040 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.146 3.040 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.173 3.040 nonbonded pdb=" NH1 ARG B 15 " pdb=" O VAL C 90 " model vdw 2.216 3.120 ... (remaining 66733 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.950 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 0.085 8744 Z= 0.241 Angle : 0.719 11.607 11900 Z= 0.441 Chirality : 0.048 0.283 1381 Planarity : 0.004 0.044 1496 Dihedral : 12.834 89.645 3015 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1108 helix: 1.65 (0.28), residues: 367 sheet: -0.36 (0.32), residues: 269 loop : -1.05 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 427 HIS 0.006 0.001 HIS B 189 PHE 0.020 0.001 PHE C 234 TYR 0.042 0.001 TYR A 426 ARG 0.009 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.19796 ( 406) hydrogen bonds : angle 7.08190 ( 1161) SS BOND : bond 0.00384 ( 3) SS BOND : angle 0.67608 ( 6) covalent geometry : bond 0.00445 ( 8741) covalent geometry : angle 0.71927 (11894) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.7797 (tt) cc_final: 0.7591 (tt) REVERT: B 48 THR cc_start: 0.8525 (m) cc_final: 0.8254 (t) REVERT: B 231 TYR cc_start: 0.6107 (m-10) cc_final: 0.5787 (m-10) REVERT: E 77 ASN cc_start: 0.8164 (p0) cc_final: 0.7925 (p0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2243 time to fit residues: 43.3454 Evaluate side-chains 111 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 0.0770 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.0470 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN E 113 GLN E 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.117656 restraints weight = 10698.530| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.91 r_work: 0.3177 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8744 Z= 0.131 Angle : 0.580 11.221 11900 Z= 0.314 Chirality : 0.044 0.224 1381 Planarity : 0.004 0.044 1496 Dihedral : 4.724 52.739 1210 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.34 % Allowed : 7.24 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1108 helix: 1.86 (0.28), residues: 374 sheet: -0.17 (0.32), residues: 276 loop : -1.08 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS B 189 PHE 0.021 0.001 PHE A 180 TYR 0.021 0.001 TYR A 131 ARG 0.006 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 406) hydrogen bonds : angle 4.98822 ( 1161) SS BOND : bond 0.00510 ( 3) SS BOND : angle 1.05477 ( 6) covalent geometry : bond 0.00280 ( 8741) covalent geometry : angle 0.57916 (11894) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.7799 (tt) cc_final: 0.7550 (tt) REVERT: A 188 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6113 (t80) REVERT: A 426 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7011 (m-80) REVERT: B 48 THR cc_start: 0.8742 (m) cc_final: 0.8512 (t) REVERT: B 231 TYR cc_start: 0.6310 (m-10) cc_final: 0.5997 (m-10) REVERT: C 268 ASN cc_start: 0.8098 (t0) cc_final: 0.7864 (t0) REVERT: D 36 ASP cc_start: 0.8428 (m-30) cc_final: 0.8178 (m-30) REVERT: E 77 ASN cc_start: 0.8052 (p0) cc_final: 0.7765 (p0) outliers start: 12 outliers final: 4 residues processed: 127 average time/residue: 0.2159 time to fit residues: 37.8263 Evaluate side-chains 116 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 0.0370 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119710 restraints weight = 11132.039| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.89 r_work: 0.3181 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8744 Z= 0.123 Angle : 0.548 11.191 11900 Z= 0.297 Chirality : 0.043 0.193 1381 Planarity : 0.004 0.043 1496 Dihedral : 4.491 47.626 1210 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.67 % Allowed : 9.69 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1108 helix: 1.91 (0.27), residues: 379 sheet: -0.01 (0.32), residues: 271 loop : -1.03 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS B 322 PHE 0.017 0.001 PHE A 180 TYR 0.022 0.001 TYR B 297 ARG 0.004 0.000 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 406) hydrogen bonds : angle 4.66675 ( 1161) SS BOND : bond 0.00553 ( 3) SS BOND : angle 0.95442 ( 6) covalent geometry : bond 0.00270 ( 8741) covalent geometry : angle 0.54810 (11894) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.7211 (tpp) cc_final: 0.6965 (mmp) REVERT: A 150 LEU cc_start: 0.7764 (tt) cc_final: 0.7478 (tt) REVERT: A 188 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.6164 (t80) REVERT: A 426 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: B 231 TYR cc_start: 0.6308 (m-10) cc_final: 0.6035 (m-10) REVERT: C 268 ASN cc_start: 0.8101 (t0) cc_final: 0.7768 (t0) REVERT: D 36 ASP cc_start: 0.8431 (m-30) cc_final: 0.8193 (m-30) outliers start: 15 outliers final: 5 residues processed: 122 average time/residue: 0.1990 time to fit residues: 33.9358 Evaluate side-chains 112 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN C 17 GLN C 340 ASN E 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113992 restraints weight = 10906.073| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.08 r_work: 0.3114 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8744 Z= 0.186 Angle : 0.611 11.504 11900 Z= 0.327 Chirality : 0.045 0.211 1381 Planarity : 0.004 0.045 1496 Dihedral : 4.764 51.593 1210 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.12 % Allowed : 11.92 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1108 helix: 1.76 (0.27), residues: 380 sheet: 0.00 (0.32), residues: 278 loop : -1.08 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.004 0.001 HIS C 142 PHE 0.021 0.002 PHE A 180 TYR 0.021 0.002 TYR B 297 ARG 0.004 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.04985 ( 406) hydrogen bonds : angle 4.65413 ( 1161) SS BOND : bond 0.00691 ( 3) SS BOND : angle 1.24167 ( 6) covalent geometry : bond 0.00441 ( 8741) covalent geometry : angle 0.61032 (11894) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 1.016 Fit side-chains REVERT: A 139 MET cc_start: 0.7165 (tpp) cc_final: 0.6963 (mmp) REVERT: A 188 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.6158 (t80) REVERT: A 426 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: B 266 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8448 (mt) REVERT: C 268 ASN cc_start: 0.8136 (t0) cc_final: 0.7808 (t0) REVERT: D 36 ASP cc_start: 0.8472 (m-30) cc_final: 0.8177 (m-30) REVERT: E 77 ASN cc_start: 0.8067 (p0) cc_final: 0.7798 (p0) outliers start: 19 outliers final: 10 residues processed: 123 average time/residue: 0.2044 time to fit residues: 35.0230 Evaluate side-chains 113 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113355 restraints weight = 10938.994| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.96 r_work: 0.3109 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8744 Z= 0.177 Angle : 0.608 11.415 11900 Z= 0.326 Chirality : 0.045 0.209 1381 Planarity : 0.004 0.045 1496 Dihedral : 4.780 51.202 1210 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.78 % Allowed : 14.03 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1108 helix: 1.70 (0.27), residues: 382 sheet: -0.07 (0.31), residues: 278 loop : -1.09 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 82 HIS 0.003 0.001 HIS B 322 PHE 0.022 0.001 PHE A 180 TYR 0.022 0.001 TYR B 297 ARG 0.004 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.04852 ( 406) hydrogen bonds : angle 4.61344 ( 1161) SS BOND : bond 0.00702 ( 3) SS BOND : angle 1.18039 ( 6) covalent geometry : bond 0.00420 ( 8741) covalent geometry : angle 0.60725 (11894) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.893 Fit side-chains REVERT: A 139 MET cc_start: 0.7135 (tpp) cc_final: 0.6926 (mmp) REVERT: A 188 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.6166 (t80) REVERT: A 426 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: C 75 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7423 (mt0) REVERT: C 268 ASN cc_start: 0.8028 (t0) cc_final: 0.7742 (t0) REVERT: D 36 ASP cc_start: 0.8447 (m-30) cc_final: 0.8214 (m-30) REVERT: E 77 ASN cc_start: 0.8076 (p0) cc_final: 0.7787 (p0) outliers start: 16 outliers final: 10 residues processed: 113 average time/residue: 0.1943 time to fit residues: 31.1866 Evaluate side-chains 112 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 21 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN C 17 GLN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.116098 restraints weight = 10756.905| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.91 r_work: 0.3151 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8744 Z= 0.128 Angle : 0.555 11.310 11900 Z= 0.300 Chirality : 0.043 0.219 1381 Planarity : 0.004 0.043 1496 Dihedral : 4.554 49.186 1210 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.67 % Allowed : 15.92 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1108 helix: 1.86 (0.27), residues: 381 sheet: -0.04 (0.31), residues: 278 loop : -1.04 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS B 322 PHE 0.019 0.001 PHE A 180 TYR 0.021 0.001 TYR B 297 ARG 0.003 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 406) hydrogen bonds : angle 4.46271 ( 1161) SS BOND : bond 0.00587 ( 3) SS BOND : angle 0.95427 ( 6) covalent geometry : bond 0.00285 ( 8741) covalent geometry : angle 0.55497 (11894) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.851 Fit side-chains REVERT: A 139 MET cc_start: 0.7202 (tpp) cc_final: 0.6982 (mmp) REVERT: A 188 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.6228 (t80) REVERT: A 426 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: B 266 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8475 (mt) REVERT: C 268 ASN cc_start: 0.8032 (t0) cc_final: 0.7749 (t0) REVERT: D 36 ASP cc_start: 0.8406 (m-30) cc_final: 0.8165 (m-30) REVERT: E 77 ASN cc_start: 0.8003 (p0) cc_final: 0.7679 (p0) outliers start: 15 outliers final: 7 residues processed: 117 average time/residue: 0.1989 time to fit residues: 32.6516 Evaluate side-chains 113 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN C 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111368 restraints weight = 10885.001| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.08 r_work: 0.3082 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8744 Z= 0.227 Angle : 0.652 11.654 11900 Z= 0.348 Chirality : 0.047 0.248 1381 Planarity : 0.005 0.046 1496 Dihedral : 4.974 53.137 1210 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.45 % Allowed : 15.37 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1108 helix: 1.67 (0.27), residues: 379 sheet: -0.32 (0.31), residues: 278 loop : -1.12 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.004 0.001 HIS C 142 PHE 0.022 0.002 PHE A 180 TYR 0.022 0.002 TYR B 297 ARG 0.005 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 406) hydrogen bonds : angle 4.62746 ( 1161) SS BOND : bond 0.00829 ( 3) SS BOND : angle 1.29305 ( 6) covalent geometry : bond 0.00548 ( 8741) covalent geometry : angle 0.65133 (11894) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.858 Fit side-chains REVERT: A 54 LEU cc_start: 0.7123 (mt) cc_final: 0.6880 (mp) REVERT: A 139 MET cc_start: 0.7114 (tpp) cc_final: 0.6906 (mmp) REVERT: A 188 PHE cc_start: 0.6613 (OUTLIER) cc_final: 0.6140 (t80) REVERT: A 426 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7200 (m-80) REVERT: A 427 TRP cc_start: 0.7102 (OUTLIER) cc_final: 0.6435 (t60) REVERT: B 14 GLU cc_start: 0.8223 (tt0) cc_final: 0.8000 (tt0) REVERT: B 266 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8423 (mt) REVERT: C 75 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7485 (mt0) REVERT: C 268 ASN cc_start: 0.8061 (t0) cc_final: 0.7783 (t0) REVERT: D 36 ASP cc_start: 0.8441 (m-30) cc_final: 0.8151 (m-30) outliers start: 22 outliers final: 12 residues processed: 119 average time/residue: 0.2046 time to fit residues: 34.3517 Evaluate side-chains 115 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114599 restraints weight = 10915.581| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.02 r_work: 0.3132 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8744 Z= 0.128 Angle : 0.570 11.217 11900 Z= 0.307 Chirality : 0.044 0.230 1381 Planarity : 0.004 0.044 1496 Dihedral : 4.648 48.700 1210 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.12 % Allowed : 16.04 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1108 helix: 1.89 (0.27), residues: 380 sheet: -0.15 (0.31), residues: 278 loop : -1.11 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS B 322 PHE 0.018 0.001 PHE A 180 TYR 0.022 0.001 TYR B 297 ARG 0.002 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 406) hydrogen bonds : angle 4.44273 ( 1161) SS BOND : bond 0.00601 ( 3) SS BOND : angle 0.99921 ( 6) covalent geometry : bond 0.00282 ( 8741) covalent geometry : angle 0.56975 (11894) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.049 Fit side-chains REVERT: A 54 LEU cc_start: 0.7074 (mt) cc_final: 0.6825 (mp) REVERT: A 139 MET cc_start: 0.7218 (tpp) cc_final: 0.6793 (mmt) REVERT: A 188 PHE cc_start: 0.6564 (OUTLIER) cc_final: 0.6145 (t80) REVERT: A 218 LYS cc_start: 0.7595 (tttt) cc_final: 0.6428 (pttm) REVERT: A 426 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7171 (m-80) REVERT: B 266 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8455 (mt) REVERT: C 75 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: C 268 ASN cc_start: 0.8072 (t0) cc_final: 0.7761 (t0) REVERT: D 36 ASP cc_start: 0.8383 (m-30) cc_final: 0.8117 (m-30) outliers start: 19 outliers final: 12 residues processed: 116 average time/residue: 0.2130 time to fit residues: 35.0059 Evaluate side-chains 116 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.0370 chunk 76 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 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 = 0.3771 r_free = 0.3771 target = 0.152776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117127 restraints weight = 10907.902| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.98 r_work: 0.3161 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8744 Z= 0.120 Angle : 0.555 11.346 11900 Z= 0.299 Chirality : 0.043 0.225 1381 Planarity : 0.004 0.043 1496 Dihedral : 4.419 45.459 1210 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.67 % Allowed : 16.59 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1108 helix: 1.99 (0.27), residues: 381 sheet: -0.02 (0.31), residues: 272 loop : -1.08 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.004 0.001 HIS B 322 PHE 0.017 0.001 PHE A 180 TYR 0.022 0.001 TYR B 297 ARG 0.003 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 406) hydrogen bonds : angle 4.31873 ( 1161) SS BOND : bond 0.00544 ( 3) SS BOND : angle 0.91684 ( 6) covalent geometry : bond 0.00263 ( 8741) covalent geometry : angle 0.55461 (11894) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.976 Fit side-chains REVERT: A 54 LEU cc_start: 0.7218 (mt) cc_final: 0.6954 (mp) REVERT: A 139 MET cc_start: 0.7261 (tpp) cc_final: 0.7037 (mmp) REVERT: A 188 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6257 (t80) REVERT: A 218 LYS cc_start: 0.7551 (tttt) cc_final: 0.6468 (pttm) REVERT: A 426 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: B 266 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8445 (mt) REVERT: C 75 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7365 (mt0) REVERT: C 268 ASN cc_start: 0.8021 (t0) cc_final: 0.7719 (t0) outliers start: 15 outliers final: 11 residues processed: 120 average time/residue: 0.2840 time to fit residues: 47.3793 Evaluate side-chains 120 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 22 optimal weight: 0.0060 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 0.7496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122091 restraints weight = 11070.152| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.21 r_work: 0.3267 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8744 Z= 0.130 Angle : 0.565 11.192 11900 Z= 0.304 Chirality : 0.044 0.223 1381 Planarity : 0.004 0.044 1496 Dihedral : 4.454 46.421 1210 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.89 % Allowed : 16.37 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1108 helix: 1.96 (0.27), residues: 381 sheet: -0.01 (0.31), residues: 272 loop : -1.05 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS B 322 PHE 0.017 0.001 PHE A 180 TYR 0.022 0.001 TYR B 297 ARG 0.002 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 406) hydrogen bonds : angle 4.32661 ( 1161) SS BOND : bond 0.00578 ( 3) SS BOND : angle 0.98545 ( 6) covalent geometry : bond 0.00292 ( 8741) covalent geometry : angle 0.56516 (11894) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.876 Fit side-chains REVERT: A 54 LEU cc_start: 0.7183 (mt) cc_final: 0.6909 (mp) REVERT: A 139 MET cc_start: 0.7209 (tpp) cc_final: 0.6952 (mmp) REVERT: A 188 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.6085 (t80) REVERT: A 218 LYS cc_start: 0.7527 (tttt) cc_final: 0.6423 (pttm) REVERT: A 426 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: B 266 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8403 (mt) REVERT: C 75 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7238 (mt0) REVERT: C 268 ASN cc_start: 0.8115 (t0) cc_final: 0.7781 (t0) outliers start: 17 outliers final: 13 residues processed: 121 average time/residue: 0.2196 time to fit residues: 37.5869 Evaluate side-chains 120 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 4 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.157888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119891 restraints weight = 11113.539| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.20 r_work: 0.3245 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8744 Z= 0.143 Angle : 0.584 11.366 11900 Z= 0.315 Chirality : 0.045 0.227 1381 Planarity : 0.004 0.044 1496 Dihedral : 4.522 47.497 1210 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.89 % Allowed : 17.04 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1108 helix: 1.90 (0.27), residues: 381 sheet: -0.06 (0.31), residues: 277 loop : -1.02 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS B 322 PHE 0.018 0.001 PHE A 180 TYR 0.023 0.001 TYR B 297 ARG 0.003 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 406) hydrogen bonds : angle 4.37875 ( 1161) SS BOND : bond 0.00613 ( 3) SS BOND : angle 1.04271 ( 6) covalent geometry : bond 0.00328 ( 8741) covalent geometry : angle 0.58399 (11894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5472.28 seconds wall clock time: 96 minutes 42.14 seconds (5802.14 seconds total)