Starting phenix.real_space_refine on Wed Mar 12 18:48:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i95_35257/03_2025/8i95_35257.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i95_35257/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8i95_35257/03_2025/8i95_35257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i95_35257/03_2025/8i95_35257.map" model { file = "/net/cci-nas-00/data/ceres_data/8i95_35257/03_2025/8i95_35257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i95_35257/03_2025/8i95_35257.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG: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: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 10} 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, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} 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: 5.92, per 1000 atoms: 0.73 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.92 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: 2.36 Time building geometry restraints manager: 2.34 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: 5.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 22.610 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.040 ------------------------------------------------------------------------------- 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 8329 Z= 0.228 Angle : 0.606 8.462 11356 Z= 0.322 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (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 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE C 107 TYR 0.021 0.002 TYR B 105 ARG 0.008 0.000 ARG B 214 *********************** 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 : 0.870 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 108 average time/residue: 1.0293 time to fit residues: 119.6413 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 : 0.864 ------------------------------------------------------------------------------- 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 92 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.168963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.128050 restraints weight = 8829.062| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.79 r_work: 0.3287 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8329 Z= 0.269 Angle : 0.578 8.364 11356 Z= 0.308 Chirality : 0.044 0.203 1329 Planarity : 0.004 0.061 1448 Dihedral : 5.371 47.507 1204 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.42 % Allowed : 14.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1098 helix: 1.33 (0.28), residues: 387 sheet: -0.26 (0.29), residues: 288 loop : -0.75 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.011 0.001 PHE C 107 TYR 0.017 0.002 TYR H 190 ARG 0.003 0.000 ARG A 198 *********************** 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 125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.891 Fit side-chains REVERT: A 254 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7789 (tp) REVERT: B 325 MET cc_start: 0.8723 (tpp) cc_final: 0.8278 (mmt) REVERT: H 82 GLN cc_start: 0.8239 (tp40) cc_final: 0.7473 (tp40) REVERT: H 140 MET cc_start: 0.8464 (mtp) cc_final: 0.8127 (mtp) REVERT: H 213 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8201 (t) REVERT: C 367 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6959 (ttt-90) outliers start: 19 outliers final: 11 residues processed: 118 average time/residue: 1.1727 time to fit residues: 149.2644 Evaluate side-chains 115 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.167750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126161 restraints weight = 9037.581| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.83 r_work: 0.3257 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8329 Z= 0.315 Angle : 0.586 8.481 11356 Z= 0.309 Chirality : 0.044 0.204 1329 Planarity : 0.004 0.056 1448 Dihedral : 4.881 40.510 1193 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.18 % Allowed : 15.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1098 helix: 1.27 (0.28), residues: 388 sheet: -0.39 (0.29), residues: 289 loop : -0.80 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE C 107 TYR 0.016 0.002 TYR B 59 ARG 0.005 0.000 ARG A 198 *********************** 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: 25 poor density : 107 time to evaluate : 0.809 Fit side-chains REVERT: A 254 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7884 (tp) REVERT: H 213 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8319 (t) REVERT: C 367 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6975 (ttt-90) outliers start: 25 outliers final: 13 residues processed: 123 average time/residue: 0.9906 time to fit residues: 130.9229 Evaluate side-chains 115 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 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 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.2980 chunk 107 optimal weight: 0.0970 chunk 55 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.170319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129431 restraints weight = 8898.801| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.83 r_work: 0.3288 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8329 Z= 0.186 Angle : 0.529 7.367 11356 Z= 0.278 Chirality : 0.042 0.203 1329 Planarity : 0.004 0.052 1448 Dihedral : 4.553 35.228 1192 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.18 % Allowed : 16.69 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1098 helix: 1.49 (0.28), residues: 388 sheet: -0.32 (0.29), residues: 286 loop : -0.76 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE B 241 TYR 0.015 0.001 TYR H 190 ARG 0.002 0.000 ARG B 214 *********************** 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 133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.798 Fit side-chains REVERT: A 254 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.7970 (tp) REVERT: B 214 ARG cc_start: 0.7634 (mmt180) cc_final: 0.7195 (mmp-170) REVERT: H 213 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8375 (t) REVERT: C 367 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6905 (ttt-90) outliers start: 25 outliers final: 10 residues processed: 125 average time/residue: 1.1272 time to fit residues: 152.3720 Evaluate side-chains 120 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 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 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 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.0020 chunk 8 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 B 340 ASN H 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.168577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.127611 restraints weight = 8872.659| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.81 r_work: 0.3245 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8329 Z= 0.277 Angle : 0.566 7.863 11356 Z= 0.295 Chirality : 0.044 0.205 1329 Planarity : 0.004 0.053 1448 Dihedral : 4.671 35.848 1192 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.95 % Allowed : 16.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1098 helix: 1.47 (0.28), residues: 383 sheet: -0.45 (0.29), residues: 288 loop : -0.83 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE C 107 TYR 0.018 0.002 TYR B 59 ARG 0.003 0.000 ARG H 160 *********************** 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 142 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.781 Fit side-chains REVERT: A 254 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7934 (tp) REVERT: B 139 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8135 (mt) REVERT: B 214 ARG cc_start: 0.7650 (mmt180) cc_final: 0.7322 (mmp-170) REVERT: H 213 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8351 (t) REVERT: C 367 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6987 (ttt-90) outliers start: 31 outliers final: 16 residues processed: 129 average time/residue: 0.9426 time to fit residues: 131.0054 Evaluate side-chains 129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 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 G residue 51 LEU 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 101 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 0.0770 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.168490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126807 restraints weight = 8923.115| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.85 r_work: 0.3246 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8329 Z= 0.262 Angle : 0.563 7.875 11356 Z= 0.291 Chirality : 0.043 0.202 1329 Planarity : 0.004 0.051 1448 Dihedral : 4.669 35.808 1192 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.82 % Allowed : 17.83 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1098 helix: 1.49 (0.28), residues: 383 sheet: -0.49 (0.29), residues: 288 loop : -0.82 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE B 335 TYR 0.020 0.002 TYR B 59 ARG 0.002 0.000 ARG H 160 *********************** 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 137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.973 Fit side-chains REVERT: A 254 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7939 (tp) REVERT: B 13 GLN cc_start: 0.7386 (tt0) cc_final: 0.6855 (tm-30) REVERT: B 46 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7371 (mmm160) REVERT: B 139 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8120 (mt) REVERT: B 214 ARG cc_start: 0.7626 (mmt180) cc_final: 0.7383 (mmp-170) REVERT: B 259 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8474 (pm20) REVERT: H 213 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8349 (t) REVERT: C 367 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6986 (ttt-90) outliers start: 30 outliers final: 15 residues processed: 126 average time/residue: 0.9853 time to fit residues: 133.8918 Evaluate side-chains 126 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 46 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 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 259 GLN 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 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 337 THR Chi-restraints excluded: chain C residue 367 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.168697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127682 restraints weight = 8949.446| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.82 r_work: 0.3248 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8329 Z= 0.258 Angle : 0.565 8.219 11356 Z= 0.291 Chirality : 0.043 0.202 1329 Planarity : 0.004 0.050 1448 Dihedral : 4.675 35.837 1192 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.44 % Allowed : 18.09 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1098 helix: 1.48 (0.28), residues: 384 sheet: -0.52 (0.29), residues: 288 loop : -0.80 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.014 0.001 PHE B 335 TYR 0.022 0.002 TYR B 59 ARG 0.002 0.000 ARG B 256 *********************** 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: 27 poor density : 108 time to evaluate : 0.831 Fit side-chains REVERT: A 254 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.7995 (tp) REVERT: B 13 GLN cc_start: 0.7397 (tt0) cc_final: 0.6848 (tm-30) REVERT: B 46 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7412 (mmm160) REVERT: B 139 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8144 (mt) REVERT: B 214 ARG cc_start: 0.7668 (mmt180) cc_final: 0.7392 (mmp-170) REVERT: H 213 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8372 (t) REVERT: C 367 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6932 (ttt-90) REVERT: D 10 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6771 (mtt-85) outliers start: 27 outliers final: 14 residues processed: 125 average time/residue: 1.0269 time to fit residues: 138.1884 Evaluate side-chains 126 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 46 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 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 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 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 7 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.168799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127767 restraints weight = 8952.101| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.84 r_work: 0.3252 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8329 Z= 0.252 Angle : 0.563 8.278 11356 Z= 0.290 Chirality : 0.043 0.198 1329 Planarity : 0.004 0.050 1448 Dihedral : 4.665 35.766 1192 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.44 % Allowed : 18.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1098 helix: 1.48 (0.28), residues: 386 sheet: -0.50 (0.29), residues: 287 loop : -0.77 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE B 335 TYR 0.020 0.002 TYR B 59 ARG 0.002 0.000 ARG H 160 *********************** 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 137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.901 Fit side-chains REVERT: A 254 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.7990 (tp) REVERT: B 13 GLN cc_start: 0.7401 (tt0) cc_final: 0.6851 (tm-30) REVERT: B 46 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7386 (mmm160) REVERT: B 139 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8157 (mt) REVERT: B 160 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8710 (p) REVERT: B 214 ARG cc_start: 0.7633 (mmt180) cc_final: 0.7359 (mmp-170) REVERT: B 259 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8464 (pm20) REVERT: H 82 GLN cc_start: 0.8319 (tp40) cc_final: 0.7956 (tp40) REVERT: H 213 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8378 (t) REVERT: C 36 LEU cc_start: 0.7909 (mp) cc_final: 0.7313 (tp) REVERT: C 367 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6799 (ttt-90) REVERT: D 10 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6546 (mtt-85) outliers start: 27 outliers final: 15 residues processed: 127 average time/residue: 1.0135 time to fit residues: 138.3928 Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 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 112 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 160 SER 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 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 51 LEU 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 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 94 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 0.0670 chunk 89 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.0050 chunk 4 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.4932 ------------------------------------------------------------------------------- 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 B 340 ASN 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 = 0.169484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128602 restraints weight = 9024.585| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.84 r_work: 0.3262 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8329 Z= 0.218 Angle : 0.552 8.045 11356 Z= 0.285 Chirality : 0.043 0.188 1329 Planarity : 0.004 0.049 1448 Dihedral : 4.616 35.366 1192 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.18 % Allowed : 19.11 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1098 helix: 1.49 (0.28), residues: 386 sheet: -0.52 (0.29), residues: 288 loop : -0.75 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS H 35 PHE 0.016 0.001 PHE B 335 TYR 0.021 0.001 TYR B 59 ARG 0.003 0.000 ARG C 362 *********************** 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 137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.835 Fit side-chains REVERT: A 254 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.7998 (tp) REVERT: B 13 GLN cc_start: 0.7402 (tt0) cc_final: 0.7201 (tt0) REVERT: B 46 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7378 (mmm160) REVERT: B 139 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8129 (mt) REVERT: B 160 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8709 (p) REVERT: B 214 ARG cc_start: 0.7680 (mmt180) cc_final: 0.7417 (mmp-170) REVERT: H 82 GLN cc_start: 0.8308 (tp40) cc_final: 0.7946 (tp40) REVERT: H 213 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8397 (t) REVERT: C 36 LEU cc_start: 0.7921 (mp) cc_final: 0.7380 (tp) REVERT: C 367 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6754 (ttt-90) REVERT: D 10 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6545 (mtt-85) outliers start: 25 outliers final: 15 residues processed: 128 average time/residue: 0.9884 time to fit residues: 136.0319 Evaluate side-chains 131 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 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 160 SER 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 G residue 51 LEU 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 337 THR 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 95 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 57 optimal weight: 0.0020 chunk 81 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 45 optimal weight: 0.0980 overall best weight: 0.2188 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.173141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.132759 restraints weight = 8840.681| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.84 r_work: 0.3324 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8329 Z= 0.148 Angle : 0.519 7.992 11356 Z= 0.267 Chirality : 0.042 0.163 1329 Planarity : 0.004 0.048 1448 Dihedral : 4.328 33.300 1192 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.04 % Allowed : 20.38 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1098 helix: 1.69 (0.28), residues: 385 sheet: -0.43 (0.30), residues: 277 loop : -0.71 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.002 0.000 HIS B 91 PHE 0.010 0.001 PHE H 27 TYR 0.015 0.001 TYR H 190 ARG 0.002 0.000 ARG D 10 ********************** 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 126 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.817 Fit side-chains REVERT: B 212 ASP cc_start: 0.8228 (p0) cc_final: 0.8024 (p0) REVERT: B 214 ARG cc_start: 0.7636 (mmt180) cc_final: 0.7341 (mmp-170) REVERT: B 325 MET cc_start: 0.8670 (tpp) cc_final: 0.8318 (tpt) REVERT: H 82 GLN cc_start: 0.8302 (tp40) cc_final: 0.7942 (tp40) REVERT: H 213 THR cc_start: 0.8668 (m) cc_final: 0.8418 (t) REVERT: C 36 LEU cc_start: 0.7915 (mp) cc_final: 0.7453 (tp) REVERT: C 358 PHE cc_start: 0.7379 (m-10) cc_final: 0.7173 (m-10) REVERT: C 367 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7033 (ttt-90) REVERT: D 10 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6339 (mtt-85) outliers start: 16 outliers final: 9 residues processed: 120 average time/residue: 1.0923 time to fit residues: 140.9901 Evaluate side-chains 116 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 63 optimal weight: 0.0770 chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.169227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128009 restraints weight = 8957.336| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.87 r_work: 0.3274 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8329 Z= 0.211 Angle : 0.537 7.480 11356 Z= 0.280 Chirality : 0.043 0.163 1329 Planarity : 0.004 0.048 1448 Dihedral : 4.291 24.554 1190 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.29 % Allowed : 19.49 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1098 helix: 1.71 (0.28), residues: 385 sheet: -0.51 (0.29), residues: 288 loop : -0.66 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE B 335 TYR 0.014 0.001 TYR H 190 ARG 0.003 0.000 ARG C 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6155.88 seconds wall clock time: 108 minutes 39.56 seconds (6519.56 seconds total)