Starting phenix.real_space_refine on Mon Jul 28 03:06:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e90_47738/07_2025/9e90_47738.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e90_47738/07_2025/9e90_47738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e90_47738/07_2025/9e90_47738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e90_47738/07_2025/9e90_47738.map" model { file = "/net/cci-nas-00/data/ceres_data/9e90_47738/07_2025/9e90_47738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e90_47738/07_2025/9e90_47738.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 S 28 5.16 5 C 6103 2.51 5 N 1675 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9672 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2109 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain: "A" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3731 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 101 Chain: "C" Number of atoms: 3769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3769 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 17, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 467 SG CYS B 57 40.233 61.353 33.829 1.00 65.56 S ATOM 798 SG CYS B 98 39.157 65.237 34.684 1.00 64.46 S ATOM 924 SG CYS B 116 41.803 63.700 32.700 1.00 66.41 S Time building chain proxies: 6.57, per 1000 atoms: 0.68 Number of scatterers: 9672 At special positions: 0 Unit cell: (94.83, 134.07, 120.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 6 15.00 O 1859 8.00 N 1675 7.00 C 6103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 116 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 98 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 57 " 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 12 sheets defined 47.6% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'B' and resid 14 through 21 removed outlier: 3.921A pdb=" N PHE B 18 " --> pdb=" O PHE B 14 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 19 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 32 Processing helix chain 'B' and resid 36 through 50 removed outlier: 3.607A pdb=" N ASP B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.612A pdb=" N GLU B 68 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.895A pdb=" N SER B 80 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.810A pdb=" N SER B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 179 through 192 removed outlier: 3.963A pdb=" N ILE B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 202 through 212 removed outlier: 3.944A pdb=" N LEU B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 229 removed outlier: 3.674A pdb=" N LEU B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 21 through 26 removed outlier: 3.845A pdb=" N GLN A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 32 Processing helix chain 'A' and resid 43 through 48 removed outlier: 4.361A pdb=" N TYR A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 48 " --> pdb=" O MET A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 98 through 118 removed outlier: 3.853A pdb=" N LEU A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 224 through 230 removed outlier: 3.502A pdb=" N ALA A 228 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 261 removed outlier: 3.557A pdb=" N THR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.963A pdb=" N PHE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 362 through 383 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 412 through 421 Processing helix chain 'A' and resid 432 through 437 removed outlier: 3.763A pdb=" N CYS A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 437' Processing helix chain 'A' and resid 438 through 439 No H-bonds generated for 'chain 'A' and resid 438 through 439' Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.523A pdb=" N LEU A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 516 removed outlier: 3.507A pdb=" N HIS A 514 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 542 removed outlier: 3.549A pdb=" N GLN A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 19 removed outlier: 3.579A pdb=" N THR C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LYS C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 31 removed outlier: 4.018A pdb=" N SER C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C 29 " --> pdb=" O TYR C 25 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL C 30 " --> pdb=" O GLN C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 54 removed outlier: 3.613A pdb=" N ASP C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.003A pdb=" N HIS C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 112 " --> pdb=" O GLY C 108 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 171 through 187 removed outlier: 3.800A pdb=" N GLU C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.762A pdb=" N ALA C 228 " --> pdb=" O LYS C 225 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR C 229 " --> pdb=" O PHE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 254 removed outlier: 3.930A pdb=" N ASN C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 removed outlier: 3.695A pdb=" N LEU C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 383 removed outlier: 3.666A pdb=" N ILE C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 421 Processing helix chain 'C' and resid 432 through 437 Processing helix chain 'C' and resid 438 through 439 No H-bonds generated for 'chain 'C' and resid 438 through 439' Processing helix chain 'C' and resid 440 through 442 No H-bonds generated for 'chain 'C' and resid 440 through 442' Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 481 through 495 removed outlier: 3.627A pdb=" N PHE C 495 " --> pdb=" O LYS C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 516 removed outlier: 3.905A pdb=" N LEU C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS C 514 " --> pdb=" O THR C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 539 removed outlier: 3.857A pdb=" N ASP C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C 538 " --> pdb=" O TRP C 534 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 70 through 73 Processing sheet with id=AA2, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.572A pdb=" N LEU A 77 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 65 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 143 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.572A pdb=" N LEU A 77 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 65 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 143 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 138 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 157 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.826A pdb=" N VAL A 91 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 197 through 198 Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 341 removed outlier: 5.063A pdb=" N ASN A 337 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 350 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 346 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.588A pdb=" N LEU C 68 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 66 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL C 63 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP C 145 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 65 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 69 " --> pdb=" O SER C 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.588A pdb=" N LEU C 68 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 66 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL C 63 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP C 145 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 65 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 69 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 157 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 428 through 429 removed outlier: 6.816A pdb=" N ILE C 89 " --> pdb=" O TRP C 445 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 194 through 198 Processing sheet with id=AB3, first strand: chain 'C' and resid 335 through 341 removed outlier: 5.383A pdb=" N ASN C 337 " --> pdb=" O ASP C 350 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP C 350 " --> pdb=" O ASN C 337 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 2.77 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: 3205 1.34 - 1.46: 2007 1.46 - 1.58: 4593 1.58 - 1.70: 14 1.70 - 1.82: 43 Bond restraints: 9862 Sorted by residual: bond pdb=" C2' ATP A 602 " pdb=" C3' ATP A 602 " ideal model delta sigma weight residual 1.531 1.260 0.271 1.20e-02 6.94e+03 5.09e+02 bond pdb=" C2' ATP A 601 " pdb=" C3' ATP A 601 " ideal model delta sigma weight residual 1.531 1.265 0.266 1.20e-02 6.94e+03 4.92e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.480 -0.143 1.10e-02 8.26e+03 1.70e+02 bond pdb=" C6 ATP A 602 " pdb=" N6 ATP A 602 " ideal model delta sigma weight residual 1.337 1.480 -0.143 1.10e-02 8.26e+03 1.68e+02 bond pdb=" C1' ATP A 602 " pdb=" C2' ATP A 602 " ideal model delta sigma weight residual 1.531 1.659 -0.128 1.20e-02 6.94e+03 1.14e+02 ... (remaining 9857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 13245 3.18 - 6.35: 85 6.35 - 9.53: 17 9.53 - 12.71: 1 12.71 - 15.88: 4 Bond angle restraints: 13352 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.99 15.88 1.00e+00 1.00e+00 2.52e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 123.99 15.88 1.00e+00 1.00e+00 2.52e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 124.10 12.73 1.00e+00 1.00e+00 1.62e+02 angle pdb=" PA ATP A 602 " pdb=" O3A ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 136.83 124.12 12.71 1.00e+00 1.00e+00 1.62e+02 angle pdb=" C5 ATP A 602 " pdb=" C4 ATP A 602 " pdb=" N3 ATP A 602 " ideal model delta sigma weight residual 126.80 119.07 7.73 1.00e+00 1.00e+00 5.97e+01 ... (remaining 13347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5498 17.58 - 35.15: 407 35.15 - 52.73: 47 52.73 - 70.31: 41 70.31 - 87.88: 4 Dihedral angle restraints: 5997 sinusoidal: 2438 harmonic: 3559 Sorted by residual: dihedral pdb=" CA PRO A 344 " pdb=" C PRO A 344 " pdb=" N LEU A 345 " pdb=" CA LEU A 345 " ideal model delta harmonic sigma weight residual 180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA ALA A 343 " pdb=" C ALA A 343 " pdb=" N PRO A 344 " pdb=" CA PRO A 344 " ideal model delta harmonic sigma weight residual -180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ASP C 145 " pdb=" C ASP C 145 " pdb=" N TYR C 146 " pdb=" CA TYR C 146 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1198 0.053 - 0.106: 239 0.106 - 0.159: 42 0.159 - 0.212: 5 0.212 - 0.265: 4 Chirality restraints: 1488 Sorted by residual: chirality pdb=" C3' ATP A 601 " pdb=" C2' ATP A 601 " pdb=" C4' ATP A 601 " pdb=" O3' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.42 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C3' ATP A 602 " pdb=" C2' ATP A 602 " pdb=" C4' ATP A 602 " pdb=" O3' ATP A 602 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1485 not shown) Planarity restraints: 1718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 246 " -0.024 2.00e-02 2.50e+03 1.78e-02 5.54e+00 pdb=" CG PHE C 246 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE C 246 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 246 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 246 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 246 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 246 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 406 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO A 407 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 89 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C ILE A 89 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE A 89 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 90 " -0.012 2.00e-02 2.50e+03 ... (remaining 1715 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 79 2.64 - 3.21: 9026 3.21 - 3.77: 13994 3.77 - 4.34: 19549 4.34 - 4.90: 32246 Nonbonded interactions: 74894 Sorted by model distance: nonbonded pdb=" OG SER C 16 " pdb=" OG SER C 24 " model vdw 2.076 3.040 nonbonded pdb=" O PRO A 188 " pdb=" NZ LYS A 225 " model vdw 2.113 3.120 nonbonded pdb=" O PRO C 193 " pdb=" OH TYR C 229 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR B 102 " pdb=" OE2 GLU B 109 " model vdw 2.183 3.040 nonbonded pdb=" NH1 ARG B 5 " pdb=" OD1 ASN B 7 " model vdw 2.265 3.120 ... (remaining 74889 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 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 11 or (resid 12 through 15 and (name N or name CA \ or name C or name O or name CB )) or resid 16 through 19 or (resid 20 through 2 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 23 through 2 \ 5 or (resid 26 through 31 and (name N or name CA or name C or name O or name CB \ )) or resid 32 through 237 or (resid 238 and (name N or name CA or name C or nam \ e O or name CB )) or resid 239 through 254 or resid 316 through 345 or (resid 34 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 347 through \ 540)) selection = (chain 'C' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 8 or (resid 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 through 12 or (resid 13 through 15 and (name N \ or name CA or name C or name O or name CB )) or resid 16 through 27 or (resid 2 \ 8 through 31 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 2 or (resid 33 through 36 and (name N or name CA or name C or name O or name CB \ )) or resid 37 or (resid 38 through 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 or (resid 46 through 50 and (name N or \ name CA or name C or name O or name CB )) or resid 51 or resid 57 through 59 or \ (resid 60 and (name N or name CA or name C or name O or name CB )) or resid 61 t \ hrough 129 or (resid 130 and (name N or name CA or name C or name O or name CB ) \ ) or resid 131 through 214 or (resid 215 through 216 and (name N or name CA or n \ ame C or name O or name CB )) or resid 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB )) or resid 219 through 254 or resid 316 through \ 540)) } 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: 0.010 Normalize map: mean=0, sd=1: 65.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.150 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 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 : 0.007 0.271 9867 Z= 0.523 Angle : 0.748 15.882 13352 Z= 0.473 Chirality : 0.046 0.265 1488 Planarity : 0.005 0.057 1718 Dihedral : 13.389 87.884 3689 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.65 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.24), residues: 1210 helix: 0.29 (0.23), residues: 503 sheet: -1.94 (0.42), residues: 130 loop : -2.24 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 27 HIS 0.005 0.001 HIS C 437 PHE 0.038 0.002 PHE C 246 TYR 0.021 0.002 TYR B 119 ARG 0.004 0.000 ARG C 378 Details of bonding type rmsd hydrogen bonds : bond 0.17462 ( 380) hydrogen bonds : angle 6.71222 ( 1131) metal coordination : bond 0.00126 ( 3) covalent geometry : bond 0.00680 ( 9862) covalent geometry : angle 0.74775 (13352) Misc. bond : bond 0.00092 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 ASP cc_start: 0.6499 (t0) cc_final: 0.6058 (t0) REVERT: B 208 HIS cc_start: 0.7145 (t70) cc_final: 0.6929 (t-90) REVERT: A 115 ARG cc_start: 0.7985 (mtt90) cc_final: 0.7651 (mtt-85) REVERT: A 200 VAL cc_start: 0.7990 (m) cc_final: 0.7689 (p) REVERT: A 243 PHE cc_start: 0.6850 (t80) cc_final: 0.6597 (t80) REVERT: A 393 THR cc_start: 0.7606 (t) cc_final: 0.7253 (m) REVERT: A 418 GLU cc_start: 0.7275 (tt0) cc_final: 0.7041 (tt0) REVERT: A 434 GLN cc_start: 0.7940 (mp-120) cc_final: 0.7636 (mp10) REVERT: A 469 GLU cc_start: 0.6295 (tt0) cc_final: 0.6093 (tt0) REVERT: A 528 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6471 (mm-30) REVERT: A 533 ILE cc_start: 0.7718 (mt) cc_final: 0.7465 (tp) REVERT: A 534 TRP cc_start: 0.7190 (t60) cc_final: 0.6175 (t60) REVERT: A 535 GLU cc_start: 0.7478 (mm-30) cc_final: 0.5581 (mm-30) REVERT: C 1 MET cc_start: 0.7351 (mtm) cc_final: 0.6906 (ppp) REVERT: C 75 GLU cc_start: 0.7732 (tp30) cc_final: 0.7469 (tm-30) REVERT: C 76 SER cc_start: 0.8225 (t) cc_final: 0.7956 (m) REVERT: C 109 LEU cc_start: 0.7316 (mm) cc_final: 0.7096 (mt) REVERT: C 127 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7377 (mt-10) REVERT: C 146 TYR cc_start: 0.7642 (t80) cc_final: 0.7064 (t80) REVERT: C 236 LYS cc_start: 0.6819 (pttm) cc_final: 0.6608 (pttm) REVERT: C 374 ASP cc_start: 0.6472 (t0) cc_final: 0.6078 (t0) REVERT: C 398 ILE cc_start: 0.7695 (mt) cc_final: 0.7346 (mp) REVERT: C 416 ARG cc_start: 0.6228 (mtm110) cc_final: 0.5534 (mmp-170) REVERT: C 418 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7205 (mt-10) REVERT: C 448 LYS cc_start: 0.8181 (tttt) cc_final: 0.7797 (ptmm) REVERT: C 469 GLU cc_start: 0.7548 (tt0) cc_final: 0.7323 (tt0) REVERT: C 470 ASN cc_start: 0.7257 (m110) cc_final: 0.6909 (m110) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.2742 time to fit residues: 111.6683 Evaluate side-chains 248 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.7980 chunk 91 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 109 optimal weight: 0.2980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 HIS ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN A 411 GLN C 111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.157320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.135554 restraints weight = 13393.114| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.37 r_work: 0.3716 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9867 Z= 0.140 Angle : 0.638 10.905 13352 Z= 0.328 Chirality : 0.044 0.213 1488 Planarity : 0.005 0.066 1718 Dihedral : 7.763 65.804 1369 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.41 % Favored : 89.34 % Rotamer: Outliers : 1.64 % Allowed : 9.46 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.24), residues: 1210 helix: 0.55 (0.23), residues: 523 sheet: -1.66 (0.44), residues: 130 loop : -2.18 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 223 HIS 0.011 0.001 HIS C 437 PHE 0.019 0.002 PHE B 30 TYR 0.021 0.002 TYR C 71 ARG 0.003 0.001 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.04572 ( 380) hydrogen bonds : angle 5.12856 ( 1131) metal coordination : bond 0.00252 ( 3) covalent geometry : bond 0.00310 ( 9862) covalent geometry : angle 0.63774 (13352) Misc. bond : bond 0.00193 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 257 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 ASP cc_start: 0.6808 (t0) cc_final: 0.6151 (t0) REVERT: B 135 THR cc_start: 0.8299 (m) cc_final: 0.7989 (m) REVERT: B 229 ASN cc_start: 0.7918 (t0) cc_final: 0.7448 (t0) REVERT: A 230 ASN cc_start: 0.7717 (m110) cc_final: 0.7488 (m110) REVERT: A 243 PHE cc_start: 0.7020 (t80) cc_final: 0.6744 (t80) REVERT: A 319 LYS cc_start: 0.6852 (mmtm) cc_final: 0.6618 (mmmt) REVERT: A 393 THR cc_start: 0.7848 (t) cc_final: 0.7528 (m) REVERT: A 445 TRP cc_start: 0.7695 (m100) cc_final: 0.7464 (m-90) REVERT: A 533 ILE cc_start: 0.7695 (mt) cc_final: 0.7491 (tp) REVERT: A 535 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7158 (tp30) REVERT: C 1 MET cc_start: 0.7425 (mtm) cc_final: 0.6854 (ppp) REVERT: C 76 SER cc_start: 0.8453 (t) cc_final: 0.8227 (m) REVERT: C 79 MET cc_start: 0.8190 (mmm) cc_final: 0.7862 (mmm) REVERT: C 83 MET cc_start: 0.8061 (mmm) cc_final: 0.7799 (mmp) REVERT: C 109 LEU cc_start: 0.7483 (mm) cc_final: 0.7122 (mt) REVERT: C 130 GLU cc_start: 0.6344 (mt-10) cc_final: 0.6137 (mt-10) REVERT: C 146 TYR cc_start: 0.7889 (t80) cc_final: 0.7688 (t80) REVERT: C 182 THR cc_start: 0.8306 (m) cc_final: 0.8060 (p) REVERT: C 398 ILE cc_start: 0.8035 (mt) cc_final: 0.7577 (mt) REVERT: C 402 ASP cc_start: 0.7001 (p0) cc_final: 0.6781 (p0) REVERT: C 416 ARG cc_start: 0.6645 (mtm110) cc_final: 0.5847 (mmp-170) REVERT: C 448 LYS cc_start: 0.8337 (tttt) cc_final: 0.7825 (ptmm) REVERT: C 449 ASN cc_start: 0.8194 (m-40) cc_final: 0.7929 (m-40) REVERT: C 468 LEU cc_start: 0.7884 (mt) cc_final: 0.7518 (tp) REVERT: C 469 GLU cc_start: 0.7972 (tt0) cc_final: 0.7746 (tt0) REVERT: C 470 ASN cc_start: 0.7685 (m110) cc_final: 0.7219 (m110) outliers start: 17 outliers final: 9 residues processed: 261 average time/residue: 0.2751 time to fit residues: 95.7713 Evaluate side-chains 252 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 243 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 393 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 116 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 251 GLN A 184 HIS A 411 GLN C 70 ASN C 317 ASN C 488 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.151841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.129844 restraints weight = 13601.653| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.30 r_work: 0.3636 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9867 Z= 0.204 Angle : 0.674 10.646 13352 Z= 0.349 Chirality : 0.045 0.169 1488 Planarity : 0.005 0.061 1718 Dihedral : 7.904 72.166 1369 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.99 % Favored : 88.76 % Rotamer: Outliers : 2.70 % Allowed : 12.93 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1210 helix: 0.63 (0.23), residues: 519 sheet: -1.61 (0.44), residues: 130 loop : -2.34 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 223 HIS 0.010 0.001 HIS C 437 PHE 0.021 0.002 PHE C 335 TYR 0.030 0.002 TYR C 71 ARG 0.006 0.001 ARG C 377 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 380) hydrogen bonds : angle 4.95745 ( 1131) metal coordination : bond 0.01107 ( 3) covalent geometry : bond 0.00467 ( 9862) covalent geometry : angle 0.67448 (13352) Misc. bond : bond 0.00226 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ASN cc_start: 0.7610 (t0) cc_final: 0.7397 (t0) REVERT: B 133 ASP cc_start: 0.6955 (t0) cc_final: 0.6389 (t0) REVERT: B 135 THR cc_start: 0.8433 (m) cc_final: 0.8185 (m) REVERT: B 229 ASN cc_start: 0.8137 (t0) cc_final: 0.7672 (t0) REVERT: A 71 TYR cc_start: 0.7796 (t80) cc_final: 0.7208 (t80) REVERT: A 115 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7889 (mtt-85) REVERT: A 230 ASN cc_start: 0.7937 (m110) cc_final: 0.7574 (m110) REVERT: A 243 PHE cc_start: 0.7305 (t80) cc_final: 0.6894 (t80) REVERT: A 319 LYS cc_start: 0.7042 (mmtm) cc_final: 0.6798 (mmmt) REVERT: A 393 THR cc_start: 0.8112 (t) cc_final: 0.7832 (m) REVERT: C 1 MET cc_start: 0.7428 (mtm) cc_final: 0.6906 (ppp) REVERT: C 109 LEU cc_start: 0.7599 (mm) cc_final: 0.7330 (mt) REVERT: C 130 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6312 (mt-10) REVERT: C 163 GLU cc_start: 0.7188 (pm20) cc_final: 0.6938 (mp0) REVERT: C 182 THR cc_start: 0.8302 (m) cc_final: 0.8031 (p) REVERT: C 398 ILE cc_start: 0.8299 (mt) cc_final: 0.7784 (mt) REVERT: C 402 ASP cc_start: 0.7115 (p0) cc_final: 0.6875 (p0) REVERT: C 416 ARG cc_start: 0.6727 (mtm110) cc_final: 0.5948 (mmp-170) REVERT: C 418 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7310 (mt-10) REVERT: C 448 LYS cc_start: 0.8451 (tttt) cc_final: 0.7980 (ptmm) REVERT: C 468 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7821 (tp) REVERT: C 470 ASN cc_start: 0.7908 (m110) cc_final: 0.7447 (m110) REVERT: C 480 GLU cc_start: 0.8454 (tp30) cc_final: 0.7957 (tp30) outliers start: 28 outliers final: 18 residues processed: 255 average time/residue: 0.2559 time to fit residues: 87.1630 Evaluate side-chains 260 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 109 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 66 optimal weight: 0.0070 chunk 80 optimal weight: 0.9980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.155170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133619 restraints weight = 13596.809| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.40 r_work: 0.3658 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9867 Z= 0.141 Angle : 0.614 10.125 13352 Z= 0.312 Chirality : 0.043 0.172 1488 Planarity : 0.004 0.050 1718 Dihedral : 7.731 81.674 1369 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.66 % Favored : 89.09 % Rotamer: Outliers : 2.80 % Allowed : 14.19 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 1210 helix: 0.74 (0.23), residues: 526 sheet: -1.53 (0.44), residues: 136 loop : -2.20 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 466 HIS 0.009 0.001 HIS C 437 PHE 0.024 0.002 PHE C 335 TYR 0.016 0.001 TYR C 71 ARG 0.003 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 380) hydrogen bonds : angle 4.69172 ( 1131) metal coordination : bond 0.00630 ( 3) covalent geometry : bond 0.00320 ( 9862) covalent geometry : angle 0.61390 (13352) Misc. bond : bond 0.00149 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 ARG cc_start: 0.7873 (tpt170) cc_final: 0.7622 (tpt-90) REVERT: B 49 ASP cc_start: 0.7209 (t0) cc_final: 0.6908 (t0) REVERT: B 86 ASN cc_start: 0.7414 (t0) cc_final: 0.7210 (t0) REVERT: B 133 ASP cc_start: 0.7000 (t0) cc_final: 0.6380 (t0) REVERT: B 135 THR cc_start: 0.8386 (m) cc_final: 0.8108 (m) REVERT: B 229 ASN cc_start: 0.7963 (t0) cc_final: 0.7457 (t0) REVERT: A 71 TYR cc_start: 0.7560 (t80) cc_final: 0.6947 (t80) REVERT: A 72 LYS cc_start: 0.7594 (mmtm) cc_final: 0.7378 (tptt) REVERT: A 181 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7844 (mmtm) REVERT: A 201 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7129 (mt-10) REVERT: A 230 ASN cc_start: 0.7779 (m110) cc_final: 0.7353 (m110) REVERT: A 243 PHE cc_start: 0.7198 (t80) cc_final: 0.6735 (t80) REVERT: A 319 LYS cc_start: 0.6797 (mmtm) cc_final: 0.6585 (mmmt) REVERT: A 393 THR cc_start: 0.7995 (t) cc_final: 0.7737 (m) REVERT: A 418 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7388 (mt-10) REVERT: A 533 ILE cc_start: 0.7734 (tp) cc_final: 0.7456 (tt) REVERT: A 534 TRP cc_start: 0.7197 (t60) cc_final: 0.5974 (t60) REVERT: A 535 GLU cc_start: 0.7376 (tp30) cc_final: 0.6321 (tp30) REVERT: C 1 MET cc_start: 0.7338 (mtm) cc_final: 0.6857 (ppp) REVERT: C 109 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7146 (mt) REVERT: C 127 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: C 130 GLU cc_start: 0.6405 (mt-10) cc_final: 0.5995 (mt-10) REVERT: C 163 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: C 398 ILE cc_start: 0.8154 (mt) cc_final: 0.7571 (mt) REVERT: C 402 ASP cc_start: 0.6921 (p0) cc_final: 0.6694 (p0) REVERT: C 416 ARG cc_start: 0.6637 (mtm110) cc_final: 0.5874 (mmp-170) REVERT: C 418 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7253 (mt-10) REVERT: C 448 LYS cc_start: 0.8381 (tttt) cc_final: 0.7897 (ptmm) REVERT: C 468 LEU cc_start: 0.8027 (mt) cc_final: 0.7667 (tp) REVERT: C 470 ASN cc_start: 0.7624 (m110) cc_final: 0.7115 (m110) outliers start: 29 outliers final: 19 residues processed: 250 average time/residue: 0.2468 time to fit residues: 82.3822 Evaluate side-chains 250 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 484 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 0.0370 chunk 47 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.153830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.132435 restraints weight = 13716.000| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.38 r_work: 0.3638 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9867 Z= 0.160 Angle : 0.643 10.159 13352 Z= 0.326 Chirality : 0.044 0.187 1488 Planarity : 0.004 0.050 1718 Dihedral : 7.770 87.512 1369 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.07 % Favored : 88.76 % Rotamer: Outliers : 2.80 % Allowed : 15.44 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.25), residues: 1210 helix: 0.77 (0.23), residues: 521 sheet: -1.47 (0.44), residues: 136 loop : -2.17 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 91 HIS 0.009 0.001 HIS C 437 PHE 0.020 0.002 PHE C 335 TYR 0.020 0.002 TYR B 39 ARG 0.003 0.000 ARG B 240 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 380) hydrogen bonds : angle 4.64039 ( 1131) metal coordination : bond 0.00797 ( 3) covalent geometry : bond 0.00366 ( 9862) covalent geometry : angle 0.64268 (13352) Misc. bond : bond 0.00156 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 ARG cc_start: 0.7976 (tpt170) cc_final: 0.7685 (tpt-90) REVERT: B 49 ASP cc_start: 0.7496 (t0) cc_final: 0.7256 (t0) REVERT: B 86 ASN cc_start: 0.7498 (t0) cc_final: 0.7285 (t0) REVERT: B 91 TRP cc_start: 0.8213 (t-100) cc_final: 0.8012 (t-100) REVERT: B 133 ASP cc_start: 0.7042 (t0) cc_final: 0.6436 (t0) REVERT: B 135 THR cc_start: 0.8473 (m) cc_final: 0.8198 (m) REVERT: B 229 ASN cc_start: 0.8045 (t0) cc_final: 0.7557 (t0) REVERT: A 71 TYR cc_start: 0.7747 (t80) cc_final: 0.7135 (t80) REVERT: A 181 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7948 (mmtm) REVERT: A 230 ASN cc_start: 0.7963 (m110) cc_final: 0.7641 (m110) REVERT: A 243 PHE cc_start: 0.7275 (t80) cc_final: 0.6813 (t80) REVERT: A 319 LYS cc_start: 0.6865 (mmtm) cc_final: 0.6654 (mmmt) REVERT: A 374 ASP cc_start: 0.7479 (t0) cc_final: 0.6990 (t0) REVERT: A 393 THR cc_start: 0.8102 (t) cc_final: 0.7829 (m) REVERT: A 416 ARG cc_start: 0.7633 (mtp85) cc_final: 0.7367 (mtt-85) REVERT: A 533 ILE cc_start: 0.7828 (tp) cc_final: 0.7532 (tt) REVERT: C 1 MET cc_start: 0.7224 (mtm) cc_final: 0.6742 (ppp) REVERT: C 109 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7247 (mt) REVERT: C 127 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: C 130 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6137 (mm-30) REVERT: C 163 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: C 374 ASP cc_start: 0.7355 (t0) cc_final: 0.7143 (t0) REVERT: C 398 ILE cc_start: 0.8284 (mt) cc_final: 0.7877 (mt) REVERT: C 402 ASP cc_start: 0.7073 (p0) cc_final: 0.6856 (p0) REVERT: C 416 ARG cc_start: 0.6748 (mtm110) cc_final: 0.5905 (mmp-170) REVERT: C 418 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7304 (mt-10) REVERT: C 448 LYS cc_start: 0.8457 (tttt) cc_final: 0.7953 (ptmm) REVERT: C 468 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7794 (tp) REVERT: C 470 ASN cc_start: 0.7785 (m110) cc_final: 0.7316 (m110) REVERT: C 480 GLU cc_start: 0.8480 (tp30) cc_final: 0.7890 (tp30) REVERT: C 537 ASP cc_start: 0.7852 (t0) cc_final: 0.7432 (t0) outliers start: 29 outliers final: 19 residues processed: 251 average time/residue: 0.2434 time to fit residues: 82.0243 Evaluate side-chains 246 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 489 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 61 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 57 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS A 169 ASN C 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.154222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132902 restraints weight = 13772.746| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.39 r_work: 0.3647 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9867 Z= 0.154 Angle : 0.628 9.348 13352 Z= 0.320 Chirality : 0.043 0.207 1488 Planarity : 0.004 0.068 1718 Dihedral : 7.765 89.123 1369 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.99 % Favored : 88.76 % Rotamer: Outliers : 3.38 % Allowed : 16.12 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.25), residues: 1210 helix: 0.85 (0.23), residues: 516 sheet: -1.41 (0.44), residues: 136 loop : -2.16 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 466 HIS 0.008 0.001 HIS C 437 PHE 0.031 0.002 PHE A 335 TYR 0.013 0.001 TYR C 71 ARG 0.006 0.000 ARG C 244 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 380) hydrogen bonds : angle 4.55010 ( 1131) metal coordination : bond 0.00678 ( 3) covalent geometry : bond 0.00352 ( 9862) covalent geometry : angle 0.62780 (13352) Misc. bond : bond 0.00142 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ASP cc_start: 0.7221 (t0) cc_final: 0.6954 (t0) REVERT: B 133 ASP cc_start: 0.6895 (t0) cc_final: 0.6287 (t0) REVERT: B 135 THR cc_start: 0.8383 (m) cc_final: 0.8099 (m) REVERT: B 229 ASN cc_start: 0.7951 (t0) cc_final: 0.7442 (t0) REVERT: A 71 TYR cc_start: 0.7593 (t80) cc_final: 0.6966 (t80) REVERT: A 181 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7871 (mmtm) REVERT: A 230 ASN cc_start: 0.7867 (m110) cc_final: 0.7547 (m110) REVERT: A 243 PHE cc_start: 0.7205 (t80) cc_final: 0.6728 (t80) REVERT: A 319 LYS cc_start: 0.6806 (mmtm) cc_final: 0.6594 (mmmt) REVERT: A 374 ASP cc_start: 0.7339 (t0) cc_final: 0.7104 (m-30) REVERT: A 393 THR cc_start: 0.8005 (t) cc_final: 0.7752 (m) REVERT: A 416 ARG cc_start: 0.7470 (mtp85) cc_final: 0.7217 (mtt-85) REVERT: A 533 ILE cc_start: 0.7722 (tp) cc_final: 0.7403 (tt) REVERT: C 1 MET cc_start: 0.7191 (mtm) cc_final: 0.6726 (ppp) REVERT: C 109 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7185 (mt) REVERT: C 127 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: C 137 TYR cc_start: 0.6883 (p90) cc_final: 0.5466 (p90) REVERT: C 398 ILE cc_start: 0.8158 (mt) cc_final: 0.7455 (mt) REVERT: C 402 ASP cc_start: 0.6994 (p0) cc_final: 0.6768 (p0) REVERT: C 416 ARG cc_start: 0.6577 (mtm110) cc_final: 0.5879 (mmp-170) REVERT: C 448 LYS cc_start: 0.8401 (tttt) cc_final: 0.7881 (ptmm) REVERT: C 468 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7725 (tp) REVERT: C 470 ASN cc_start: 0.7537 (m110) cc_final: 0.7045 (m110) REVERT: C 537 ASP cc_start: 0.7645 (t0) cc_final: 0.7254 (t0) outliers start: 35 outliers final: 21 residues processed: 247 average time/residue: 0.3469 time to fit residues: 117.5973 Evaluate side-chains 248 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 497 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 106 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 11 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 20 optimal weight: 0.1980 chunk 18 optimal weight: 0.2980 chunk 75 optimal weight: 9.9990 chunk 105 optimal weight: 0.0980 overall best weight: 0.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN A 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.154479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.133027 restraints weight = 13751.976| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.41 r_work: 0.3656 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9867 Z= 0.120 Angle : 0.608 8.788 13352 Z= 0.309 Chirality : 0.042 0.158 1488 Planarity : 0.004 0.058 1718 Dihedral : 7.568 88.132 1369 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.91 % Favored : 88.84 % Rotamer: Outliers : 2.51 % Allowed : 18.92 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.24), residues: 1210 helix: 0.99 (0.23), residues: 517 sheet: -1.51 (0.43), residues: 136 loop : -2.16 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 466 HIS 0.008 0.001 HIS C 437 PHE 0.031 0.001 PHE A 335 TYR 0.019 0.001 TYR A 499 ARG 0.004 0.000 ARG C 244 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 380) hydrogen bonds : angle 4.42156 ( 1131) metal coordination : bond 0.00407 ( 3) covalent geometry : bond 0.00269 ( 9862) covalent geometry : angle 0.60832 (13352) Misc. bond : bond 0.00111 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ASP cc_start: 0.7259 (t0) cc_final: 0.6983 (t0) REVERT: B 133 ASP cc_start: 0.6977 (t0) cc_final: 0.6335 (t0) REVERT: B 135 THR cc_start: 0.8401 (m) cc_final: 0.8104 (m) REVERT: B 229 ASN cc_start: 0.7889 (t0) cc_final: 0.7316 (t0) REVERT: A 71 TYR cc_start: 0.7516 (t80) cc_final: 0.6887 (t80) REVERT: A 181 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7862 (mmtm) REVERT: A 230 ASN cc_start: 0.7849 (m110) cc_final: 0.7522 (m110) REVERT: A 243 PHE cc_start: 0.7134 (t80) cc_final: 0.6647 (t80) REVERT: A 319 LYS cc_start: 0.6849 (mmtm) cc_final: 0.6612 (mmmt) REVERT: A 374 ASP cc_start: 0.7318 (t0) cc_final: 0.7033 (m-30) REVERT: A 393 THR cc_start: 0.8001 (t) cc_final: 0.7764 (m) REVERT: A 416 ARG cc_start: 0.7422 (mtp85) cc_final: 0.7192 (mtt-85) REVERT: A 445 TRP cc_start: 0.7270 (m100) cc_final: 0.7031 (m-90) REVERT: A 448 LYS cc_start: 0.7924 (tmtt) cc_final: 0.7534 (tmtt) REVERT: C 1 MET cc_start: 0.7174 (mtm) cc_final: 0.6713 (ppp) REVERT: C 109 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7178 (mt) REVERT: C 127 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7508 (mp0) REVERT: C 195 ILE cc_start: 0.7915 (mp) cc_final: 0.7546 (mm) REVERT: C 331 PHE cc_start: 0.6865 (m-80) cc_final: 0.6245 (t80) REVERT: C 398 ILE cc_start: 0.8146 (mt) cc_final: 0.7696 (mt) REVERT: C 402 ASP cc_start: 0.6971 (p0) cc_final: 0.6748 (p0) REVERT: C 416 ARG cc_start: 0.6566 (mtm110) cc_final: 0.5864 (mmp-170) REVERT: C 468 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7690 (tp) REVERT: C 470 ASN cc_start: 0.7539 (m110) cc_final: 0.7053 (m110) REVERT: C 537 ASP cc_start: 0.7681 (t0) cc_final: 0.7367 (t0) outliers start: 26 outliers final: 18 residues processed: 236 average time/residue: 0.2910 time to fit residues: 92.5571 Evaluate side-chains 243 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 497 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 47 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 73 optimal weight: 0.0670 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN A 121 HIS A 476 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.153121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131523 restraints weight = 13718.274| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.39 r_work: 0.3642 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9867 Z= 0.148 Angle : 0.635 12.186 13352 Z= 0.322 Chirality : 0.043 0.164 1488 Planarity : 0.004 0.057 1718 Dihedral : 7.579 86.359 1369 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.74 % Favored : 89.01 % Rotamer: Outliers : 2.70 % Allowed : 18.92 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.24), residues: 1210 helix: 0.95 (0.23), residues: 524 sheet: -1.17 (0.45), residues: 126 loop : -2.15 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 91 HIS 0.008 0.001 HIS C 437 PHE 0.029 0.002 PHE A 335 TYR 0.014 0.001 TYR B 39 ARG 0.004 0.000 ARG C 244 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 380) hydrogen bonds : angle 4.45712 ( 1131) metal coordination : bond 0.00696 ( 3) covalent geometry : bond 0.00340 ( 9862) covalent geometry : angle 0.63493 (13352) Misc. bond : bond 0.00127 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6893 (t0) REVERT: B 65 ASN cc_start: 0.8064 (m-40) cc_final: 0.7715 (m-40) REVERT: B 133 ASP cc_start: 0.6871 (t0) cc_final: 0.6259 (t0) REVERT: B 135 THR cc_start: 0.8390 (m) cc_final: 0.8111 (m) REVERT: B 229 ASN cc_start: 0.7891 (t0) cc_final: 0.7303 (t0) REVERT: B 241 ASP cc_start: 0.7609 (m-30) cc_final: 0.7354 (t0) REVERT: A 71 TYR cc_start: 0.7598 (t80) cc_final: 0.6951 (t80) REVERT: A 136 ASN cc_start: 0.6785 (p0) cc_final: 0.6081 (m110) REVERT: A 181 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7897 (mmtm) REVERT: A 230 ASN cc_start: 0.7858 (m110) cc_final: 0.7537 (m110) REVERT: A 243 PHE cc_start: 0.7104 (t80) cc_final: 0.6611 (t80) REVERT: A 319 LYS cc_start: 0.6949 (mmtm) cc_final: 0.6729 (mmmt) REVERT: A 339 LYS cc_start: 0.6185 (ttmt) cc_final: 0.5925 (mtmm) REVERT: A 374 ASP cc_start: 0.7316 (t0) cc_final: 0.7029 (m-30) REVERT: A 393 THR cc_start: 0.8063 (t) cc_final: 0.7818 (m) REVERT: A 445 TRP cc_start: 0.7387 (m100) cc_final: 0.7183 (m-90) REVERT: A 448 LYS cc_start: 0.7963 (tmtt) cc_final: 0.7598 (tmtt) REVERT: C 1 MET cc_start: 0.7138 (mtm) cc_final: 0.6701 (ppp) REVERT: C 109 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7179 (mt) REVERT: C 127 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7553 (mp0) REVERT: C 130 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6059 (mm-30) REVERT: C 142 ILE cc_start: 0.8351 (mt) cc_final: 0.8089 (mm) REVERT: C 195 ILE cc_start: 0.7914 (mp) cc_final: 0.7526 (mm) REVERT: C 331 PHE cc_start: 0.6933 (m-80) cc_final: 0.6293 (t80) REVERT: C 398 ILE cc_start: 0.8185 (mt) cc_final: 0.7714 (mt) REVERT: C 402 ASP cc_start: 0.6993 (p0) cc_final: 0.6760 (p0) REVERT: C 416 ARG cc_start: 0.6608 (mtm110) cc_final: 0.5971 (mmp-170) REVERT: C 468 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7722 (tp) REVERT: C 470 ASN cc_start: 0.7533 (m110) cc_final: 0.7035 (m110) REVERT: C 537 ASP cc_start: 0.7632 (t0) cc_final: 0.7336 (t0) outliers start: 28 outliers final: 20 residues processed: 243 average time/residue: 0.4203 time to fit residues: 140.4135 Evaluate side-chains 248 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN B 148 HIS B 227 GLN A 476 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.149691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.127982 restraints weight = 13709.651| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.35 r_work: 0.3584 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9867 Z= 0.260 Angle : 0.729 12.160 13352 Z= 0.372 Chirality : 0.047 0.166 1488 Planarity : 0.005 0.072 1718 Dihedral : 7.980 88.725 1369 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.24 % Favored : 88.60 % Rotamer: Outliers : 2.61 % Allowed : 19.31 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.24), residues: 1210 helix: 0.67 (0.22), residues: 526 sheet: -1.05 (0.49), residues: 116 loop : -2.26 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 91 HIS 0.012 0.002 HIS A 437 PHE 0.022 0.003 PHE A 335 TYR 0.026 0.002 TYR C 137 ARG 0.005 0.001 ARG C 244 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 380) hydrogen bonds : angle 4.74810 ( 1131) metal coordination : bond 0.01476 ( 3) covalent geometry : bond 0.00600 ( 9862) covalent geometry : angle 0.72898 (13352) Misc. bond : bond 0.00200 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7189 (t0) REVERT: B 65 ASN cc_start: 0.8133 (m-40) cc_final: 0.7741 (m-40) REVERT: B 133 ASP cc_start: 0.6994 (t0) cc_final: 0.6401 (t0) REVERT: B 135 THR cc_start: 0.8515 (m) cc_final: 0.8235 (m) REVERT: B 229 ASN cc_start: 0.8116 (t0) cc_final: 0.7537 (t0) REVERT: B 241 ASP cc_start: 0.7845 (m-30) cc_final: 0.7609 (t0) REVERT: A 71 TYR cc_start: 0.7891 (t80) cc_final: 0.7224 (t80) REVERT: A 136 ASN cc_start: 0.7022 (p0) cc_final: 0.6367 (m110) REVERT: A 181 LYS cc_start: 0.8337 (mmmt) cc_final: 0.8005 (mmtm) REVERT: A 230 ASN cc_start: 0.8002 (m110) cc_final: 0.7654 (m110) REVERT: A 243 PHE cc_start: 0.7281 (t80) cc_final: 0.6866 (t80) REVERT: A 319 LYS cc_start: 0.7098 (mmtm) cc_final: 0.6888 (mmmt) REVERT: A 374 ASP cc_start: 0.7484 (t0) cc_final: 0.7001 (t0) REVERT: A 448 LYS cc_start: 0.8145 (tmtt) cc_final: 0.7769 (tmtt) REVERT: A 524 GLU cc_start: 0.7793 (tp30) cc_final: 0.7410 (mm-30) REVERT: C 1 MET cc_start: 0.7198 (mtm) cc_final: 0.6652 (ppp) REVERT: C 109 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7432 (mt) REVERT: C 127 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7623 (mp0) REVERT: C 142 ILE cc_start: 0.8361 (mt) cc_final: 0.8109 (mm) REVERT: C 398 ILE cc_start: 0.8383 (mt) cc_final: 0.7924 (mt) REVERT: C 402 ASP cc_start: 0.7330 (p0) cc_final: 0.7106 (p0) REVERT: C 416 ARG cc_start: 0.6874 (mtm110) cc_final: 0.6018 (mmp-170) REVERT: C 468 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7853 (tp) REVERT: C 470 ASN cc_start: 0.7812 (m110) cc_final: 0.7300 (m110) REVERT: C 537 ASP cc_start: 0.7877 (t0) cc_final: 0.7487 (t0) outliers start: 27 outliers final: 22 residues processed: 240 average time/residue: 0.2316 time to fit residues: 75.6148 Evaluate side-chains 251 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 246 PHE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 50 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 111 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 92 optimal weight: 0.0670 chunk 81 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 194 ASN B 227 GLN C 411 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.151455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.129538 restraints weight = 13848.415| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.41 r_work: 0.3599 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9867 Z= 0.215 Angle : 0.708 12.223 13352 Z= 0.360 Chirality : 0.046 0.192 1488 Planarity : 0.005 0.073 1718 Dihedral : 7.947 88.070 1369 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.16 % Favored : 88.68 % Rotamer: Outliers : 2.61 % Allowed : 19.69 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.24), residues: 1210 helix: 0.69 (0.23), residues: 523 sheet: -1.29 (0.48), residues: 118 loop : -2.31 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 445 HIS 0.009 0.001 HIS C 437 PHE 0.020 0.002 PHE A 335 TYR 0.041 0.002 TYR C 499 ARG 0.004 0.000 ARG C 244 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 380) hydrogen bonds : angle 4.72787 ( 1131) metal coordination : bond 0.01338 ( 3) covalent geometry : bond 0.00497 ( 9862) covalent geometry : angle 0.70814 (13352) Misc. bond : bond 0.00170 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6889 (t0) REVERT: B 65 ASN cc_start: 0.8029 (m-40) cc_final: 0.7668 (m-40) REVERT: B 133 ASP cc_start: 0.6747 (t0) cc_final: 0.6141 (t0) REVERT: B 135 THR cc_start: 0.8416 (m) cc_final: 0.8125 (m) REVERT: B 229 ASN cc_start: 0.8008 (t0) cc_final: 0.7412 (t0) REVERT: B 241 ASP cc_start: 0.7666 (m-30) cc_final: 0.7397 (t0) REVERT: A 71 TYR cc_start: 0.7713 (t80) cc_final: 0.7043 (t80) REVERT: A 136 ASN cc_start: 0.6809 (p0) cc_final: 0.6204 (m110) REVERT: A 181 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7928 (mmtm) REVERT: A 230 ASN cc_start: 0.7898 (m110) cc_final: 0.7557 (m110) REVERT: A 243 PHE cc_start: 0.7088 (t80) cc_final: 0.6653 (t80) REVERT: A 319 LYS cc_start: 0.7020 (mmtm) cc_final: 0.6799 (mmmt) REVERT: A 328 MET cc_start: 0.7756 (mtm) cc_final: 0.7516 (ptp) REVERT: A 339 LYS cc_start: 0.6279 (ttmt) cc_final: 0.6039 (mtmm) REVERT: A 374 ASP cc_start: 0.7426 (t0) cc_final: 0.7055 (t0) REVERT: A 448 LYS cc_start: 0.7923 (tmtt) cc_final: 0.7613 (tmtt) REVERT: C 1 MET cc_start: 0.7186 (mtm) cc_final: 0.6721 (ppp) REVERT: C 127 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7550 (mp0) REVERT: C 130 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6047 (mm-30) REVERT: C 153 MET cc_start: 0.7924 (ttt) cc_final: 0.7588 (ptp) REVERT: C 195 ILE cc_start: 0.8008 (mp) cc_final: 0.7753 (mm) REVERT: C 398 ILE cc_start: 0.8274 (mt) cc_final: 0.7803 (mt) REVERT: C 402 ASP cc_start: 0.7193 (p0) cc_final: 0.6977 (p0) REVERT: C 416 ARG cc_start: 0.6677 (mtm110) cc_final: 0.6004 (mmp-170) REVERT: C 468 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7723 (tp) REVERT: C 470 ASN cc_start: 0.7552 (m110) cc_final: 0.7041 (m110) REVERT: C 537 ASP cc_start: 0.7672 (t0) cc_final: 0.7263 (t0) outliers start: 27 outliers final: 22 residues processed: 235 average time/residue: 0.2551 time to fit residues: 83.0028 Evaluate side-chains 242 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 73 optimal weight: 0.0030 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 113 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN A 121 HIS A 476 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.152874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131383 restraints weight = 13566.074| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.37 r_work: 0.3632 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9867 Z= 0.135 Angle : 0.659 12.644 13352 Z= 0.332 Chirality : 0.043 0.177 1488 Planarity : 0.005 0.068 1718 Dihedral : 7.680 89.910 1369 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.50 % Favored : 89.34 % Rotamer: Outliers : 2.22 % Allowed : 20.08 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.24), residues: 1210 helix: 0.97 (0.23), residues: 522 sheet: -1.26 (0.47), residues: 116 loop : -2.26 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 466 HIS 0.008 0.001 HIS C 437 PHE 0.015 0.001 PHE A 335 TYR 0.059 0.002 TYR C 499 ARG 0.004 0.000 ARG C 477 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 380) hydrogen bonds : angle 4.48446 ( 1131) metal coordination : bond 0.00316 ( 3) covalent geometry : bond 0.00306 ( 9862) covalent geometry : angle 0.65854 (13352) Misc. bond : bond 0.00097 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5622.92 seconds wall clock time: 100 minutes 38.87 seconds (6038.87 seconds total)