Starting phenix.real_space_refine on Fri Oct 23 04:58:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wpq_66146/10_2026/9wpq_66146.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wpq_66146/10_2026/9wpq_66146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wpq_66146/10_2026/9wpq_66146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wpq_66146/10_2026/9wpq_66146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wpq_66146/10_2026/9wpq_66146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wpq_66146/10_2026/9wpq_66146.map" } resolution = 3.15 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= 0.026 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 49 5.16 5 C 5364 2.51 5 N 1418 2.21 5 O 1542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8373 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1958 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2495 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 5, 'ASP:plan': 8, 'ASN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1733 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 414 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1749 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'7LD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.10, per 1000 atoms: 0.13 Number of scatterers: 8373 At special positions: 0 Unit cell: (91.52, 121.472, 129.792, 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 49 16.00 O 1542 8.00 N 1418 7.00 C 5364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 268.5 milliseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 38.6% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 81 through 101 removed outlier: 3.622A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 88 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 105 Processing helix chain 'A' and resid 111 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 147 through 179 Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.519A pdb=" N SER A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 207 removed outlier: 3.559A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.679A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 243 through 262 Processing helix chain 'A' and resid 316 through 348 Proline residue: A 338 - end of helix removed outlier: 3.547A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 382 removed outlier: 4.023A pdb=" N LEU A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Proline residue: A 377 - end of helix removed outlier: 3.504A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.583A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.615A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.287A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 183 through 203 removed outlier: 3.535A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.554A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.876A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.261A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.564A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.094A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS C 121 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 139 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.502A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 187 through 192 removed outlier: 4.157A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.716A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.183A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 76 removed outlier: 5.263A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 109 through 111 Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.747A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.030A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN E 39 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 137 removed outlier: 3.511A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 137 removed outlier: 3.511A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 148 removed outlier: 3.512A pdb=" N VAL E 143 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 202 " --> pdb=" O ILE E 145 " (cutoff:3.500A) 441 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: 0.84 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2699 1.34 - 1.46: 1587 1.46 - 1.57: 4194 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8552 Sorted by residual: bond pdb=" C6 7LD A 501 " pdb=" C9 7LD A 501 " ideal model delta sigma weight residual 1.471 1.392 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C10 7LD A 501 " pdb=" C9 7LD A 501 " ideal model delta sigma weight residual 1.333 1.388 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" C3 7LD A 501 " pdb=" C7 7LD A 501 " ideal model delta sigma weight residual 1.414 1.361 0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" C16 7LD A 501 " pdb=" O1 7LD A 501 " ideal model delta sigma weight residual 1.226 1.272 -0.046 2.00e-02 2.50e+03 5.19e+00 bond pdb=" N GLU C 3 " pdb=" CA GLU C 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 ... (remaining 8547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 11205 1.11 - 2.23: 348 2.23 - 3.34: 59 3.34 - 4.46: 27 4.46 - 5.57: 3 Bond angle restraints: 11642 Sorted by residual: angle pdb=" C SER A 145 " pdb=" N LYS A 146 " pdb=" CA LYS A 146 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.51e+00 angle pdb=" N VAL A 221 " pdb=" CA VAL A 221 " pdb=" C VAL A 221 " ideal model delta sigma weight residual 113.20 110.65 2.55 9.60e-01 1.09e+00 7.03e+00 angle pdb=" N TYR A 139 " pdb=" CA TYR A 139 " pdb=" CB TYR A 139 " ideal model delta sigma weight residual 113.65 110.42 3.23 1.47e+00 4.63e-01 4.83e+00 angle pdb=" N TYR E 223 " pdb=" CA TYR E 223 " pdb=" C TYR E 223 " ideal model delta sigma weight residual 109.81 114.54 -4.73 2.21e+00 2.05e-01 4.58e+00 angle pdb=" C14 7LD A 501 " pdb=" C16 7LD A 501 " pdb=" N3 7LD A 501 " ideal model delta sigma weight residual 117.57 123.05 -5.48 3.00e+00 1.11e-01 3.33e+00 ... (remaining 11637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 4894 33.91 - 67.83: 119 67.83 - 101.74: 8 101.74 - 135.65: 0 135.65 - 169.56: 1 Dihedral angle restraints: 5022 sinusoidal: 1790 harmonic: 3232 Sorted by residual: dihedral pdb=" CB CYS A 148 " pdb=" SG CYS A 148 " pdb=" SG CYS A 227 " pdb=" CB CYS A 227 " ideal model delta sinusoidal sigma weight residual -86.00 -163.73 77.73 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" C16 7LD A 501 " pdb=" C17 7LD A 501 " pdb=" N3 7LD A 501 " pdb=" C18 7LD A 501 " ideal model delta sinusoidal sigma weight residual 91.75 -77.81 169.56 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA MET E 180 " pdb=" C MET E 180 " pdb=" N SER E 181 " pdb=" CA SER E 181 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 805 0.028 - 0.057: 366 0.057 - 0.085: 101 0.085 - 0.113: 60 0.113 - 0.142: 21 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA VAL C 327 " pdb=" N VAL C 327 " pdb=" C VAL C 327 " pdb=" CB VAL C 327 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE C 81 " pdb=" N ILE C 81 " pdb=" C ILE C 81 " pdb=" CB ILE C 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE C 123 " pdb=" N ILE C 123 " pdb=" C ILE C 123 " pdb=" CB ILE C 123 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1350 not shown) Planarity restraints: 1473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 7LD A 501 " 0.032 2.00e-02 2.50e+03 2.63e-02 1.04e+01 pdb=" C16 7LD A 501 " -0.004 2.00e-02 2.50e+03 pdb=" C17 7LD A 501 " -0.031 2.00e-02 2.50e+03 pdb=" C19 7LD A 501 " 0.031 2.00e-02 2.50e+03 pdb=" N3 7LD A 501 " 0.006 2.00e-02 2.50e+03 pdb=" O1 7LD A 501 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 223 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO E 224 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 224 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 224 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 134 " 0.134 9.50e-02 1.11e+02 6.02e-02 2.50e+00 pdb=" NE ARG C 134 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 134 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 134 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 134 " 0.002 2.00e-02 2.50e+03 ... (remaining 1470 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2520 2.81 - 3.33: 8234 3.33 - 3.86: 13850 3.86 - 4.38: 16888 4.38 - 4.90: 29461 Nonbonded interactions: 70953 Sorted by model distance: nonbonded pdb=" O ASP C 66 " pdb=" OG SER C 67 " model vdw 2.288 3.040 nonbonded pdb=" O SER A 207 " pdb=" OG SER A 207 " model vdw 2.376 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.389 3.040 nonbonded pdb=" OD2 ASP A 155 " pdb=" OH TYR A 370 " model vdw 2.454 3.040 nonbonded pdb=" O THR B 136 " pdb=" OG1 THR B 136 " model vdw 2.461 3.040 ... (remaining 70948 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: 0.930 Set stop_for_unknowns flag: 0.010 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.100 Find NCS groups from input model: 0.030 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:0.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 0.079 8553 Z= 0.189 Angle : 0.504 5.571 11644 Z= 0.269 Chirality : 0.040 0.142 1353 Planarity : 0.004 0.060 1473 Dihedral : 14.895 169.563 2931 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.59 % Allowed : 14.25 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.27), residues: 1095 helix: 1.96 (0.29), residues: 371 sheet: -1.41 (0.32), residues: 270 loop : -0.26 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 134 TYR 0.009 0.001 TYR E 178 PHE 0.017 0.001 PHE A 339 TRP 0.013 0.001 TRP A 367 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 8552) covalent geometry : angle 0.50350 / 0.27 (11642) SS BOND : bond 0.00628 / 0.33 ( 1) SS BOND : angle 0.93958 / 0.50 ( 2) hydrogen bonds : bond 0.16417 / 10.26 ( 435) hydrogen bonds : angle 7.97330 / 5.78 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8233 (mmt) cc_final: 0.7666 (mmt) REVERT: A 213 PHE cc_start: 0.7872 (m-10) cc_final: 0.7633 (m-10) REVERT: B 101 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8684 (p0) REVERT: B 131 ASN cc_start: 0.8893 (t0) cc_final: 0.8540 (t0) REVERT: D 21 MET cc_start: 0.7360 (ttp) cc_final: 0.7060 (tmm) REVERT: E 167 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7469 (tp40) outliers start: 5 outliers final: 3 residues processed: 147 average time/residue: 0.0529 time to fit residues: 10.9684 Evaluate side-chains 133 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain E residue 167 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN C 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.166359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133413 restraints weight = 9898.437| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.97 r_work: 0.3288 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8553 Z= 0.189 Angle : 0.562 7.749 11644 Z= 0.297 Chirality : 0.043 0.164 1353 Planarity : 0.004 0.051 1473 Dihedral : 8.002 177.173 1231 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.97 % Allowed : 15.44 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.27), residues: 1095 helix: 1.98 (0.28), residues: 372 sheet: -1.21 (0.32), residues: 269 loop : -0.13 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.018 0.002 TYR B 115 PHE 0.016 0.002 PHE A 234 TRP 0.015 0.002 TRP A 367 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 ( 8552) covalent geometry : angle 0.56229 / 0.30 (11642) SS BOND : bond 0.00761 / 0.40 ( 1) SS BOND : angle 1.11254 / 0.59 ( 2) hydrogen bonds : bond 0.03827 / 2.52 ( 435) hydrogen bonds : angle 5.68835 / 4.12 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 384 ASN cc_start: 0.7805 (t0) cc_final: 0.7316 (t0) REVERT: C 234 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.7986 (t80) REVERT: C 270 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7933 (pp) REVERT: B 131 ASN cc_start: 0.8954 (t0) cc_final: 0.8626 (t0) REVERT: E 83 MET cc_start: 0.7578 (mtp) cc_final: 0.7362 (mmt) outliers start: 25 outliers final: 13 residues processed: 158 average time/residue: 0.0740 time to fit residues: 17.0974 Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 85 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [23, 67, 95, 61, 16, 3, 30, 25, 76, 4, 43] chunk 23 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN C 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.168260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135959 restraints weight = 9796.368| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.00 r_work: 0.3295 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8553 Z= 0.142 Angle : 0.530 7.025 11644 Z= 0.277 Chirality : 0.042 0.164 1353 Planarity : 0.004 0.048 1473 Dihedral : 7.515 178.668 1223 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.97 % Allowed : 15.44 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.27), residues: 1095 helix: 2.09 (0.28), residues: 375 sheet: -1.08 (0.31), residues: 283 loop : 0.03 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.029 0.002 TYR E 223 PHE 0.014 0.001 PHE A 234 TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 8552) covalent geometry : angle 0.52999 / 0.28 (11642) SS BOND : bond 0.00601 / 0.32 ( 1) SS BOND : angle 1.01782 / 0.54 ( 2) hydrogen bonds : bond 0.03400 / 2.26 ( 435) hydrogen bonds : angle 5.25006 / 3.80 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.311 Fit side-chains REVERT: A 384 ASN cc_start: 0.7548 (t0) cc_final: 0.7172 (t0) REVERT: C 234 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.7889 (t80) REVERT: B 101 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8791 (p0) REVERT: B 131 ASN cc_start: 0.8892 (t0) cc_final: 0.8586 (t0) REVERT: E 223 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.6297 (t80) outliers start: 25 outliers final: 16 residues processed: 160 average time/residue: 0.0773 time to fit residues: 17.8703 Evaluate side-chains 150 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [37, 38, 24, 44, 64, 12, 79, 5, 43, 77, 11] chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN C 91 HIS C 268 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137554 restraints weight = 9951.942| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.05 r_work: 0.3312 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8553 Z= 0.131 Angle : 0.511 7.198 11644 Z= 0.268 Chirality : 0.041 0.168 1353 Planarity : 0.004 0.051 1473 Dihedral : 7.401 176.697 1223 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.09 % Allowed : 15.32 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.27), residues: 1095 helix: 2.21 (0.28), residues: 373 sheet: -1.00 (0.31), residues: 273 loop : 0.08 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 134 TYR 0.024 0.001 TYR E 223 PHE 0.014 0.001 PHE A 234 TRP 0.012 0.001 TRP A 367 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 8552) covalent geometry : angle 0.51101 / 0.27 (11642) SS BOND : bond 0.00560 / 0.29 ( 1) SS BOND : angle 0.88323 / 0.47 ( 2) hydrogen bonds : bond 0.03224 / 2.15 ( 435) hydrogen bonds : angle 4.95073 / 3.58 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 384 ASN cc_start: 0.7517 (t0) cc_final: 0.7178 (t0) REVERT: C 234 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.7839 (t80) REVERT: C 270 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7871 (pt) REVERT: B 101 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8782 (p0) REVERT: B 131 ASN cc_start: 0.8883 (t0) cc_final: 0.8557 (t0) outliers start: 26 outliers final: 18 residues processed: 159 average time/residue: 0.0727 time to fit residues: 16.9512 Evaluate side-chains 157 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 85 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [58, 44, 3, 84, 9, 23, 81, 97, 5, 108, 21] chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.0270 chunk 3 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 268 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.170557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138522 restraints weight = 9835.128| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.01 r_work: 0.3317 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8553 Z= 0.130 Angle : 0.513 7.363 11644 Z= 0.266 Chirality : 0.041 0.161 1353 Planarity : 0.004 0.051 1473 Dihedral : 7.353 175.935 1223 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.33 % Allowed : 15.56 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.27), residues: 1095 helix: 2.23 (0.28), residues: 377 sheet: -0.94 (0.31), residues: 274 loop : 0.19 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 134 TYR 0.031 0.002 TYR E 223 PHE 0.017 0.001 PHE E 80 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 8552) covalent geometry : angle 0.51319 / 0.27 (11642) SS BOND : bond 0.00550 / 0.29 ( 1) SS BOND : angle 0.82592 / 0.44 ( 2) hydrogen bonds : bond 0.03139 / 2.10 ( 435) hydrogen bonds : angle 4.81524 / 3.48 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 ASN cc_start: 0.7471 (t0) cc_final: 0.7139 (t0) REVERT: C 234 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.7823 (t80) REVERT: C 270 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7941 (pt) REVERT: B 93 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7830 (ptt90) REVERT: B 101 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8795 (p0) REVERT: B 131 ASN cc_start: 0.8883 (t0) cc_final: 0.8559 (t0) outliers start: 28 outliers final: 21 residues processed: 156 average time/residue: 0.0821 time to fit residues: 18.2437 Evaluate side-chains 153 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [93, 64, 85, 56, 68, 66, 92, 65, 1, 81, 25] chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.0070 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.170613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138470 restraints weight = 9839.741| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.02 r_work: 0.3337 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8553 Z= 0.132 Angle : 0.515 7.247 11644 Z= 0.266 Chirality : 0.041 0.168 1353 Planarity : 0.004 0.053 1473 Dihedral : 7.320 175.443 1223 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.56 % Allowed : 16.15 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.27), residues: 1095 helix: 2.33 (0.28), residues: 373 sheet: -0.84 (0.31), residues: 268 loop : 0.25 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 134 TYR 0.024 0.001 TYR E 223 PHE 0.017 0.001 PHE A 234 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 8552) covalent geometry : angle 0.51504 / 0.27 (11642) SS BOND : bond 0.00526 / 0.28 ( 1) SS BOND : angle 0.84805 / 0.45 ( 2) hydrogen bonds : bond 0.03139 / 2.11 ( 435) hydrogen bonds : angle 4.67708 / 3.37 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7819 (mm) REVERT: A 384 ASN cc_start: 0.7624 (t0) cc_final: 0.7291 (t0) REVERT: C 234 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.7910 (t80) REVERT: C 270 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7962 (pt) REVERT: B 101 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8825 (p0) REVERT: B 131 ASN cc_start: 0.8953 (t0) cc_final: 0.8619 (t0) REVERT: E 223 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.6095 (t80) outliers start: 30 outliers final: 21 residues processed: 158 average time/residue: 0.0768 time to fit residues: 17.7006 Evaluate side-chains 154 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [79, 36, 16, 24, 70, 100, 59, 34, 105, 39, 85] chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.167434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135079 restraints weight = 9989.501| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.99 r_work: 0.3288 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8553 Z= 0.194 Angle : 0.561 8.069 11644 Z= 0.291 Chirality : 0.043 0.189 1353 Planarity : 0.004 0.054 1473 Dihedral : 7.507 178.611 1223 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.56 % Allowed : 16.27 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.27), residues: 1095 helix: 2.08 (0.28), residues: 371 sheet: -0.74 (0.32), residues: 255 loop : 0.07 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 134 TYR 0.026 0.002 TYR E 223 PHE 0.021 0.002 PHE A 234 TRP 0.017 0.001 TRP A 367 HIS 0.002 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 ( 8552) covalent geometry : angle 0.56098 / 0.29 (11642) SS BOND : bond 0.00730 / 0.38 ( 1) SS BOND : angle 1.15629 / 0.61 ( 2) hydrogen bonds : bond 0.03468 / 2.31 ( 435) hydrogen bonds : angle 4.76861 / 3.43 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 213 PHE cc_start: 0.7661 (m-10) cc_final: 0.7284 (m-10) REVERT: A 215 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7851 (mm) REVERT: A 384 ASN cc_start: 0.7717 (t0) cc_final: 0.7383 (t0) REVERT: C 234 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.7976 (t80) REVERT: C 270 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7968 (pt) REVERT: B 101 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8857 (p0) REVERT: B 131 ASN cc_start: 0.9019 (t0) cc_final: 0.8687 (t0) REVERT: E 223 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.6209 (t80) outliers start: 30 outliers final: 21 residues processed: 149 average time/residue: 0.0747 time to fit residues: 16.2782 Evaluate side-chains 148 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 223 TYR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [96, 6, 79, 14, 84, 105, 89, 86, 28, 74, 106] chunk 96 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 106 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138075 restraints weight = 9914.884| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.06 r_work: 0.3320 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8553 Z= 0.131 Angle : 0.519 7.648 11644 Z= 0.268 Chirality : 0.041 0.181 1353 Planarity : 0.004 0.054 1473 Dihedral : 7.332 175.041 1223 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.33 % Allowed : 16.75 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.27), residues: 1095 helix: 2.25 (0.28), residues: 373 sheet: -0.79 (0.31), residues: 267 loop : 0.22 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 134 TYR 0.022 0.001 TYR E 223 PHE 0.015 0.001 PHE A 234 TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 8552) covalent geometry : angle 0.51918 / 0.27 (11642) SS BOND : bond 0.00472 / 0.25 ( 1) SS BOND : angle 0.90025 / 0.47 ( 2) hydrogen bonds : bond 0.03148 / 2.12 ( 435) hydrogen bonds : angle 4.62194 / 3.32 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 213 PHE cc_start: 0.7539 (m-10) cc_final: 0.7311 (m-10) REVERT: A 384 ASN cc_start: 0.7446 (t0) cc_final: 0.7151 (t0) REVERT: C 234 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.7892 (t80) REVERT: C 270 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7959 (pt) REVERT: B 101 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8793 (p0) REVERT: B 131 ASN cc_start: 0.8909 (t0) cc_final: 0.8571 (t0) REVERT: E 223 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5961 (t80) outliers start: 28 outliers final: 22 residues processed: 152 average time/residue: 0.0772 time to fit residues: 17.1532 Evaluate side-chains 151 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 223 TYR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [43, 12, 51, 64, 104, 10, 99, 67, 22, 59, 21] chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138934 restraints weight = 9887.620| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.84 r_work: 0.3376 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8553 Z= 0.123 Angle : 0.523 7.802 11644 Z= 0.268 Chirality : 0.042 0.187 1353 Planarity : 0.004 0.056 1473 Dihedral : 7.262 173.807 1223 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.33 % Allowed : 16.63 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.27), residues: 1095 helix: 2.38 (0.28), residues: 366 sheet: -0.70 (0.31), residues: 267 loop : 0.16 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.021 0.001 TYR E 223 PHE 0.015 0.001 PHE A 234 TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 8552) covalent geometry : angle 0.52270 / 0.27 (11642) SS BOND : bond 0.00463 / 0.24 ( 1) SS BOND : angle 0.70659 / 0.37 ( 2) hydrogen bonds : bond 0.03092 / 2.07 ( 435) hydrogen bonds : angle 4.57802 / 3.30 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.8440 (mtt) cc_final: 0.7620 (mtt) REVERT: A 213 PHE cc_start: 0.7507 (m-10) cc_final: 0.7166 (m-10) REVERT: A 384 ASN cc_start: 0.7515 (t0) cc_final: 0.7215 (t0) REVERT: C 234 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.7986 (t80) REVERT: C 270 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7939 (pt) REVERT: B 101 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8842 (p0) REVERT: B 131 ASN cc_start: 0.8962 (t0) cc_final: 0.8639 (t0) REVERT: E 82 GLN cc_start: 0.8268 (tp40) cc_final: 0.8000 (tp40) REVERT: E 223 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.6133 (t80) outliers start: 28 outliers final: 22 residues processed: 151 average time/residue: 0.0732 time to fit residues: 16.5391 Evaluate side-chains 149 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 223 TYR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [0, 72, 1, 60, 29, 55, 12, 71, 68, 28, 103] chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 0.0570 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.172470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142495 restraints weight = 9806.246| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.92 r_work: 0.3389 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8553 Z= 0.113 Angle : 0.513 7.477 11644 Z= 0.263 Chirality : 0.041 0.222 1353 Planarity : 0.004 0.055 1473 Dihedral : 7.139 172.057 1223 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.85 % Allowed : 17.22 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 1095 helix: 2.46 (0.28), residues: 366 sheet: -0.64 (0.31), residues: 267 loop : 0.21 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.019 0.001 TYR E 223 PHE 0.013 0.001 PHE A 234 TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 8552) covalent geometry : angle 0.51254 / 0.26 (11642) SS BOND : bond 0.00382 / 0.20 ( 1) SS BOND : angle 0.66463 / 0.35 ( 2) hydrogen bonds : bond 0.02999 / 2.02 ( 435) hydrogen bonds : angle 4.50673 / 3.25 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.8313 (mtt) cc_final: 0.7486 (mtt) REVERT: A 213 PHE cc_start: 0.7398 (m-10) cc_final: 0.7189 (m-10) REVERT: A 384 ASN cc_start: 0.7366 (t0) cc_final: 0.6973 (t0) REVERT: C 234 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.7890 (t80) REVERT: C 270 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7967 (pt) REVERT: B 25 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7512 (mt-10) REVERT: B 101 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8777 (p0) REVERT: B 131 ASN cc_start: 0.8877 (t0) cc_final: 0.8543 (t0) REVERT: B 242 GLU cc_start: 0.8487 (tt0) cc_final: 0.8260 (tt0) REVERT: E 82 GLN cc_start: 0.8224 (tp40) cc_final: 0.7932 (tp40) outliers start: 24 outliers final: 19 residues processed: 152 average time/residue: 0.0729 time to fit residues: 16.4609 Evaluate side-chains 151 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [89, 55, 27, 40, 21, 74, 8, 14, 5, 56, 66] chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.172849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141822 restraints weight = 9921.089| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.94 r_work: 0.3382 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8553 Z= 0.117 Angle : 0.516 8.717 11644 Z= 0.263 Chirality : 0.041 0.208 1353 Planarity : 0.004 0.050 1473 Dihedral : 6.936 171.706 1221 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.61 % Allowed : 17.46 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.27), residues: 1095 helix: 2.46 (0.28), residues: 367 sheet: -0.62 (0.31), residues: 267 loop : 0.23 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.031 0.001 TYR E 223 PHE 0.014 0.001 PHE A 234 TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 8552) covalent geometry : angle 0.51638 / 0.26 (11642) SS BOND : bond 0.00410 / 0.22 ( 1) SS BOND : angle 0.65951 / 0.35 ( 2) hydrogen bonds : bond 0.02969 / 1.99 ( 435) hydrogen bonds : angle 4.47292 / 3.22 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2310.00 seconds wall clock time: 40 minutes 15.02 seconds (2415.02 seconds total)