Starting phenix.real_space_refine on Wed Mar 4 08:59:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t8x_25748/03_2026/7t8x_25748_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t8x_25748/03_2026/7t8x_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 { model { file = "/net/cci-nas-00/data/ceres_data/7t8x_25748/03_2026/7t8x_25748_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t8x_25748/03_2026/7t8x_25748_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t8x_25748/03_2026/7t8x_25748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t8x_25748/03_2026/7t8x_25748.map" } resolution = 3.21 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= -0.004 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): 0.00s 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: 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, 'ASP:plan': 1, 'GLU: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: {'GLU:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} 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: {'ARG:plan': 2, 'GLU:plan': 1} 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, 'ASP:plan': 1, 'ARG:plan': 2} 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: 2.08, per 1000 atoms: 0.24 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: 0.65 Conformation dependent library (CDL) restraints added in 291.1 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: 0.28 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: 1.30 Time building geometry restraints manager: 0.89 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.460 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- 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 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: 0.02 (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 ARG 0.009 0.001 ARG B 209 TYR 0.042 0.001 TYR A 426 PHE 0.020 0.001 PHE C 234 TRP 0.023 0.002 TRP A 427 HIS 0.006 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8741) covalent geometry : angle 0.71927 (11894) SS BOND : bond 0.00384 ( 3) SS BOND : angle 0.67608 ( 6) hydrogen bonds : bond 0.19796 ( 406) hydrogen bonds : angle 7.08190 ( 1161) *********************** 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 : 0.298 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.7798 (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: 0.0969 time to fit residues: 18.8251 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 : 0.261 ------------------------------------------------------------------------------- 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: 0.4980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 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 = 0.3764 r_free = 0.3764 target = 0.151898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116146 restraints weight = 10864.070| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.91 r_work: 0.3153 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8744 Z= 0.160 Angle : 0.610 11.382 11900 Z= 0.329 Chirality : 0.045 0.234 1381 Planarity : 0.005 0.045 1496 Dihedral : 4.864 53.902 1210 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.45 % Allowed : 7.46 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % 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: 0.15 (0.26), residues: 1108 helix: 1.78 (0.27), residues: 376 sheet: -0.18 (0.32), residues: 276 loop : -1.13 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 209 TYR 0.021 0.002 TYR A 131 PHE 0.022 0.001 PHE A 180 TRP 0.019 0.001 TRP C 82 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8741) covalent geometry : angle 0.60952 (11894) SS BOND : bond 0.00659 ( 3) SS BOND : angle 1.12289 ( 6) hydrogen bonds : bond 0.05090 ( 406) hydrogen bonds : angle 5.00410 ( 1161) *********************** 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 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 131 TYR cc_start: 0.7533 (t80) cc_final: 0.7325 (t80) REVERT: A 150 LEU cc_start: 0.7818 (tt) cc_final: 0.7566 (tt) REVERT: A 188 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.6041 (t80) REVERT: A 426 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: B 48 THR cc_start: 0.8744 (m) cc_final: 0.8501 (t) REVERT: C 268 ASN cc_start: 0.8112 (t0) cc_final: 0.7875 (t0) REVERT: D 36 ASP cc_start: 0.8422 (m-30) cc_final: 0.8087 (m-30) REVERT: E 77 ASN cc_start: 0.8052 (p0) cc_final: 0.7783 (p0) REVERT: E 183 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7913 (mt0) outliers start: 13 outliers final: 4 residues processed: 127 average time/residue: 0.0906 time to fit residues: 15.9150 Evaluate side-chains 119 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 183 GLN 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 41 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.153261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117108 restraints weight = 10822.823| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.90 r_work: 0.3172 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8744 Z= 0.120 Angle : 0.549 11.190 11900 Z= 0.297 Chirality : 0.043 0.194 1381 Planarity : 0.004 0.044 1496 Dihedral : 4.563 47.971 1210 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.11 % Allowed : 10.58 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % 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: 0.32 (0.26), residues: 1108 helix: 1.88 (0.27), residues: 379 sheet: 0.01 (0.32), residues: 271 loop : -1.08 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 209 TYR 0.021 0.001 TYR B 297 PHE 0.017 0.001 PHE A 447 TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8741) covalent geometry : angle 0.54826 (11894) SS BOND : bond 0.00556 ( 3) SS BOND : angle 0.93202 ( 6) hydrogen bonds : bond 0.04382 ( 406) hydrogen bonds : angle 4.70464 ( 1161) *********************** 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 126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.277 Fit side-chains REVERT: A 139 MET cc_start: 0.7208 (tpp) cc_final: 0.6948 (mmp) REVERT: A 150 LEU cc_start: 0.7744 (tt) cc_final: 0.7472 (tt) REVERT: A 188 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.6130 (t80) REVERT: A 426 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: B 231 TYR cc_start: 0.6280 (m-10) cc_final: 0.5948 (m-10) REVERT: C 268 ASN cc_start: 0.8117 (t0) cc_final: 0.7793 (t0) REVERT: D 36 ASP cc_start: 0.8438 (m-30) cc_final: 0.8177 (m-30) outliers start: 10 outliers final: 4 residues processed: 124 average time/residue: 0.0854 time to fit residues: 14.6923 Evaluate side-chains 112 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 76 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- 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 ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN E 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116033 restraints weight = 11100.949| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.03 r_work: 0.3142 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8744 Z= 0.153 Angle : 0.576 11.394 11900 Z= 0.310 Chirality : 0.044 0.206 1381 Planarity : 0.004 0.044 1496 Dihedral : 4.622 49.839 1210 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.12 % Allowed : 12.14 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % 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: 0.31 (0.26), residues: 1108 helix: 1.80 (0.27), residues: 382 sheet: -0.01 (0.32), residues: 280 loop : -1.05 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.018 0.001 TYR B 297 PHE 0.018 0.001 PHE A 180 TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8741) covalent geometry : angle 0.57582 (11894) SS BOND : bond 0.00622 ( 3) SS BOND : angle 1.11933 ( 6) hydrogen bonds : bond 0.04605 ( 406) hydrogen bonds : angle 4.60284 ( 1161) *********************** 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 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.238 Fit side-chains REVERT: A 139 MET cc_start: 0.7138 (tpp) cc_final: 0.6900 (mmp) REVERT: A 150 LEU cc_start: 0.7771 (tt) cc_final: 0.7441 (tt) REVERT: A 179 GLN cc_start: 0.7323 (tt0) cc_final: 0.7098 (tt0) REVERT: A 188 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.6124 (t80) REVERT: A 426 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7011 (m-80) REVERT: B 266 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8433 (mt) REVERT: C 268 ASN cc_start: 0.8122 (t0) cc_final: 0.7785 (t0) REVERT: D 36 ASP cc_start: 0.8441 (m-30) cc_final: 0.8139 (m-30) outliers start: 19 outliers final: 10 residues processed: 128 average time/residue: 0.0855 time to fit residues: 15.2693 Evaluate side-chains 118 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 0.0980 chunk 27 optimal weight: 0.6980 chunk 84 optimal weight: 0.0770 chunk 16 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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** C 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.154081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118184 restraints weight = 10867.346| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.95 r_work: 0.3179 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8744 Z= 0.114 Angle : 0.543 11.096 11900 Z= 0.293 Chirality : 0.043 0.193 1381 Planarity : 0.004 0.043 1496 Dihedral : 4.380 46.468 1210 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.11 % Allowed : 13.81 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % 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: 0.43 (0.26), residues: 1108 helix: 1.94 (0.27), residues: 381 sheet: 0.12 (0.32), residues: 276 loop : -1.05 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.022 0.001 TYR B 297 PHE 0.016 0.001 PHE A 180 TRP 0.018 0.001 TRP C 82 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8741) covalent geometry : angle 0.54270 (11894) SS BOND : bond 0.00519 ( 3) SS BOND : angle 0.88507 ( 6) hydrogen bonds : bond 0.04009 ( 406) hydrogen bonds : angle 4.44571 ( 1161) *********************** 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 123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.294 Fit side-chains REVERT: A 139 MET cc_start: 0.7090 (tpp) cc_final: 0.6839 (mmp) REVERT: A 150 LEU cc_start: 0.7718 (tt) cc_final: 0.7405 (tt) REVERT: A 179 GLN cc_start: 0.7314 (tt0) cc_final: 0.7092 (tt0) REVERT: A 188 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.6207 (t80) REVERT: A 426 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7220 (m-80) REVERT: C 268 ASN cc_start: 0.8031 (t0) cc_final: 0.7726 (t0) REVERT: D 36 ASP cc_start: 0.8389 (m-30) cc_final: 0.8128 (m-30) outliers start: 10 outliers final: 6 residues processed: 119 average time/residue: 0.0882 time to fit residues: 14.7038 Evaluate side-chains 117 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 186 VAL 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 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.0060 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS ** 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 = 0.3934 r_free = 0.3934 target = 0.160956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124620 restraints weight = 11049.204| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.13 r_work: 0.3313 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8744 Z= 0.111 Angle : 0.533 11.093 11900 Z= 0.288 Chirality : 0.043 0.208 1381 Planarity : 0.004 0.039 1496 Dihedral : 4.260 45.270 1210 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.56 % Allowed : 14.92 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % 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: 0.48 (0.26), residues: 1108 helix: 2.00 (0.27), residues: 381 sheet: 0.15 (0.32), residues: 272 loop : -1.02 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.022 0.001 TYR B 297 PHE 0.016 0.001 PHE A 180 TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8741) covalent geometry : angle 0.53277 (11894) SS BOND : bond 0.00505 ( 3) SS BOND : angle 0.84978 ( 6) hydrogen bonds : bond 0.03856 ( 406) hydrogen bonds : angle 4.35265 ( 1161) *********************** 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 127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.310 Fit side-chains REVERT: A 150 LEU cc_start: 0.7664 (tt) cc_final: 0.7385 (tt) REVERT: A 179 GLN cc_start: 0.7407 (tt0) cc_final: 0.7194 (tt0) REVERT: A 188 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.6182 (t80) REVERT: A 426 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: C 268 ASN cc_start: 0.8087 (t0) cc_final: 0.7778 (t0) REVERT: D 36 ASP cc_start: 0.8298 (m-30) cc_final: 0.8033 (m-30) outliers start: 14 outliers final: 7 residues processed: 123 average time/residue: 0.0834 time to fit residues: 14.3747 Evaluate side-chains 118 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3772 r_free = 0.3772 target = 0.152774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117588 restraints weight = 11027.672| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.08 r_work: 0.3159 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1899 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= 0.133 Angle : 0.562 11.215 11900 Z= 0.303 Chirality : 0.044 0.235 1381 Planarity : 0.004 0.040 1496 Dihedral : 4.413 48.403 1210 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.67 % Allowed : 15.59 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.44 (0.26), residues: 1108 helix: 1.99 (0.27), residues: 381 sheet: 0.02 (0.32), residues: 275 loop : -1.00 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.023 0.001 TYR B 297 PHE 0.018 0.001 PHE A 180 TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8741) covalent geometry : angle 0.56180 (11894) SS BOND : bond 0.00581 ( 3) SS BOND : angle 1.00053 ( 6) hydrogen bonds : bond 0.04148 ( 406) hydrogen bonds : angle 4.38194 ( 1161) *********************** 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 127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.192 Fit side-chains REVERT: A 54 LEU cc_start: 0.7179 (mt) cc_final: 0.6921 (mp) REVERT: A 150 LEU cc_start: 0.7732 (tt) cc_final: 0.7433 (tt) REVERT: A 179 GLN cc_start: 0.7376 (tt0) cc_final: 0.7169 (tt0) REVERT: A 188 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.6258 (t80) REVERT: A 218 LYS cc_start: 0.7554 (tttt) cc_final: 0.6467 (pttm) REVERT: A 426 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: B 266 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8433 (mt) REVERT: C 75 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7304 (mt0) REVERT: C 268 ASN cc_start: 0.8044 (t0) cc_final: 0.7736 (t0) REVERT: D 36 ASP cc_start: 0.8373 (m-30) cc_final: 0.8138 (m-30) outliers start: 15 outliers final: 10 residues processed: 122 average time/residue: 0.0896 time to fit residues: 15.1340 Evaluate side-chains 121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 186 VAL 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 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3745 r_free = 0.3745 target = 0.150482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115017 restraints weight = 10919.251| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.06 r_work: 0.3123 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8744 Z= 0.173 Angle : 0.601 11.438 11900 Z= 0.322 Chirality : 0.045 0.222 1381 Planarity : 0.004 0.040 1496 Dihedral : 4.666 51.287 1210 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.23 % Allowed : 15.26 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % 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: 0.36 (0.25), residues: 1108 helix: 1.88 (0.27), residues: 382 sheet: -0.05 (0.31), residues: 278 loop : -1.01 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 304 TYR 0.022 0.001 TYR B 297 PHE 0.019 0.001 PHE A 180 TRP 0.015 0.001 TRP C 82 HIS 0.009 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8741) covalent geometry : angle 0.60032 (11894) SS BOND : bond 0.00711 ( 3) SS BOND : angle 1.14790 ( 6) hydrogen bonds : bond 0.04629 ( 406) hydrogen bonds : angle 4.48391 ( 1161) *********************** 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 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7221 (mt) cc_final: 0.6988 (mp) REVERT: A 188 PHE cc_start: 0.6599 (OUTLIER) cc_final: 0.6227 (t80) REVERT: A 218 LYS cc_start: 0.7575 (tttt) cc_final: 0.6472 (pttm) REVERT: A 426 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7223 (m-80) REVERT: B 266 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8449 (mt) REVERT: C 75 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7355 (mt0) REVERT: C 268 ASN cc_start: 0.8042 (t0) cc_final: 0.7750 (t0) outliers start: 20 outliers final: 10 residues processed: 125 average time/residue: 0.0863 time to fit residues: 14.9900 Evaluate side-chains 123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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 D residue 42 GLU 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 81 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.157549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.120408 restraints weight = 10979.877| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.09 r_work: 0.3269 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8744 Z= 0.120 Angle : 0.558 11.143 11900 Z= 0.300 Chirality : 0.043 0.225 1381 Planarity : 0.004 0.040 1496 Dihedral : 4.459 47.664 1210 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.56 % Allowed : 16.93 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % 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: 0.48 (0.26), residues: 1108 helix: 2.03 (0.27), residues: 381 sheet: 0.02 (0.31), residues: 277 loop : -0.98 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.022 0.001 TYR B 297 PHE 0.021 0.001 PHE A 180 TRP 0.017 0.001 TRP C 82 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8741) covalent geometry : angle 0.55781 (11894) SS BOND : bond 0.00554 ( 3) SS BOND : angle 0.93522 ( 6) hydrogen bonds : bond 0.04049 ( 406) hydrogen bonds : angle 4.37665 ( 1161) *********************** 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 126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.282 Fit side-chains REVERT: A 54 LEU cc_start: 0.7143 (mt) cc_final: 0.6869 (mp) REVERT: A 188 PHE cc_start: 0.6462 (OUTLIER) cc_final: 0.6129 (t80) REVERT: A 218 LYS cc_start: 0.7540 (tttt) cc_final: 0.6434 (pttm) REVERT: A 426 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: B 266 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8441 (mt) REVERT: C 75 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7237 (mt0) REVERT: C 268 ASN cc_start: 0.8104 (t0) cc_final: 0.7801 (t0) REVERT: D 36 ASP cc_start: 0.8329 (m-30) cc_final: 0.8059 (m-30) outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 0.0839 time to fit residues: 14.1484 Evaluate side-chains 123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 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 = 0.3727 r_free = 0.3727 target = 0.148923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113661 restraints weight = 10901.968| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.02 r_work: 0.3108 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8744 Z= 0.190 Angle : 0.626 11.509 11900 Z= 0.335 Chirality : 0.046 0.231 1381 Planarity : 0.004 0.040 1496 Dihedral : 4.798 52.755 1210 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.67 % Allowed : 16.26 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.32 (0.25), residues: 1108 helix: 1.91 (0.27), residues: 379 sheet: -0.10 (0.31), residues: 278 loop : -1.04 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 304 TYR 0.023 0.002 TYR B 297 PHE 0.020 0.002 PHE A 180 TRP 0.017 0.002 TRP C 82 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 8741) covalent geometry : angle 0.62600 (11894) SS BOND : bond 0.00744 ( 3) SS BOND : angle 1.25090 ( 6) hydrogen bonds : bond 0.04849 ( 406) hydrogen bonds : angle 4.51072 ( 1161) ********************** 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 123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.315 Fit side-chains REVERT: A 54 LEU cc_start: 0.7248 (mt) cc_final: 0.7022 (mp) REVERT: A 188 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.6179 (t80) REVERT: A 218 LYS cc_start: 0.7604 (tttt) cc_final: 0.6438 (pttm) REVERT: A 426 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: B 266 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8424 (mt) REVERT: C 75 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7404 (mt0) REVERT: C 268 ASN cc_start: 0.8039 (t0) cc_final: 0.7761 (t0) REVERT: D 36 ASP cc_start: 0.8438 (m-30) cc_final: 0.8171 (m-30) outliers start: 15 outliers final: 10 residues processed: 119 average time/residue: 0.0817 time to fit residues: 13.7201 Evaluate side-chains 119 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 44 optimal weight: 0.0570 chunk 75 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.158973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.121894 restraints weight = 10983.256| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.13 r_work: 0.3269 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2090 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= 0.123 Angle : 0.566 11.150 11900 Z= 0.305 Chirality : 0.044 0.230 1381 Planarity : 0.004 0.040 1496 Dihedral : 4.534 47.947 1210 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.56 % Allowed : 16.59 % 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 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: 0.48 (0.25), residues: 1108 helix: 2.04 (0.27), residues: 380 sheet: 0.01 (0.31), residues: 277 loop : -0.97 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.022 0.001 TYR B 297 PHE 0.015 0.001 PHE A 180 TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8741) covalent geometry : angle 0.56552 (11894) SS BOND : bond 0.00549 ( 3) SS BOND : angle 0.96085 ( 6) hydrogen bonds : bond 0.04087 ( 406) hydrogen bonds : angle 4.38003 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2433.66 seconds wall clock time: 42 minutes 15.11 seconds (2535.11 seconds total)