Starting phenix.real_space_refine on Fri Aug 22 21:59:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i95_35257/08_2025/8i95_35257.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i95_35257/08_2025/8i95_35257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i95_35257/08_2025/8i95_35257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i95_35257/08_2025/8i95_35257.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i95_35257/08_2025/8i95_35257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i95_35257/08_2025/8i95_35257.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5205 2.51 5 N 1403 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8153 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1550 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2416 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 400 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2057 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 14, 'TRANS': 265} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'TRP:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 1.64, per 1000 atoms: 0.20 Number of scatterers: 8153 At special positions: 0 Unit cell: (85.56, 119.6, 123.28, 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 52 16.00 O 1493 8.00 N 1403 7.00 C 5205 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.05 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " 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 Links applied TRANS " DAL D 9 " - " LEU D 8 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 296.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 9 " Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.796A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.560A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 4.130A pdb=" N ILE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.549A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.757A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 50 removed outlier: 3.555A pdb=" N SER C 26 " --> pdb=" O PRO C 22 " (cutoff:3.500A) Proline residue: C 39 - end of helix removed outlier: 3.576A pdb=" N VAL C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 74 removed outlier: 4.104A pdb=" N TRP C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.824A pdb=" N SER C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 126 Proline residue: C 99 - end of helix removed outlier: 5.197A pdb=" N VAL C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 110 " --> pdb=" O MET C 106 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.562A pdb=" N ASN C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 154 Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.766A pdb=" N TYR C 160 " --> pdb=" O PRO C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 363 removed outlier: 5.256A pdb=" N LEU C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 373 through 403 Proline residue: C 392 - end of helix removed outlier: 3.953A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 402 " --> pdb=" O VAL C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 431 removed outlier: 6.367A pdb=" N LEU C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N CYS C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 435 through 438 removed outlier: 3.820A pdb=" N LEU C 438 " --> pdb=" O TYR C 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 435 through 438' Processing helix chain 'C' and resid 439 through 451 removed outlier: 3.827A pdb=" N GLN C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.164A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.813A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.923A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.546A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.569A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.727A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.514A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.648A pdb=" N ARG H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.527A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.527A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.623A pdb=" N VAL H 149 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.969A pdb=" N PHE C 164 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG C 171 " --> pdb=" O PHE C 164 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1236 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: 1.09 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1623 1.33 - 1.45: 2170 1.45 - 1.58: 4468 1.58 - 1.70: 1 1.70 - 1.83: 67 Bond restraints: 8329 Sorted by residual: bond pdb=" CA THR C 331 " pdb=" CB THR C 331 " ideal model delta sigma weight residual 1.540 1.642 -0.102 2.70e-02 1.37e+03 1.44e+01 bond pdb=" C PRO C 156 " pdb=" O PRO C 156 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.32e-02 5.74e+03 6.79e+00 bond pdb=" N ILE C 155 " pdb=" CA ILE C 155 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.23e-02 6.61e+03 6.67e+00 bond pdb=" CA THR C 331 " pdb=" C THR C 331 " ideal model delta sigma weight residual 1.525 1.576 -0.051 2.10e-02 2.27e+03 5.96e+00 bond pdb=" N PRO C 156 " pdb=" CA PRO C 156 " ideal model delta sigma weight residual 1.471 1.443 0.028 1.32e-02 5.74e+03 4.49e+00 ... (remaining 8324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 11121 1.69 - 3.38: 171 3.38 - 5.08: 47 5.08 - 6.77: 13 6.77 - 8.46: 4 Bond angle restraints: 11356 Sorted by residual: angle pdb=" CA THR C 331 " pdb=" C THR C 331 " pdb=" N PRO C 332 " ideal model delta sigma weight residual 116.90 124.88 -7.98 1.50e+00 4.44e-01 2.83e+01 angle pdb=" C PRO C 156 " pdb=" N VAL C 157 " pdb=" CA VAL C 157 " ideal model delta sigma weight residual 121.77 114.35 7.42 1.44e+00 4.82e-01 2.65e+01 angle pdb=" C CYS C 154 " pdb=" N ILE C 155 " pdb=" CA ILE C 155 " ideal model delta sigma weight residual 122.13 115.07 7.06 1.85e+00 2.92e-01 1.46e+01 angle pdb=" N PRO C 156 " pdb=" CA PRO C 156 " pdb=" C PRO C 156 " ideal model delta sigma weight residual 113.84 109.29 4.55 1.30e+00 5.92e-01 1.22e+01 angle pdb=" C ARG D 10 " pdb=" CA ARG D 10 " pdb=" CB ARG D 10 " ideal model delta sigma weight residual 110.10 116.53 -6.43 1.90e+00 2.77e-01 1.15e+01 ... (remaining 11351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4377 17.53 - 35.05: 382 35.05 - 52.58: 75 52.58 - 70.11: 8 70.11 - 87.63: 8 Dihedral angle restraints: 4850 sinusoidal: 1619 harmonic: 3231 Sorted by residual: dihedral pdb=" CB CYS H 159 " pdb=" SG CYS H 159 " pdb=" SG CYS H 229 " pdb=" CB CYS H 229 " ideal model delta sinusoidal sigma weight residual 93.00 37.84 55.16 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CB CYS C 95 " pdb=" SG CYS C 95 " pdb=" SG CYS C 172 " pdb=" CB CYS C 172 " ideal model delta sinusoidal sigma weight residual -86.00 -121.90 35.90 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" CA PRO C 99 " pdb=" C PRO C 99 " pdb=" N SER C 100 " pdb=" CA SER C 100 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 4847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1079 0.052 - 0.104: 206 0.104 - 0.156: 42 0.156 - 0.207: 1 0.207 - 0.259: 1 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA DAL D 9 " pdb=" N DAL D 9 " pdb=" C DAL D 9 " pdb=" CB DAL D 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.23 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA THR C 391 " pdb=" N THR C 391 " pdb=" C THR C 391 " pdb=" CB THR C 391 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB ILE C 155 " pdb=" CA ILE C 155 " pdb=" CG1 ILE C 155 " pdb=" CG2 ILE C 155 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1326 not shown) Planarity restraints: 1449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 21 " -0.063 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO C 22 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO C 22 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 22 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 347 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO C 348 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 348 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 348 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 258 " -0.010 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ASP B 258 " 0.033 2.00e-02 2.50e+03 pdb=" O ASP B 258 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN B 259 " -0.011 2.00e-02 2.50e+03 ... (remaining 1446 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 565 2.74 - 3.28: 8023 3.28 - 3.82: 13786 3.82 - 4.36: 16328 4.36 - 4.90: 29141 Nonbonded interactions: 67843 Sorted by model distance: nonbonded pdb=" O LEU C 387 " pdb=" OG1 THR C 391 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.211 3.040 nonbonded pdb=" NZ LYS C 96 " pdb=" O ARG C 161 " model vdw 2.241 3.120 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.272 3.040 ... (remaining 67838 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: 6.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.690 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 0.102 8333 Z= 0.171 Angle : 0.617 8.794 11365 Z= 0.327 Chirality : 0.043 0.259 1329 Planarity : 0.005 0.094 1448 Dihedral : 14.095 87.632 2752 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.15 % Allowed : 14.01 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.26), residues: 1098 helix: 1.29 (0.28), residues: 380 sheet: -0.22 (0.29), residues: 304 loop : -0.77 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.021 0.002 TYR B 105 PHE 0.012 0.001 PHE C 107 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8329) covalent geometry : angle 0.60598 (11356) SS BOND : bond 0.01081 ( 3) SS BOND : angle 4.76495 ( 6) hydrogen bonds : bond 0.16975 ( 424) hydrogen bonds : angle 6.95701 ( 1236) link_TRANS : bond 0.01061 ( 1) link_TRANS : angle 2.86819 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.289 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 108 average time/residue: 0.3994 time to fit residues: 46.3011 Evaluate side-chains 108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain D residue 10 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.167265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125881 restraints weight = 8913.069| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.80 r_work: 0.3266 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8333 Z= 0.199 Angle : 0.596 8.602 11365 Z= 0.317 Chirality : 0.044 0.216 1329 Planarity : 0.004 0.061 1448 Dihedral : 5.446 48.108 1204 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.80 % Allowed : 13.89 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.26), residues: 1098 helix: 1.27 (0.28), residues: 387 sheet: -0.32 (0.29), residues: 291 loop : -0.76 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.017 0.002 TYR H 190 PHE 0.012 0.001 PHE C 107 TRP 0.014 0.002 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8329) covalent geometry : angle 0.59386 (11356) SS BOND : bond 0.00462 ( 3) SS BOND : angle 2.06256 ( 6) hydrogen bonds : bond 0.04649 ( 424) hydrogen bonds : angle 5.27377 ( 1236) link_TRANS : bond 0.00341 ( 1) link_TRANS : angle 1.60608 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.302 Fit side-chains REVERT: A 254 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7849 (tp) REVERT: H 82 GLN cc_start: 0.8261 (tp40) cc_final: 0.8033 (tp40) REVERT: H 213 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8268 (t) REVERT: C 367 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7021 (ttt-90) outliers start: 22 outliers final: 12 residues processed: 118 average time/residue: 0.4026 time to fit residues: 51.2299 Evaluate side-chains 115 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 399 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 14 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN H 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128455 restraints weight = 8856.782| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.78 r_work: 0.3288 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8333 Z= 0.168 Angle : 0.559 7.671 11365 Z= 0.295 Chirality : 0.043 0.193 1329 Planarity : 0.004 0.055 1448 Dihedral : 4.869 52.291 1193 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.06 % Allowed : 15.67 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.26), residues: 1098 helix: 1.38 (0.28), residues: 387 sheet: -0.34 (0.29), residues: 288 loop : -0.76 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 10 TYR 0.015 0.001 TYR H 190 PHE 0.015 0.001 PHE C 107 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8329) covalent geometry : angle 0.55739 (11356) SS BOND : bond 0.00417 ( 3) SS BOND : angle 1.58645 ( 6) hydrogen bonds : bond 0.04200 ( 424) hydrogen bonds : angle 5.01372 ( 1236) link_TRANS : bond 0.00268 ( 1) link_TRANS : angle 1.40823 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.376 Fit side-chains REVERT: A 254 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.7953 (tp) REVERT: B 325 MET cc_start: 0.8740 (tpp) cc_final: 0.8258 (mmt) REVERT: H 213 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8388 (t) REVERT: C 367 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6955 (ttt-90) outliers start: 24 outliers final: 12 residues processed: 123 average time/residue: 0.4190 time to fit residues: 55.4270 Evaluate side-chains 120 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain D residue 4 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 107 optimal weight: 0.0000 chunk 22 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.170007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.129264 restraints weight = 9000.978| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.84 r_work: 0.3273 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8333 Z= 0.140 Angle : 0.538 7.710 11365 Z= 0.282 Chirality : 0.042 0.190 1329 Planarity : 0.004 0.052 1448 Dihedral : 4.783 55.724 1192 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.18 % Allowed : 16.82 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.26), residues: 1098 helix: 1.49 (0.28), residues: 385 sheet: -0.38 (0.29), residues: 288 loop : -0.76 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 10 TYR 0.016 0.001 TYR B 59 PHE 0.011 0.001 PHE B 241 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8329) covalent geometry : angle 0.53698 (11356) SS BOND : bond 0.00372 ( 3) SS BOND : angle 1.44701 ( 6) hydrogen bonds : bond 0.03837 ( 424) hydrogen bonds : angle 4.86700 ( 1236) link_TRANS : bond 0.00272 ( 1) link_TRANS : angle 1.42331 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.285 Fit side-chains REVERT: A 254 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.7951 (tp) REVERT: H 213 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8339 (t) REVERT: C 340 ARG cc_start: 0.7211 (ttp-170) cc_final: 0.6983 (ttm170) REVERT: C 367 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6837 (ttt-90) outliers start: 25 outliers final: 12 residues processed: 123 average time/residue: 0.4060 time to fit residues: 53.9690 Evaluate side-chains 120 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 367 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 43 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN H 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.169430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128484 restraints weight = 8944.623| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.82 r_work: 0.3262 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8333 Z= 0.158 Angle : 0.555 7.394 11365 Z= 0.289 Chirality : 0.043 0.191 1329 Planarity : 0.004 0.051 1448 Dihedral : 4.797 54.388 1192 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.57 % Allowed : 17.32 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.26), residues: 1098 helix: 1.47 (0.28), residues: 385 sheet: -0.44 (0.29), residues: 288 loop : -0.78 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 160 TYR 0.017 0.001 TYR B 59 PHE 0.012 0.001 PHE B 241 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8329) covalent geometry : angle 0.55348 (11356) SS BOND : bond 0.00370 ( 3) SS BOND : angle 1.38489 ( 6) hydrogen bonds : bond 0.03836 ( 424) hydrogen bonds : angle 4.81913 ( 1236) link_TRANS : bond 0.00233 ( 1) link_TRANS : angle 1.28575 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.218 Fit side-chains REVERT: A 254 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.7990 (tp) REVERT: B 46 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7404 (mmm160) REVERT: B 139 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8135 (mt) REVERT: H 213 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8377 (t) REVERT: C 367 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6871 (ttt-90) outliers start: 28 outliers final: 15 residues processed: 125 average time/residue: 0.3629 time to fit residues: 49.2778 Evaluate side-chains 125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 367 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 0.0040 chunk 7 optimal weight: 0.0870 chunk 30 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.0010 chunk 13 optimal weight: 0.0070 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN H 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.174949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135193 restraints weight = 8828.532| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.82 r_work: 0.3360 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8333 Z= 0.097 Angle : 0.505 7.322 11365 Z= 0.262 Chirality : 0.041 0.166 1329 Planarity : 0.004 0.047 1448 Dihedral : 4.421 51.955 1192 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.55 % Allowed : 18.73 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.26), residues: 1098 helix: 1.72 (0.28), residues: 385 sheet: -0.33 (0.30), residues: 277 loop : -0.68 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 10 TYR 0.015 0.001 TYR H 190 PHE 0.010 0.001 PHE H 27 TRP 0.013 0.001 TRP B 211 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 8329) covalent geometry : angle 0.50461 (11356) SS BOND : bond 0.00314 ( 3) SS BOND : angle 1.17247 ( 6) hydrogen bonds : bond 0.03227 ( 424) hydrogen bonds : angle 4.50498 ( 1236) link_TRANS : bond 0.00230 ( 1) link_TRANS : angle 1.16544 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.301 Fit side-chains REVERT: B 325 MET cc_start: 0.8632 (tpp) cc_final: 0.8086 (mmt) REVERT: H 60 TYR cc_start: 0.8827 (m-80) cc_final: 0.8624 (m-80) REVERT: H 82 GLN cc_start: 0.8305 (tp40) cc_final: 0.8028 (tp40) REVERT: H 213 THR cc_start: 0.8633 (m) cc_final: 0.8368 (t) REVERT: C 36 LEU cc_start: 0.7900 (mp) cc_final: 0.7371 (tp) REVERT: C 358 PHE cc_start: 0.7308 (m-10) cc_final: 0.7096 (m-10) REVERT: C 367 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7061 (ttt-90) REVERT: D 10 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6592 (mmt-90) outliers start: 20 outliers final: 10 residues processed: 124 average time/residue: 0.4070 time to fit residues: 54.5274 Evaluate side-chains 116 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain D residue 10 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 0.0060 chunk 107 optimal weight: 0.0070 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.171509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130257 restraints weight = 9044.477| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.87 r_work: 0.3293 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8333 Z= 0.124 Angle : 0.524 7.649 11365 Z= 0.270 Chirality : 0.042 0.164 1329 Planarity : 0.004 0.047 1448 Dihedral : 4.310 48.222 1190 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.06 % Allowed : 17.96 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.26), residues: 1098 helix: 1.73 (0.28), residues: 385 sheet: -0.32 (0.30), residues: 283 loop : -0.61 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 367 TYR 0.014 0.001 TYR H 190 PHE 0.011 0.001 PHE C 107 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8329) covalent geometry : angle 0.52300 (11356) SS BOND : bond 0.00314 ( 3) SS BOND : angle 1.26483 ( 6) hydrogen bonds : bond 0.03446 ( 424) hydrogen bonds : angle 4.53348 ( 1236) link_TRANS : bond 0.00178 ( 1) link_TRANS : angle 1.08599 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.200 Fit side-chains REVERT: B 13 GLN cc_start: 0.7530 (tt0) cc_final: 0.6908 (tm-30) REVERT: B 139 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8087 (mt) REVERT: B 212 ASP cc_start: 0.8247 (p0) cc_final: 0.8043 (p0) REVERT: B 215 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7727 (mm-30) REVERT: H 82 GLN cc_start: 0.8345 (tp40) cc_final: 0.8008 (tp40) REVERT: H 213 THR cc_start: 0.8641 (m) cc_final: 0.8373 (t) REVERT: C 36 LEU cc_start: 0.7878 (mp) cc_final: 0.7343 (tp) REVERT: C 358 PHE cc_start: 0.7353 (m-10) cc_final: 0.7133 (m-10) REVERT: C 367 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6840 (ttt-90) REVERT: D 10 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6583 (mtt-85) outliers start: 24 outliers final: 14 residues processed: 127 average time/residue: 0.4057 time to fit residues: 55.4791 Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain D residue 10 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 36 optimal weight: 0.0470 chunk 88 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 41 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN H 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.171939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.131247 restraints weight = 8919.969| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.85 r_work: 0.3306 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8333 Z= 0.121 Angle : 0.524 8.106 11365 Z= 0.270 Chirality : 0.042 0.152 1329 Planarity : 0.004 0.046 1448 Dihedral : 4.303 46.382 1190 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.06 % Allowed : 18.85 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.26), residues: 1098 helix: 1.77 (0.28), residues: 385 sheet: -0.36 (0.29), residues: 288 loop : -0.61 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 10 TYR 0.014 0.001 TYR H 190 PHE 0.012 0.001 PHE B 335 TRP 0.010 0.001 TRP B 211 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8329) covalent geometry : angle 0.52281 (11356) SS BOND : bond 0.00347 ( 3) SS BOND : angle 1.38273 ( 6) hydrogen bonds : bond 0.03403 ( 424) hydrogen bonds : angle 4.52378 ( 1236) link_TRANS : bond 0.00171 ( 1) link_TRANS : angle 1.02139 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.248 Fit side-chains REVERT: B 13 GLN cc_start: 0.7516 (tt0) cc_final: 0.6884 (tm-30) REVERT: B 46 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7316 (mmm160) REVERT: B 139 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8116 (mt) REVERT: B 212 ASP cc_start: 0.8236 (p0) cc_final: 0.8012 (p0) REVERT: B 215 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7784 (mm-30) REVERT: H 82 GLN cc_start: 0.8354 (tp40) cc_final: 0.8043 (tp40) REVERT: H 213 THR cc_start: 0.8651 (m) cc_final: 0.8387 (t) REVERT: C 36 LEU cc_start: 0.7917 (mp) cc_final: 0.7423 (tp) REVERT: C 358 PHE cc_start: 0.7389 (m-10) cc_final: 0.7160 (m-10) REVERT: C 367 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6841 (ttt-90) REVERT: D 10 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6530 (mtt-85) outliers start: 24 outliers final: 12 residues processed: 124 average time/residue: 0.4419 time to fit residues: 58.6943 Evaluate side-chains 125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain D residue 10 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 0.8980 chunk 57 optimal weight: 0.0370 chunk 69 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 0.0570 chunk 47 optimal weight: 0.9980 chunk 64 optimal weight: 0.0170 chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN H 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.170561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.129396 restraints weight = 8959.598| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.88 r_work: 0.3294 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8333 Z= 0.123 Angle : 0.526 7.759 11365 Z= 0.271 Chirality : 0.042 0.151 1329 Planarity : 0.004 0.045 1448 Dihedral : 4.233 37.677 1190 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.80 % Allowed : 19.11 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.26), residues: 1098 helix: 1.81 (0.28), residues: 384 sheet: -0.37 (0.29), residues: 288 loop : -0.62 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 362 TYR 0.014 0.001 TYR H 190 PHE 0.012 0.001 PHE B 335 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8329) covalent geometry : angle 0.52512 (11356) SS BOND : bond 0.00351 ( 3) SS BOND : angle 1.43092 ( 6) hydrogen bonds : bond 0.03419 ( 424) hydrogen bonds : angle 4.51576 ( 1236) link_TRANS : bond 0.00145 ( 1) link_TRANS : angle 0.99417 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.307 Fit side-chains REVERT: B 46 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7201 (mmm160) REVERT: B 139 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8088 (mt) REVERT: B 212 ASP cc_start: 0.8206 (p0) cc_final: 0.7964 (p0) REVERT: B 215 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7762 (mm-30) REVERT: B 325 MET cc_start: 0.8695 (tpp) cc_final: 0.8379 (tpt) REVERT: H 82 GLN cc_start: 0.8345 (tp40) cc_final: 0.8009 (tp40) REVERT: H 213 THR cc_start: 0.8610 (m) cc_final: 0.8331 (t) REVERT: C 36 LEU cc_start: 0.7893 (mp) cc_final: 0.7444 (tt) REVERT: C 358 PHE cc_start: 0.7304 (m-10) cc_final: 0.7079 (m-10) REVERT: C 367 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6993 (ttt-90) REVERT: D 10 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6474 (mmt-90) outliers start: 22 outliers final: 13 residues processed: 127 average time/residue: 0.3890 time to fit residues: 53.0988 Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain D residue 10 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 12 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 56 optimal weight: 0.4980 chunk 11 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN H 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.170777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129636 restraints weight = 8878.843| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.87 r_work: 0.3299 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8333 Z= 0.124 Angle : 0.532 8.384 11365 Z= 0.274 Chirality : 0.042 0.153 1329 Planarity : 0.004 0.045 1448 Dihedral : 4.193 28.064 1190 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.17 % Allowed : 19.87 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1098 helix: 1.80 (0.28), residues: 384 sheet: -0.36 (0.29), residues: 288 loop : -0.61 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 362 TYR 0.014 0.001 TYR H 190 PHE 0.012 0.001 PHE B 335 TRP 0.010 0.001 TRP B 211 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8329) covalent geometry : angle 0.53104 (11356) SS BOND : bond 0.00360 ( 3) SS BOND : angle 1.44548 ( 6) hydrogen bonds : bond 0.03438 ( 424) hydrogen bonds : angle 4.54645 ( 1236) link_TRANS : bond 0.00141 ( 1) link_TRANS : angle 0.98305 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.307 Fit side-chains REVERT: B 46 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7198 (mmm160) REVERT: B 139 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8091 (mt) REVERT: B 212 ASP cc_start: 0.8278 (p0) cc_final: 0.8073 (p0) REVERT: B 215 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7808 (mm-30) REVERT: H 82 GLN cc_start: 0.8337 (tp40) cc_final: 0.8011 (tp40) REVERT: H 213 THR cc_start: 0.8611 (m) cc_final: 0.8330 (t) REVERT: C 36 LEU cc_start: 0.7912 (mp) cc_final: 0.7505 (tt) REVERT: C 358 PHE cc_start: 0.7318 (m-10) cc_final: 0.7086 (m-10) REVERT: C 362 ARG cc_start: 0.6929 (tpt170) cc_final: 0.6188 (tpt90) REVERT: C 367 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7010 (ttt-90) outliers start: 17 outliers final: 13 residues processed: 123 average time/residue: 0.3818 time to fit residues: 50.5473 Evaluate side-chains 125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 367 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 102 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 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 75 GLN H 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125396 restraints weight = 8944.303| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.84 r_work: 0.3264 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8333 Z= 0.171 Angle : 0.566 8.171 11365 Z= 0.294 Chirality : 0.043 0.183 1329 Planarity : 0.004 0.046 1448 Dihedral : 4.393 26.867 1190 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.80 % Allowed : 19.75 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.26), residues: 1098 helix: 1.74 (0.28), residues: 382 sheet: -0.40 (0.29), residues: 288 loop : -0.71 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 362 TYR 0.016 0.001 TYR H 103 PHE 0.015 0.001 PHE B 335 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8329) covalent geometry : angle 0.56516 (11356) SS BOND : bond 0.00407 ( 3) SS BOND : angle 1.59347 ( 6) hydrogen bonds : bond 0.03767 ( 424) hydrogen bonds : angle 4.73628 ( 1236) link_TRANS : bond 0.00066 ( 1) link_TRANS : angle 0.99497 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2734.13 seconds wall clock time: 47 minutes 22.07 seconds (2842.07 seconds total)