Starting phenix.real_space_refine on Wed Feb 4 02:20:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kz2_62651/02_2026/9kz2_62651.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kz2_62651/02_2026/9kz2_62651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kz2_62651/02_2026/9kz2_62651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kz2_62651/02_2026/9kz2_62651.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kz2_62651/02_2026/9kz2_62651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kz2_62651/02_2026/9kz2_62651.map" } resolution = 3.43 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= 0.001 sd= 0.018 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 55 5.16 5 C 5258 2.51 5 N 1413 2.21 5 O 1509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8235 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 70 Classifications: {'peptide': 8} Link IDs: {'NMTRANS': 1, 'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLE:plan-1': 1} Unresolved non-hydrogen planarities: 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} Chain: "B" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2421 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1575 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 51 Chain: "G" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 398 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 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: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1698 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2056 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TRP:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 1.43, per 1000 atoms: 0.17 Number of scatterers: 8235 At special positions: 0 Unit cell: (85.5925, 123.918, 123.918, 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 55 16.00 O 1509 8.00 N 1413 7.00 C 5258 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=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 205.7 milliseconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 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: 2088 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 36.4% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.623A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.969A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.613A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.572A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS A 215 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 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 352 removed outlier: 3.968A pdb=" N VAL A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.568A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.719A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.634A pdb=" N ASP H 223 " --> pdb=" O GLU H 220 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 220 through 224' Processing helix chain 'C' and resid 20 through 50 Proline residue: C 39 - end of helix Processing helix chain 'C' and resid 57 through 85 removed outlier: 3.954A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 91 through 126 removed outlier: 3.598A pdb=" N CYS C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Proline residue: C 99 - end of helix removed outlier: 5.257A pdb=" N VAL C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.983A pdb=" N ASN C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 155 Processing helix chain 'C' and resid 156 through 159 removed outlier: 3.673A pdb=" N VAL C 159 " --> pdb=" O PRO C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 159' Processing helix chain 'C' and resid 332 through 363 removed outlier: 5.032A 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 374 through 403 removed outlier: 3.555A pdb=" N TRP C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) Proline residue: C 392 - end of helix removed outlier: 3.517A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 436 removed outlier: 3.905A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 439 through 450 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.514A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.953A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.994A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.743A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.585A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.513A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.714A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.629A pdb=" N LEU A 38 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.669A pdb=" N LEU H 117 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA H 92 " --> pdb=" O LEU H 117 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.667A pdb=" N ILE H 157 " --> pdb=" O LEU H 214 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.664A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 162 through 163 removed outlier: 3.582A pdb=" N GLU C 162 " --> pdb=" O GLY C 173 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1152 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: 0.96 Time building geometry restraints manager: 0.66 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: 2668 1.34 - 1.46: 1972 1.46 - 1.58: 3704 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8417 Sorted by residual: bond pdb=" CB LYS A 24 " pdb=" CG LYS A 24 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.99e-01 bond pdb=" C ILE C 98 " pdb=" N PRO C 99 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.41e-01 bond pdb=" CA ASN A 43 " pdb=" CB ASN A 43 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.51e-01 bond pdb=" C PRO C 21 " pdb=" N PRO C 22 " ideal model delta sigma weight residual 1.335 1.347 -0.011 1.36e-02 5.41e+03 6.84e-01 bond pdb=" CA ILE B 270 " pdb=" CB ILE B 270 " ideal model delta sigma weight residual 1.540 1.551 -0.011 1.36e-02 5.41e+03 6.67e-01 ... (remaining 8412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 11227 1.44 - 2.88: 186 2.88 - 4.32: 38 4.32 - 5.76: 13 5.76 - 7.19: 5 Bond angle restraints: 11469 Sorted by residual: angle pdb=" CB LYS A 24 " pdb=" CG LYS A 24 " pdb=" CD LYS A 24 " ideal model delta sigma weight residual 111.30 118.49 -7.19 2.30e+00 1.89e-01 9.79e+00 angle pdb=" C ASP A 42 " pdb=" N ASN A 43 " pdb=" CA ASN A 43 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.26e+00 angle pdb=" C VAL H 48 " pdb=" CA VAL H 48 " pdb=" CB VAL H 48 " ideal model delta sigma weight residual 111.71 109.74 1.97 8.50e-01 1.38e+00 5.38e+00 angle pdb=" N THR B 87 " pdb=" CA THR B 87 " pdb=" CB THR B 87 " ideal model delta sigma weight residual 113.65 110.26 3.39 1.47e+00 4.63e-01 5.33e+00 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N ALA A 41 " ideal model delta sigma weight residual 114.52 116.88 -2.36 1.09e+00 8.42e-01 4.70e+00 ... (remaining 11464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 4476 17.59 - 35.17: 353 35.17 - 52.76: 57 52.76 - 70.35: 9 70.35 - 87.94: 9 Dihedral angle restraints: 4904 sinusoidal: 1668 harmonic: 3236 Sorted by residual: 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 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLN C 372 " pdb=" C GLN C 372 " pdb=" N SER C 373 " pdb=" CA SER C 373 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB GLU A 277 " pdb=" CG GLU A 277 " pdb=" CD GLU A 277 " pdb=" OE1 GLU A 277 " ideal model delta sinusoidal sigma weight residual 0.00 87.94 -87.94 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 4901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 927 0.038 - 0.076: 291 0.076 - 0.114: 93 0.114 - 0.152: 17 0.152 - 0.190: 1 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CA ASP B 163 " pdb=" N ASP B 163 " pdb=" C ASP B 163 " pdb=" CB ASP B 163 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CB VAL C 123 " pdb=" CA VAL C 123 " pdb=" CG1 VAL C 123 " pdb=" CG2 VAL C 123 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1326 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 6 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO D 7 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 7 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 7 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.014 2.00e-02 2.50e+03 1.17e-02 3.45e+00 pdb=" CG TRP H 47 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 20 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO C 21 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 21 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 21 " 0.020 5.00e-02 4.00e+02 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 590 2.74 - 3.28: 8165 3.28 - 3.82: 13203 3.82 - 4.36: 14590 4.36 - 4.90: 26258 Nonbonded interactions: 62806 Sorted by model distance: nonbonded pdb=" OG1 THR C 55 " pdb=" OD1 ASN C 57 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 177 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.235 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.247 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.252 3.040 ... (remaining 62801 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: 0.970 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 : 0.003 0.101 8421 Z= 0.155 Angle : 0.528 7.195 11475 Z= 0.277 Chirality : 0.042 0.190 1329 Planarity : 0.004 0.052 1464 Dihedral : 13.154 87.936 2807 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.27), residues: 1100 helix: 2.20 (0.28), residues: 371 sheet: -0.44 (0.32), residues: 281 loop : -0.56 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 367 TYR 0.011 0.001 TYR A 303 PHE 0.014 0.001 PHE A 308 TRP 0.032 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8417) covalent geometry : angle 0.52734 (11469) SS BOND : bond 0.00164 ( 3) SS BOND : angle 0.77901 ( 6) hydrogen bonds : bond 0.20536 ( 407) hydrogen bonds : angle 7.11868 ( 1152) Misc. bond : bond 0.10054 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLN cc_start: 0.7427 (tm-30) cc_final: 0.7095 (tm-30) REVERT: B 49 ARG cc_start: 0.8031 (mmt-90) cc_final: 0.7694 (mmt180) REVERT: B 52 ARG cc_start: 0.7088 (mtt90) cc_final: 0.6817 (mtm-85) REVERT: B 75 GLN cc_start: 0.8004 (mm110) cc_final: 0.7763 (mm-40) REVERT: B 110 ASN cc_start: 0.7812 (m110) cc_final: 0.7573 (m110) REVERT: B 111 TYR cc_start: 0.8011 (m-80) cc_final: 0.7772 (m-80) REVERT: B 137 ARG cc_start: 0.7816 (ttm-80) cc_final: 0.7081 (mmt90) REVERT: B 154 ASP cc_start: 0.7349 (m-30) cc_final: 0.7140 (m-30) REVERT: B 214 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7068 (mtm110) REVERT: B 292 PHE cc_start: 0.8326 (m-10) cc_final: 0.8095 (m-80) REVERT: B 323 ASP cc_start: 0.6135 (p0) cc_final: 0.5906 (p0) REVERT: B 325 MET cc_start: 0.7736 (mtt) cc_final: 0.7171 (mtt) REVERT: A 14 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6605 (tm-30) REVERT: A 24 LYS cc_start: 0.7475 (mmmt) cc_final: 0.7176 (mmmt) REVERT: A 32 LYS cc_start: 0.8537 (mttt) cc_final: 0.7971 (mttt) REVERT: A 193 LYS cc_start: 0.8661 (mttt) cc_final: 0.8441 (mtpp) REVERT: A 209 ARG cc_start: 0.7401 (mmt90) cc_final: 0.7174 (mtt-85) REVERT: A 211 LYS cc_start: 0.8454 (mmmt) cc_final: 0.8057 (mmmm) REVERT: A 212 TRP cc_start: 0.7274 (p-90) cc_final: 0.6463 (p-90) REVERT: A 214 HIS cc_start: 0.8672 (p90) cc_final: 0.8283 (p90) REVERT: A 228 LEU cc_start: 0.8186 (mp) cc_final: 0.7921 (mp) REVERT: A 247 SER cc_start: 0.7966 (t) cc_final: 0.7757 (t) REVERT: A 303 TYR cc_start: 0.7470 (t80) cc_final: 0.6778 (t80) REVERT: A 307 GLN cc_start: 0.8177 (mm110) cc_final: 0.7270 (mp10) REVERT: A 309 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7806 (mt-10) REVERT: A 322 HIS cc_start: 0.7991 (t70) cc_final: 0.7674 (t70) REVERT: A 331 ASN cc_start: 0.7896 (p0) cc_final: 0.7655 (p0) REVERT: A 349 ARG cc_start: 0.7671 (ttp-110) cc_final: 0.7197 (ttm-80) REVERT: G 38 MET cc_start: 0.7668 (ttp) cc_final: 0.7425 (ttm) REVERT: G 60 PRO cc_start: 0.8465 (Cg_endo) cc_final: 0.8260 (Cg_exo) REVERT: H 18 ARG cc_start: 0.6266 (ttm-80) cc_final: 0.4951 (ttt180) REVERT: H 101 TYR cc_start: 0.7139 (m-80) cc_final: 0.6902 (m-80) REVERT: H 179 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7399 (tm-30) REVERT: H 193 SER cc_start: 0.7565 (t) cc_final: 0.7089 (t) REVERT: H 194 ASN cc_start: 0.7241 (m110) cc_final: 0.7041 (m-40) REVERT: H 195 LEU cc_start: 0.8379 (tp) cc_final: 0.8167 (tp) REVERT: H 233 LEU cc_start: 0.8235 (tp) cc_final: 0.7682 (tp) REVERT: H 238 THR cc_start: 0.7262 (p) cc_final: 0.6986 (p) REVERT: C 27 MET cc_start: 0.7265 (tmm) cc_final: 0.6888 (tmm) REVERT: C 65 THR cc_start: 0.7441 (p) cc_final: 0.7164 (t) REVERT: C 106 MET cc_start: 0.7160 (mtt) cc_final: 0.6851 (mtt) REVERT: C 130 CYS cc_start: 0.7871 (m) cc_final: 0.7591 (m) REVERT: C 151 PHE cc_start: 0.7769 (t80) cc_final: 0.7421 (t80) REVERT: C 336 ILE cc_start: 0.8015 (tt) cc_final: 0.7713 (pt) REVERT: C 398 VAL cc_start: 0.8328 (t) cc_final: 0.8098 (m) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.0795 time to fit residues: 30.6102 Evaluate side-chains 246 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.0040 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.0020 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 156 GLN B 259 GLN A 189 HIS ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.132501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115425 restraints weight = 14547.203| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.92 r_work: 0.3417 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8421 Z= 0.139 Angle : 0.575 6.923 11475 Z= 0.300 Chirality : 0.044 0.209 1329 Planarity : 0.004 0.043 1464 Dihedral : 4.069 42.248 1195 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.74 % Allowed : 12.19 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1100 helix: 2.14 (0.28), residues: 375 sheet: -0.13 (0.32), residues: 283 loop : -0.61 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 283 TYR 0.011 0.001 TYR A 303 PHE 0.025 0.002 PHE A 275 TRP 0.019 0.002 TRP H 47 HIS 0.008 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8417) covalent geometry : angle 0.57457 (11469) SS BOND : bond 0.00702 ( 3) SS BOND : angle 0.97812 ( 6) hydrogen bonds : bond 0.04297 ( 407) hydrogen bonds : angle 5.18450 ( 1152) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 251 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7522 (tm-30) REVERT: B 50 THR cc_start: 0.8012 (m) cc_final: 0.7692 (m) REVERT: B 52 ARG cc_start: 0.7363 (mtt90) cc_final: 0.7099 (mtt90) REVERT: B 137 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7516 (mmt90) REVERT: B 214 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7428 (mtm110) REVERT: B 218 CYS cc_start: 0.7331 (m) cc_final: 0.7088 (m) REVERT: B 219 ARG cc_start: 0.7637 (mmt-90) cc_final: 0.7182 (mmm160) REVERT: A 24 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7496 (mmmt) REVERT: A 32 LYS cc_start: 0.8687 (mttt) cc_final: 0.8265 (mttt) REVERT: A 187 GLU cc_start: 0.7898 (tt0) cc_final: 0.7497 (tt0) REVERT: A 198 ARG cc_start: 0.8327 (mtm180) cc_final: 0.7846 (mtp85) REVERT: A 209 ARG cc_start: 0.7654 (mmt90) cc_final: 0.7433 (mtt-85) REVERT: A 212 TRP cc_start: 0.7458 (p-90) cc_final: 0.7211 (p-90) REVERT: A 303 TYR cc_start: 0.7835 (t80) cc_final: 0.7330 (t80) REVERT: A 349 ARG cc_start: 0.7878 (ttp-110) cc_final: 0.7622 (ttm-80) REVERT: G 21 MET cc_start: 0.8289 (tpp) cc_final: 0.7697 (tmm) REVERT: G 60 PRO cc_start: 0.8451 (Cg_endo) cc_final: 0.8241 (Cg_exo) REVERT: H 18 ARG cc_start: 0.6857 (ttm-80) cc_final: 0.5754 (ttt180) REVERT: H 27 PHE cc_start: 0.8830 (p90) cc_final: 0.8036 (p90) REVERT: H 69 THR cc_start: 0.8090 (m) cc_final: 0.7552 (p) REVERT: H 179 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7532 (tm-30) REVERT: H 193 SER cc_start: 0.7656 (t) cc_final: 0.7196 (t) REVERT: H 194 ASN cc_start: 0.7450 (m110) cc_final: 0.7240 (m-40) REVERT: H 195 LEU cc_start: 0.8615 (tp) cc_final: 0.8411 (tp) REVERT: H 233 LEU cc_start: 0.8383 (tp) cc_final: 0.8132 (tp) REVERT: C 27 MET cc_start: 0.7547 (tmm) cc_final: 0.7164 (tmm) REVERT: C 65 THR cc_start: 0.7857 (p) cc_final: 0.7505 (t) REVERT: C 106 MET cc_start: 0.7404 (mtt) cc_final: 0.7059 (mtt) REVERT: C 151 PHE cc_start: 0.7972 (t80) cc_final: 0.7649 (t80) REVERT: C 336 ILE cc_start: 0.8284 (tt) cc_final: 0.8055 (pt) REVERT: C 398 VAL cc_start: 0.8219 (t) cc_final: 0.7995 (m) outliers start: 14 outliers final: 11 residues processed: 257 average time/residue: 0.0807 time to fit residues: 28.1990 Evaluate side-chains 250 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 239 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 407 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.0570 chunk 44 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 chunk 86 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 256 ASN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.132249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114728 restraints weight = 14090.682| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.00 r_work: 0.3387 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8421 Z= 0.137 Angle : 0.540 6.747 11475 Z= 0.284 Chirality : 0.043 0.243 1329 Planarity : 0.004 0.037 1464 Dihedral : 4.060 34.219 1195 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.86 % Allowed : 15.17 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.27), residues: 1100 helix: 2.12 (0.28), residues: 375 sheet: 0.01 (0.32), residues: 285 loop : -0.66 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 49 TYR 0.011 0.001 TYR A 303 PHE 0.016 0.001 PHE B 180 TRP 0.013 0.002 TRP H 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8417) covalent geometry : angle 0.53919 (11469) SS BOND : bond 0.01067 ( 3) SS BOND : angle 0.96577 ( 6) hydrogen bonds : bond 0.03919 ( 407) hydrogen bonds : angle 4.78129 ( 1152) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 253 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7426 (tm-30) REVERT: B 50 THR cc_start: 0.8049 (m) cc_final: 0.7730 (m) REVERT: B 52 ARG cc_start: 0.7472 (mtt90) cc_final: 0.7244 (ptp90) REVERT: B 214 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7427 (mtm110) REVERT: A 17 LYS cc_start: 0.7627 (mmtt) cc_final: 0.7347 (mmtt) REVERT: A 24 LYS cc_start: 0.7789 (mmmt) cc_final: 0.7553 (mmmt) REVERT: A 32 LYS cc_start: 0.8711 (mttt) cc_final: 0.8480 (mttt) REVERT: A 209 ARG cc_start: 0.7717 (mmt90) cc_final: 0.7498 (mtt-85) REVERT: A 212 TRP cc_start: 0.7476 (p-90) cc_final: 0.7038 (p-90) REVERT: A 303 TYR cc_start: 0.7888 (t80) cc_final: 0.7384 (t80) REVERT: A 349 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7646 (ttm-80) REVERT: G 21 MET cc_start: 0.8375 (tpp) cc_final: 0.7776 (tmm) REVERT: H 18 ARG cc_start: 0.7054 (ttm-80) cc_final: 0.5810 (ttt180) REVERT: H 27 PHE cc_start: 0.8818 (p90) cc_final: 0.7892 (p90) REVERT: H 60 TYR cc_start: 0.8119 (m-80) cc_final: 0.7861 (m-80) REVERT: H 69 THR cc_start: 0.8048 (m) cc_final: 0.7331 (p) REVERT: H 101 TYR cc_start: 0.7425 (m-80) cc_final: 0.6877 (m-80) REVERT: H 179 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7473 (tm-30) REVERT: H 193 SER cc_start: 0.7806 (t) cc_final: 0.7366 (t) REVERT: C 27 MET cc_start: 0.7531 (tmm) cc_final: 0.7108 (tmm) REVERT: C 65 THR cc_start: 0.8127 (p) cc_final: 0.7804 (t) REVERT: C 84 LEU cc_start: 0.7313 (tp) cc_final: 0.7052 (mm) REVERT: C 106 MET cc_start: 0.7438 (mtt) cc_final: 0.7111 (mtt) REVERT: C 151 PHE cc_start: 0.7921 (t80) cc_final: 0.7635 (t80) REVERT: C 336 ILE cc_start: 0.8276 (tt) cc_final: 0.8020 (pt) REVERT: C 376 PHE cc_start: 0.7946 (t80) cc_final: 0.7728 (t80) REVERT: C 398 VAL cc_start: 0.8195 (t) cc_final: 0.7978 (m) outliers start: 23 outliers final: 18 residues processed: 261 average time/residue: 0.0854 time to fit residues: 30.3730 Evaluate side-chains 274 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 256 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 407 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** H 142 GLN ** 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 = 0.3706 r_free = 0.3706 target = 0.128555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111273 restraints weight = 14366.409| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.89 r_work: 0.3344 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8421 Z= 0.205 Angle : 0.606 8.043 11475 Z= 0.320 Chirality : 0.046 0.301 1329 Planarity : 0.004 0.039 1464 Dihedral : 4.339 29.047 1195 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.73 % Allowed : 18.28 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1100 helix: 1.83 (0.27), residues: 371 sheet: -0.04 (0.32), residues: 285 loop : -0.83 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 129 TYR 0.018 0.002 TYR H 173 PHE 0.024 0.002 PHE B 180 TRP 0.016 0.002 TRP B 169 HIS 0.010 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 8417) covalent geometry : angle 0.60567 (11469) SS BOND : bond 0.00509 ( 3) SS BOND : angle 1.36092 ( 6) hydrogen bonds : bond 0.04607 ( 407) hydrogen bonds : angle 4.81516 ( 1152) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7514 (tm-30) REVERT: B 82 TRP cc_start: 0.7319 (m-10) cc_final: 0.6036 (m-10) REVERT: B 137 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7660 (mmt90) REVERT: B 205 ASP cc_start: 0.8214 (p0) cc_final: 0.7996 (p0) REVERT: B 214 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7536 (mtm110) REVERT: B 230 ASN cc_start: 0.8454 (m-40) cc_final: 0.8158 (t0) REVERT: B 298 ASP cc_start: 0.7412 (t70) cc_final: 0.6784 (t70) REVERT: A 9 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7720 (mt-10) REVERT: A 17 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7337 (mmtt) REVERT: A 24 LYS cc_start: 0.7897 (mmmt) cc_final: 0.7665 (mmmt) REVERT: A 32 LYS cc_start: 0.8673 (mttt) cc_final: 0.8470 (mttt) REVERT: A 209 ARG cc_start: 0.7880 (mmt90) cc_final: 0.7625 (mtt-85) REVERT: A 303 TYR cc_start: 0.7977 (t80) cc_final: 0.7750 (t80) REVERT: A 317 LYS cc_start: 0.7983 (ptmm) cc_final: 0.7587 (ptpt) REVERT: A 347 ASN cc_start: 0.7799 (m-40) cc_final: 0.7502 (t0) REVERT: G 21 MET cc_start: 0.8357 (tpp) cc_final: 0.7836 (tmm) REVERT: H 30 SER cc_start: 0.8855 (t) cc_final: 0.8515 (p) REVERT: H 60 TYR cc_start: 0.8216 (m-80) cc_final: 0.7726 (m-80) REVERT: H 69 THR cc_start: 0.8136 (m) cc_final: 0.7399 (p) REVERT: H 77 ASN cc_start: 0.8254 (m-40) cc_final: 0.8023 (m-40) REVERT: H 101 TYR cc_start: 0.7586 (m-80) cc_final: 0.7231 (m-80) REVERT: H 179 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7464 (tm-30) REVERT: H 180 ARG cc_start: 0.8403 (mtt-85) cc_final: 0.8051 (mtt-85) REVERT: H 193 SER cc_start: 0.7984 (t) cc_final: 0.7633 (t) REVERT: C 27 MET cc_start: 0.7613 (tmm) cc_final: 0.7141 (tmm) REVERT: C 64 LEU cc_start: 0.8095 (tp) cc_final: 0.7889 (tp) REVERT: C 65 THR cc_start: 0.8108 (p) cc_final: 0.7775 (t) REVERT: C 84 LEU cc_start: 0.7640 (tp) cc_final: 0.7387 (mm) REVERT: C 93 PHE cc_start: 0.7056 (t80) cc_final: 0.6798 (t80) REVERT: C 151 PHE cc_start: 0.7888 (t80) cc_final: 0.7638 (t80) REVERT: C 336 ILE cc_start: 0.8348 (tt) cc_final: 0.8138 (pt) REVERT: C 398 VAL cc_start: 0.8278 (t) cc_final: 0.8054 (m) outliers start: 30 outliers final: 20 residues processed: 282 average time/residue: 0.0832 time to fit residues: 32.0179 Evaluate side-chains 273 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 253 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 346 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 108 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 156 GLN A 307 GLN ** H 142 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.129005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111769 restraints weight = 14331.646| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.90 r_work: 0.3351 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8421 Z= 0.174 Angle : 0.577 6.982 11475 Z= 0.305 Chirality : 0.044 0.169 1329 Planarity : 0.004 0.037 1464 Dihedral : 4.293 27.831 1195 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.48 % Allowed : 19.53 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 1100 helix: 1.85 (0.27), residues: 371 sheet: -0.10 (0.31), residues: 287 loop : -0.98 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 129 TYR 0.015 0.002 TYR C 174 PHE 0.021 0.002 PHE B 180 TRP 0.014 0.002 TRP B 169 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8417) covalent geometry : angle 0.57701 (11469) SS BOND : bond 0.00419 ( 3) SS BOND : angle 1.12037 ( 6) hydrogen bonds : bond 0.04232 ( 407) hydrogen bonds : angle 4.75148 ( 1152) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 LYS cc_start: 0.6689 (tttt) cc_final: 0.6413 (tptm) REVERT: B 82 TRP cc_start: 0.7442 (m-10) cc_final: 0.6348 (m-10) REVERT: B 137 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7749 (mmt-90) REVERT: B 214 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7474 (mtm110) REVERT: B 234 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: B 298 ASP cc_start: 0.7415 (t70) cc_final: 0.6757 (t70) REVERT: A 17 LYS cc_start: 0.7567 (mmtt) cc_final: 0.7339 (mmtt) REVERT: A 24 LYS cc_start: 0.7936 (mmmt) cc_final: 0.7699 (mmmt) REVERT: A 32 LYS cc_start: 0.8675 (mttt) cc_final: 0.8439 (mttt) REVERT: A 212 TRP cc_start: 0.7481 (p-90) cc_final: 0.7156 (p-90) REVERT: A 231 TYR cc_start: 0.5723 (OUTLIER) cc_final: 0.4980 (p90) REVERT: A 317 LYS cc_start: 0.7945 (ptmm) cc_final: 0.7580 (ptpt) REVERT: A 349 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7458 (ttm-80) REVERT: H 18 ARG cc_start: 0.7254 (ttm-80) cc_final: 0.6803 (mmm160) REVERT: H 30 SER cc_start: 0.8858 (t) cc_final: 0.8531 (p) REVERT: H 77 ASN cc_start: 0.8276 (m-40) cc_final: 0.8021 (m110) REVERT: H 101 TYR cc_start: 0.7561 (m-80) cc_final: 0.7130 (m-80) REVERT: H 179 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7539 (tm-30) REVERT: H 180 ARG cc_start: 0.8265 (mtt-85) cc_final: 0.7895 (mtt-85) REVERT: C 27 MET cc_start: 0.7617 (tmm) cc_final: 0.7132 (tmm) REVERT: C 64 LEU cc_start: 0.8013 (tp) cc_final: 0.7802 (tp) REVERT: C 65 THR cc_start: 0.8144 (p) cc_final: 0.7831 (t) REVERT: C 84 LEU cc_start: 0.7604 (tp) cc_final: 0.7367 (mm) REVERT: C 151 PHE cc_start: 0.7869 (t80) cc_final: 0.7598 (t80) REVERT: C 336 ILE cc_start: 0.8360 (tt) cc_final: 0.8152 (pt) REVERT: C 398 VAL cc_start: 0.8231 (t) cc_final: 0.8016 (m) outliers start: 36 outliers final: 24 residues processed: 272 average time/residue: 0.0825 time to fit residues: 30.5584 Evaluate side-chains 272 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 394 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 0.0570 chunk 7 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 56 optimal weight: 0.0670 chunk 35 optimal weight: 0.6980 chunk 76 optimal weight: 0.0170 chunk 85 optimal weight: 0.9990 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 176 GLN H 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.131833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.114319 restraints weight = 14003.612| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.97 r_work: 0.3382 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8421 Z= 0.111 Angle : 0.560 8.115 11475 Z= 0.286 Chirality : 0.043 0.263 1329 Planarity : 0.004 0.035 1464 Dihedral : 4.046 27.343 1195 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.48 % Allowed : 22.39 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.46 (0.27), residues: 1100 helix: 2.01 (0.28), residues: 374 sheet: -0.14 (0.31), residues: 291 loop : -0.84 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.021 0.001 TYR H 190 PHE 0.016 0.001 PHE C 376 TRP 0.015 0.001 TRP H 47 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8417) covalent geometry : angle 0.55928 (11469) SS BOND : bond 0.00494 ( 3) SS BOND : angle 1.03866 ( 6) hydrogen bonds : bond 0.03536 ( 407) hydrogen bonds : angle 4.51273 ( 1152) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 LYS cc_start: 0.6638 (OUTLIER) cc_final: 0.6330 (tptm) REVERT: B 137 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7770 (mmt90) REVERT: B 214 ARG cc_start: 0.7798 (mtt180) cc_final: 0.7428 (mtm110) REVERT: B 298 ASP cc_start: 0.7358 (t70) cc_final: 0.6692 (t70) REVERT: A 17 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7267 (mmtt) REVERT: A 24 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7644 (mmmt) REVERT: A 32 LYS cc_start: 0.8692 (mttt) cc_final: 0.8437 (mttt) REVERT: A 317 LYS cc_start: 0.7913 (ptmm) cc_final: 0.7508 (ptpt) REVERT: G 21 MET cc_start: 0.8410 (tpp) cc_final: 0.7901 (tmm) REVERT: G 61 PHE cc_start: 0.7546 (m-80) cc_final: 0.7281 (m-80) REVERT: H 18 ARG cc_start: 0.7233 (ttm-80) cc_final: 0.6834 (mmm160) REVERT: H 30 SER cc_start: 0.8828 (t) cc_final: 0.8512 (p) REVERT: H 77 ASN cc_start: 0.8296 (m-40) cc_final: 0.8092 (m110) REVERT: H 101 TYR cc_start: 0.7470 (m-80) cc_final: 0.7105 (m-80) REVERT: H 179 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7469 (tm-30) REVERT: H 180 ARG cc_start: 0.8184 (mtt-85) cc_final: 0.7856 (mtt-85) REVERT: C 27 MET cc_start: 0.7589 (tmm) cc_final: 0.7153 (tmm) REVERT: C 65 THR cc_start: 0.8173 (p) cc_final: 0.7910 (t) REVERT: C 93 PHE cc_start: 0.6779 (t80) cc_final: 0.6493 (t80) REVERT: C 124 VAL cc_start: 0.8323 (t) cc_final: 0.8063 (p) REVERT: C 151 PHE cc_start: 0.7866 (t80) cc_final: 0.7621 (t80) REVERT: C 398 VAL cc_start: 0.8123 (t) cc_final: 0.7917 (m) outliers start: 28 outliers final: 20 residues processed: 258 average time/residue: 0.0824 time to fit residues: 28.6560 Evaluate side-chains 262 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 394 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 0.0470 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 156 GLN B 259 GLN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.130182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112899 restraints weight = 14292.309| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.89 r_work: 0.3372 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8421 Z= 0.148 Angle : 0.590 9.313 11475 Z= 0.302 Chirality : 0.044 0.293 1329 Planarity : 0.004 0.035 1464 Dihedral : 4.123 27.781 1195 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.10 % Allowed : 23.63 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.27), residues: 1100 helix: 1.98 (0.28), residues: 370 sheet: -0.07 (0.31), residues: 290 loop : -0.89 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.018 0.002 TYR H 190 PHE 0.015 0.001 PHE B 180 TRP 0.031 0.002 TRP C 88 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8417) covalent geometry : angle 0.58924 (11469) SS BOND : bond 0.00527 ( 3) SS BOND : angle 1.38523 ( 6) hydrogen bonds : bond 0.03850 ( 407) hydrogen bonds : angle 4.53120 ( 1152) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6553 (tptm) REVERT: B 214 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7486 (mtm110) REVERT: B 298 ASP cc_start: 0.7389 (t70) cc_final: 0.6736 (t70) REVERT: A 17 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7305 (mmtt) REVERT: A 24 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7680 (mmmt) REVERT: A 32 LYS cc_start: 0.8672 (mttt) cc_final: 0.8430 (mttt) REVERT: A 192 PHE cc_start: 0.8260 (t80) cc_final: 0.8025 (t80) REVERT: A 231 TYR cc_start: 0.5892 (OUTLIER) cc_final: 0.5133 (p90) REVERT: A 317 LYS cc_start: 0.7977 (ptmm) cc_final: 0.7594 (ptpt) REVERT: G 21 MET cc_start: 0.8379 (tpp) cc_final: 0.7877 (tmm) REVERT: G 51 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7952 (pp) REVERT: H 18 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.6914 (mmm-85) REVERT: H 30 SER cc_start: 0.8862 (t) cc_final: 0.8535 (p) REVERT: H 77 ASN cc_start: 0.8312 (m-40) cc_final: 0.8075 (m110) REVERT: C 27 MET cc_start: 0.7631 (tmm) cc_final: 0.7171 (tmm) REVERT: C 65 THR cc_start: 0.8186 (p) cc_final: 0.7865 (t) REVERT: C 124 VAL cc_start: 0.8375 (t) cc_final: 0.8104 (p) REVERT: C 151 PHE cc_start: 0.7866 (t80) cc_final: 0.7620 (t80) REVERT: C 398 VAL cc_start: 0.8183 (t) cc_final: 0.7977 (m) outliers start: 33 outliers final: 28 residues processed: 261 average time/residue: 0.0829 time to fit residues: 29.0237 Evaluate side-chains 279 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 394 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 0.4980 chunk 77 optimal weight: 0.0060 chunk 103 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.130579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113382 restraints weight = 14149.891| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.87 r_work: 0.3380 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8421 Z= 0.142 Angle : 0.591 8.676 11475 Z= 0.303 Chirality : 0.044 0.164 1329 Planarity : 0.004 0.034 1464 Dihedral : 4.154 27.621 1195 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.48 % Allowed : 23.13 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.27), residues: 1100 helix: 1.93 (0.28), residues: 370 sheet: -0.09 (0.31), residues: 291 loop : -0.83 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 129 TYR 0.017 0.002 TYR H 190 PHE 0.015 0.001 PHE C 376 TRP 0.029 0.002 TRP C 88 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8417) covalent geometry : angle 0.59062 (11469) SS BOND : bond 0.00496 ( 3) SS BOND : angle 1.11384 ( 6) hydrogen bonds : bond 0.03794 ( 407) hydrogen bonds : angle 4.51619 ( 1152) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6633 (tptm) REVERT: B 82 TRP cc_start: 0.7429 (m-10) cc_final: 0.6164 (m-10) REVERT: B 137 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7721 (mmt90) REVERT: B 214 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7489 (mtm110) REVERT: B 298 ASP cc_start: 0.7291 (t70) cc_final: 0.6657 (t70) REVERT: A 24 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7675 (mmmt) REVERT: A 32 LYS cc_start: 0.8666 (mttt) cc_final: 0.8426 (mttt) REVERT: A 192 PHE cc_start: 0.8257 (t80) cc_final: 0.8034 (t80) REVERT: A 211 LYS cc_start: 0.8008 (mmmm) cc_final: 0.7655 (mmmm) REVERT: A 231 TYR cc_start: 0.5918 (OUTLIER) cc_final: 0.5153 (p90) REVERT: A 275 PHE cc_start: 0.7155 (t80) cc_final: 0.6922 (t80) REVERT: A 317 LYS cc_start: 0.7934 (ptmm) cc_final: 0.7584 (ptpt) REVERT: A 349 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7451 (ttm-80) REVERT: G 21 MET cc_start: 0.8397 (tpp) cc_final: 0.7869 (tmm) REVERT: G 51 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7960 (pp) REVERT: H 18 ARG cc_start: 0.7254 (ttm-80) cc_final: 0.6645 (mmm-85) REVERT: H 30 SER cc_start: 0.8856 (t) cc_final: 0.8541 (p) REVERT: H 77 ASN cc_start: 0.8301 (m-40) cc_final: 0.8061 (m110) REVERT: C 27 MET cc_start: 0.7649 (tmm) cc_final: 0.7186 (tmm) REVERT: C 65 THR cc_start: 0.8182 (p) cc_final: 0.7933 (t) REVERT: C 124 VAL cc_start: 0.8376 (t) cc_final: 0.8105 (p) REVERT: C 398 VAL cc_start: 0.8181 (t) cc_final: 0.7976 (m) outliers start: 36 outliers final: 27 residues processed: 267 average time/residue: 0.0834 time to fit residues: 29.9254 Evaluate side-chains 269 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 394 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.0270 chunk 56 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 259 GLN ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.129668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112468 restraints weight = 14215.325| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.89 r_work: 0.3367 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8421 Z= 0.182 Angle : 0.638 10.568 11475 Z= 0.326 Chirality : 0.046 0.404 1329 Planarity : 0.004 0.035 1464 Dihedral : 4.292 28.374 1195 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.23 % Allowed : 23.88 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.27), residues: 1100 helix: 1.83 (0.28), residues: 370 sheet: -0.14 (0.31), residues: 291 loop : -0.89 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 219 TYR 0.017 0.002 TYR H 173 PHE 0.020 0.002 PHE B 180 TRP 0.030 0.002 TRP C 88 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8417) covalent geometry : angle 0.63718 (11469) SS BOND : bond 0.00702 ( 3) SS BOND : angle 1.84959 ( 6) hydrogen bonds : bond 0.04148 ( 407) hydrogen bonds : angle 4.68126 ( 1152) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 249 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6701 (tptm) REVERT: B 82 TRP cc_start: 0.7454 (m-10) cc_final: 0.6055 (m-10) REVERT: B 214 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7483 (mtm110) REVERT: B 298 ASP cc_start: 0.7270 (t70) cc_final: 0.6762 (t70) REVERT: A 24 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7668 (mmmt) REVERT: A 32 LYS cc_start: 0.8690 (mttt) cc_final: 0.8437 (mttt) REVERT: A 192 PHE cc_start: 0.8270 (t80) cc_final: 0.8024 (t80) REVERT: A 231 TYR cc_start: 0.5433 (OUTLIER) cc_final: 0.4907 (p90) REVERT: A 317 LYS cc_start: 0.7952 (ptmm) cc_final: 0.7576 (ptpt) REVERT: A 349 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7458 (ttm-80) REVERT: G 21 MET cc_start: 0.8350 (tpp) cc_final: 0.7886 (tmm) REVERT: G 51 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7965 (pp) REVERT: H 30 SER cc_start: 0.8875 (t) cc_final: 0.8578 (p) REVERT: H 77 ASN cc_start: 0.8343 (m-40) cc_final: 0.8111 (m110) REVERT: C 27 MET cc_start: 0.7622 (tmm) cc_final: 0.7160 (tmm) REVERT: C 65 THR cc_start: 0.8224 (p) cc_final: 0.7912 (t) REVERT: C 124 VAL cc_start: 0.8392 (t) cc_final: 0.8122 (p) REVERT: C 151 PHE cc_start: 0.7834 (t80) cc_final: 0.7587 (t80) REVERT: C 398 VAL cc_start: 0.8212 (t) cc_final: 0.8004 (m) outliers start: 34 outliers final: 30 residues processed: 267 average time/residue: 0.0793 time to fit residues: 28.6789 Evaluate side-chains 289 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 256 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 394 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 30 optimal weight: 0.0570 chunk 87 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.130782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113507 restraints weight = 14063.750| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.88 r_work: 0.3384 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8421 Z= 0.133 Angle : 0.614 8.590 11475 Z= 0.311 Chirality : 0.044 0.162 1329 Planarity : 0.004 0.035 1464 Dihedral : 4.204 28.271 1195 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.10 % Allowed : 23.76 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.27), residues: 1100 helix: 1.91 (0.28), residues: 370 sheet: -0.10 (0.31), residues: 289 loop : -0.86 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 129 TYR 0.013 0.001 TYR C 174 PHE 0.016 0.001 PHE C 376 TRP 0.035 0.002 TRP C 88 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8417) covalent geometry : angle 0.61345 (11469) SS BOND : bond 0.00516 ( 3) SS BOND : angle 1.19224 ( 6) hydrogen bonds : bond 0.03759 ( 407) hydrogen bonds : angle 4.56362 ( 1152) Misc. bond : bond 0.00021 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.7428 (m-10) cc_final: 0.6028 (m-10) REVERT: B 137 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7734 (mmt90) REVERT: B 214 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7484 (mtm110) REVERT: B 298 ASP cc_start: 0.7265 (t70) cc_final: 0.6757 (t70) REVERT: A 24 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7669 (mmmt) REVERT: A 32 LYS cc_start: 0.8684 (mttt) cc_final: 0.8418 (mttt) REVERT: A 192 PHE cc_start: 0.8292 (t80) cc_final: 0.8088 (t80) REVERT: A 198 ARG cc_start: 0.8386 (mtm180) cc_final: 0.8078 (mtp85) REVERT: A 231 TYR cc_start: 0.5346 (OUTLIER) cc_final: 0.4716 (p90) REVERT: A 275 PHE cc_start: 0.7175 (t80) cc_final: 0.6887 (t80) REVERT: A 317 LYS cc_start: 0.7931 (ptmm) cc_final: 0.7576 (ptpt) REVERT: A 349 ARG cc_start: 0.7981 (ttp-110) cc_final: 0.7471 (ttm-80) REVERT: G 51 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7953 (pp) REVERT: H 30 SER cc_start: 0.8871 (t) cc_final: 0.8551 (p) REVERT: H 60 TYR cc_start: 0.8291 (m-80) cc_final: 0.7994 (m-80) REVERT: H 77 ASN cc_start: 0.8348 (m-40) cc_final: 0.8134 (m110) REVERT: C 27 MET cc_start: 0.7657 (tmm) cc_final: 0.7186 (tmm) REVERT: C 65 THR cc_start: 0.8158 (p) cc_final: 0.7951 (t) REVERT: C 93 PHE cc_start: 0.6813 (t80) cc_final: 0.6326 (t80) REVERT: C 124 VAL cc_start: 0.8378 (t) cc_final: 0.8103 (p) REVERT: C 398 VAL cc_start: 0.8181 (t) cc_final: 0.7976 (m) outliers start: 33 outliers final: 27 residues processed: 266 average time/residue: 0.0848 time to fit residues: 30.1875 Evaluate side-chains 270 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 394 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 47 optimal weight: 0.0030 chunk 66 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.131393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114013 restraints weight = 14154.969| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.90 r_work: 0.3390 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8421 Z= 0.127 Angle : 0.615 9.396 11475 Z= 0.309 Chirality : 0.045 0.390 1329 Planarity : 0.003 0.035 1464 Dihedral : 4.124 28.620 1195 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.48 % Allowed : 24.88 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.27), residues: 1100 helix: 1.97 (0.28), residues: 370 sheet: -0.13 (0.31), residues: 289 loop : -0.88 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 129 TYR 0.013 0.001 TYR C 174 PHE 0.016 0.001 PHE C 376 TRP 0.027 0.002 TRP C 88 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8417) covalent geometry : angle 0.61515 (11469) SS BOND : bond 0.00460 ( 3) SS BOND : angle 1.01560 ( 6) hydrogen bonds : bond 0.03592 ( 407) hydrogen bonds : angle 4.47060 ( 1152) Misc. bond : bond 0.00012 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1576.58 seconds wall clock time: 27 minutes 43.19 seconds (1663.19 seconds total)