Starting phenix.real_space_refine on Wed Feb 4 06:55:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sdy_54794/02_2026/9sdy_54794.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sdy_54794/02_2026/9sdy_54794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sdy_54794/02_2026/9sdy_54794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sdy_54794/02_2026/9sdy_54794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sdy_54794/02_2026/9sdy_54794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sdy_54794/02_2026/9sdy_54794.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.012 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: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 68 5.16 5 C 5767 2.51 5 N 1581 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9073 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 995 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "R" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 661 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 4418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4418 Classifications: {'peptide': 574} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 16, 'TRANS': 557} Chain breaks: 6 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 22, 'ASN:plan1': 2, 'GLN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 182 Chain: "H" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2992 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 3 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1177 SG CYS R 50 89.509 50.228 68.505 1.00 81.69 S ATOM 1196 SG CYS R 53 86.558 52.397 67.397 1.00 98.31 S ATOM 1454 SG CYS R 88 89.167 53.886 69.743 1.00 93.22 S ATOM 1257 SG CYS R 61 90.770 57.947 66.661 1.00100.92 S ATOM 1282 SG CYS R 64 93.350 60.667 66.105 1.00117.89 S ATOM 1335 SG CYS R 73 93.806 57.364 64.673 1.00103.90 S ATOM 1448 SG CYS R 87 94.043 57.878 68.649 1.00115.88 S ATOM 1389 SG CYS R 80 95.243 40.261 75.240 1.00111.43 S ATOM 1544 SG CYS R 99 94.046 42.732 77.155 1.00137.37 S ATOM 1565 SG CYS R 102 92.167 39.481 77.445 1.00100.37 S ATOM 7730 SG CYS H 257 56.775 43.583 69.995 1.00 94.21 S ATOM 7756 SG CYS H 260 55.086 43.778 73.414 1.00 99.19 S ATOM 7839 SG CYS H 270 58.036 41.392 72.874 1.00 85.89 S ATOM 6781 SG CYS H 139 18.615 17.382 78.632 1.00112.72 S ATOM 6799 SG CYS H 142 16.178 20.158 79.725 1.00 78.38 S ATOM 6949 SG CYS H 161 15.916 19.033 76.329 1.00 99.23 S ATOM 6972 SG CYS H 164 19.016 20.813 77.035 1.00111.49 S ATOM 7501 SG CYS H 228 45.895 50.016 65.451 1.00 82.51 S ATOM 7531 SG CYS H 233 42.938 51.403 63.473 1.00105.70 S ATOM 7664 SG CYS H 249 46.523 51.349 61.941 1.00 90.46 S ATOM 7689 SG CYS H 252 45.557 53.668 64.861 1.00 97.66 S ATOM 6904 SG CYS H 156 30.214 14.418 73.427 1.00 92.71 S ATOM 7106 SG CYS H 183 28.532 17.380 75.279 1.00 97.97 S ATOM 7142 SG CYS H 188 31.858 16.172 76.546 1.00 67.54 S Time building chain proxies: 2.22, per 1000 atoms: 0.24 Number of scatterers: 9073 At special positions: 0 Unit cell: (129.382, 134.49, 127.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 68 16.00 O 1650 8.00 N 1581 7.00 C 5767 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=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 341.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 265 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 260 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 270 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 257 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" SG CYS H 161 " pdb="ZN ZN H 502 " - pdb=" SG CYS H 142 " pdb="ZN ZN H 502 " - pdb=" SG CYS H 164 " pdb="ZN ZN H 502 " - pdb=" SG CYS H 139 " pdb=" ZN H 503 " pdb="ZN ZN H 503 " - pdb=" SG CYS H 228 " pdb="ZN ZN H 503 " - pdb=" SG CYS H 252 " pdb="ZN ZN H 503 " - pdb=" SG CYS H 233 " pdb="ZN ZN H 503 " - pdb=" SG CYS H 249 " pdb=" ZN H 504 " pdb="ZN ZN H 504 " - pdb=" ND1 HIS H 158 " pdb="ZN ZN H 504 " - pdb=" SG CYS H 183 " pdb="ZN ZN H 504 " - pdb=" SG CYS H 188 " pdb="ZN ZN H 504 " - pdb=" SG CYS H 156 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 85 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 88 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 50 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 61 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 64 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 73 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 87 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 99 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 102 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 80 " Number of angles added : 30 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 60.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'G' and resid 4 through 18 Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 100 through 114 Processing helix chain 'G' and resid 122 through 130 Processing helix chain 'G' and resid 133 through 138 Processing helix chain 'G' and resid 138 through 147 Processing helix chain 'R' and resid 61 through 67 Processing helix chain 'R' and resid 86 through 94 Processing helix chain 'C' and resid 155 through 169 Processing helix chain 'C' and resid 175 through 188 removed outlier: 4.576A pdb=" N CYS C 188 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 201 Processing helix chain 'C' and resid 202 through 249 Proline residue: C 219 - end of helix removed outlier: 7.143A pdb=" N VAL C 227 " --> pdb=" O GLN C 223 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N GLN C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N MET C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 270 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 280 through 286 removed outlier: 4.157A pdb=" N LYS C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 301 removed outlier: 3.727A pdb=" N LEU C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 329 removed outlier: 3.548A pdb=" N ALA C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 360 Processing helix chain 'C' and resid 362 through 378 Processing helix chain 'C' and resid 403 through 417 Processing helix chain 'C' and resid 419 through 424 Processing helix chain 'C' and resid 426 through 442 Processing helix chain 'C' and resid 446 through 465 removed outlier: 4.394A pdb=" N PHE C 450 " --> pdb=" O ASN C 446 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET C 451 " --> pdb=" O LYS C 447 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG C 452 " --> pdb=" O ASP C 448 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 removed outlier: 3.719A pdb=" N VAL C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU C 478 " --> pdb=" O GLU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 514 removed outlier: 3.644A pdb=" N VAL C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 501 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 524 No H-bonds generated for 'chain 'C' and resid 522 through 524' Processing helix chain 'C' and resid 548 through 566 removed outlier: 3.593A pdb=" N ILE C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Proline residue: C 556 - end of helix removed outlier: 4.261A pdb=" N ASN C 565 " --> pdb=" O PHE C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 604 Processing helix chain 'C' and resid 605 through 607 No H-bonds generated for 'chain 'C' and resid 605 through 607' Processing helix chain 'C' and resid 616 through 624 Processing helix chain 'C' and resid 626 through 639 Processing helix chain 'C' and resid 656 through 660 Processing helix chain 'C' and resid 700 through 725 removed outlier: 4.131A pdb=" N ASN C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 Processing helix chain 'C' and resid 749 through 764 Processing helix chain 'H' and resid 65 through 84 removed outlier: 3.819A pdb=" N SER H 82 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 98 removed outlier: 3.527A pdb=" N ASN H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.629A pdb=" N LYS H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ALA H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLN H 115 " --> pdb=" O SER H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 149 No H-bonds generated for 'chain 'H' and resid 147 through 149' Processing helix chain 'H' and resid 162 through 176 removed outlier: 3.515A pdb=" N CYS H 169 " --> pdb=" O TRP H 165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER H 170 " --> pdb=" O GLU H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 197 Processing helix chain 'H' and resid 208 through 222 Processing helix chain 'H' and resid 269 through 280 removed outlier: 3.688A pdb=" N ARG H 274 " --> pdb=" O CYS H 270 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS H 275 " --> pdb=" O ALA H 271 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP H 276 " --> pdb=" O THR H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 379 removed outlier: 4.463A pdb=" N ARG H 371 " --> pdb=" O PHE H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 399 Processing helix chain 'H' and resid 403 through 407 Processing helix chain 'H' and resid 408 through 426 removed outlier: 3.853A pdb=" N ASN H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 427 through 432 Processing helix chain 'H' and resid 437 through 463 Processing helix chain 'H' and resid 468 through 487 removed outlier: 3.894A pdb=" N LEU H 486 " --> pdb=" O ARG H 482 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU H 487 " --> pdb=" O ARG H 483 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 34 through 37 removed outlier: 3.699A pdb=" N TRP G 35 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR G 69 " --> pdb=" O GLU G 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 526 through 532 Processing sheet with id=AA3, first strand: chain 'C' and resid 526 through 532 removed outlier: 5.684A pdb=" N LEU R 32 " --> pdb=" O THR C 583 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N THR C 583 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N ILE C 686 " --> pdb=" O GLN C 590 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP C 592 " --> pdb=" O ILE C 686 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 83 through 85 removed outlier: 3.825A pdb=" N ARG R 110 " --> pdb=" O TRP R 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 614 through 615 Processing sheet with id=AA6, first strand: chain 'H' and resid 62 through 64 Processing sheet with id=AA7, first strand: chain 'H' and resid 151 through 153 removed outlier: 3.644A pdb=" N PHE H 160 " --> pdb=" O LEU H 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 246 through 248 518 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 0.97 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: 2991 1.34 - 1.46: 1812 1.46 - 1.58: 4339 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 9242 Sorted by residual: bond pdb=" N CYS R 80 " pdb=" CA CYS R 80 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.18e-02 7.18e+03 8.30e+00 bond pdb=" N GLN H 380 " pdb=" CA GLN H 380 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.62e+00 bond pdb=" CA GLN H 384 " pdb=" C GLN H 384 " ideal model delta sigma weight residual 1.524 1.543 -0.019 1.29e-02 6.01e+03 2.21e+00 bond pdb=" CG1 ILE C 712 " pdb=" CD1 ILE C 712 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.81e+00 bond pdb=" C LEU H 381 " pdb=" O LEU H 381 " ideal model delta sigma weight residual 1.236 1.222 0.014 1.35e-02 5.49e+03 1.08e+00 ... (remaining 9237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 12309 1.82 - 3.63: 179 3.63 - 5.45: 37 5.45 - 7.26: 3 7.26 - 9.08: 2 Bond angle restraints: 12530 Sorted by residual: angle pdb=" N LEU H 381 " pdb=" CA LEU H 381 " pdb=" C LEU H 381 " ideal model delta sigma weight residual 113.20 107.97 5.23 1.21e+00 6.83e-01 1.87e+01 angle pdb=" N GLN H 380 " pdb=" CA GLN H 380 " pdb=" C GLN H 380 " ideal model delta sigma weight residual 110.80 102.63 8.17 2.13e+00 2.20e-01 1.47e+01 angle pdb=" C PRO C 304 " pdb=" N ASN C 305 " pdb=" CA ASN C 305 " ideal model delta sigma weight residual 121.54 127.46 -5.92 1.91e+00 2.74e-01 9.61e+00 angle pdb=" N CYS R 80 " pdb=" CA CYS R 80 " pdb=" C CYS R 80 " ideal model delta sigma weight residual 112.72 109.22 3.50 1.14e+00 7.69e-01 9.42e+00 angle pdb=" C CYS R 47 " pdb=" N ASP R 48 " pdb=" CA ASP R 48 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.13e+00 ... (remaining 12525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5070 17.75 - 35.51: 441 35.51 - 53.26: 58 53.26 - 71.02: 18 71.02 - 88.77: 7 Dihedral angle restraints: 5594 sinusoidal: 2115 harmonic: 3479 Sorted by residual: dihedral pdb=" CA ASP G 132 " pdb=" C ASP G 132 " pdb=" N ARG G 133 " pdb=" CA ARG G 133 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA GLU H 205 " pdb=" C GLU H 205 " pdb=" N LEU H 206 " pdb=" CA LEU H 206 " ideal model delta harmonic sigma weight residual 180.00 156.65 23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LEU H 84 " pdb=" C LEU H 84 " pdb=" N LYS H 85 " pdb=" CA LYS H 85 " ideal model delta harmonic sigma weight residual 180.00 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1009 0.040 - 0.081: 327 0.081 - 0.121: 74 0.121 - 0.161: 10 0.161 - 0.202: 1 Chirality restraints: 1421 Sorted by residual: chirality pdb=" CA GLN H 380 " pdb=" N GLN H 380 " pdb=" C GLN H 380 " pdb=" CB GLN H 380 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ASP R 48 " pdb=" N ASP R 48 " pdb=" C ASP R 48 " pdb=" CB ASP R 48 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ARG C 287 " pdb=" N ARG C 287 " pdb=" C ARG C 287 " pdb=" CB ARG C 287 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 1418 not shown) Planarity restraints: 1609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 656 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO C 657 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 657 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 657 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 96 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO G 97 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO G 97 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 97 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 35 " -0.017 2.00e-02 2.50e+03 1.27e-02 4.03e+00 pdb=" CG TRP G 35 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP G 35 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP G 35 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 35 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 35 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 35 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 35 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 35 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP G 35 " -0.005 2.00e-02 2.50e+03 ... (remaining 1606 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1033 2.75 - 3.29: 8795 3.29 - 3.82: 14238 3.82 - 4.36: 15426 4.36 - 4.90: 27612 Nonbonded interactions: 67104 Sorted by model distance: nonbonded pdb=" N HIS H 138 " pdb=" O GLN H 144 " model vdw 2.212 3.120 nonbonded pdb=" OH TYR C 214 " pdb=" OE2 GLU C 241 " model vdw 2.245 3.040 nonbonded pdb=" OE2 GLU H 395 " pdb=" ND2 ASN H 399 " model vdw 2.257 3.120 nonbonded pdb=" N GLN C 735 " pdb=" OE1 GLN C 735 " model vdw 2.260 3.120 nonbonded pdb=" O PRO G 77 " pdb=" N LEU G 121 " model vdw 2.303 3.120 ... (remaining 67099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.050 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.410 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9270 Z= 0.143 Angle : 0.632 21.030 12560 Z= 0.316 Chirality : 0.041 0.202 1421 Planarity : 0.004 0.056 1609 Dihedral : 13.812 88.774 3312 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1142 helix: 2.03 (0.21), residues: 642 sheet: -1.24 (0.71), residues: 51 loop : -1.87 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 110 TYR 0.018 0.002 TYR H 59 PHE 0.025 0.002 PHE C 604 TRP 0.033 0.001 TRP G 35 HIS 0.005 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9242) covalent geometry : angle 0.57412 (12530) hydrogen bonds : bond 0.13678 ( 512) hydrogen bonds : angle 5.01403 ( 1512) metal coordination : bond 0.01283 ( 28) metal coordination : angle 5.42781 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: G 5 SER cc_start: 0.7743 (p) cc_final: 0.7416 (p) REVERT: G 25 ILE cc_start: 0.8838 (tt) cc_final: 0.8613 (tp) REVERT: R 57 VAL cc_start: 0.8674 (p) cc_final: 0.8439 (t) REVERT: H 108 ARG cc_start: 0.8157 (ttm110) cc_final: 0.7854 (ttm110) REVERT: H 203 ASN cc_start: 0.8213 (t0) cc_final: 0.7864 (p0) REVERT: H 206 LEU cc_start: 0.9070 (pp) cc_final: 0.8868 (pp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1135 time to fit residues: 23.1975 Evaluate side-chains 109 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 95 GLN C 653 GLN H 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.065204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.055028 restraints weight = 35314.169| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.83 r_work: 0.3154 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9270 Z= 0.143 Angle : 0.576 8.085 12560 Z= 0.293 Chirality : 0.041 0.177 1421 Planarity : 0.004 0.050 1609 Dihedral : 4.135 26.427 1252 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.87 % Allowed : 6.33 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1142 helix: 2.23 (0.21), residues: 651 sheet: -0.56 (0.75), residues: 47 loop : -1.92 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 463 TYR 0.019 0.002 TYR H 59 PHE 0.015 0.001 PHE C 604 TRP 0.025 0.001 TRP G 35 HIS 0.005 0.001 HIS H 222 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9242) covalent geometry : angle 0.55042 (12530) hydrogen bonds : bond 0.04755 ( 512) hydrogen bonds : angle 4.07817 ( 1512) metal coordination : bond 0.00814 ( 28) metal coordination : angle 3.54545 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 5 SER cc_start: 0.7565 (p) cc_final: 0.6984 (p) REVERT: R 57 VAL cc_start: 0.8668 (p) cc_final: 0.8434 (t) REVERT: C 513 MET cc_start: 0.8768 (tmm) cc_final: 0.7987 (ttt) REVERT: C 711 ARG cc_start: 0.8279 (mtt180) cc_final: 0.7919 (ttm170) REVERT: C 738 LEU cc_start: 0.9294 (mm) cc_final: 0.9069 (mm) REVERT: H 463 ARG cc_start: 0.7634 (mpp80) cc_final: 0.7391 (mpp80) outliers start: 8 outliers final: 3 residues processed: 125 average time/residue: 0.1139 time to fit residues: 19.0850 Evaluate side-chains 114 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain C residue 650 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN H 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.064994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.054777 restraints weight = 34927.073| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.80 r_work: 0.3148 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9270 Z= 0.132 Angle : 0.545 7.257 12560 Z= 0.279 Chirality : 0.040 0.173 1421 Planarity : 0.004 0.041 1609 Dihedral : 4.057 24.778 1252 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.55 % Allowed : 8.08 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1142 helix: 2.24 (0.21), residues: 652 sheet: -0.83 (0.68), residues: 47 loop : -1.83 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 52 TYR 0.017 0.001 TYR H 59 PHE 0.014 0.001 PHE C 604 TRP 0.016 0.001 TRP G 35 HIS 0.003 0.001 HIS C 566 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9242) covalent geometry : angle 0.52077 (12530) hydrogen bonds : bond 0.04524 ( 512) hydrogen bonds : angle 3.98938 ( 1512) metal coordination : bond 0.00721 ( 28) metal coordination : angle 3.36058 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 5 SER cc_start: 0.7481 (p) cc_final: 0.7113 (p) REVERT: R 54 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.8068 (mmt180) REVERT: R 57 VAL cc_start: 0.8709 (p) cc_final: 0.8441 (t) REVERT: R 83 SER cc_start: 0.8299 (p) cc_final: 0.8053 (p) REVERT: C 738 LEU cc_start: 0.9286 (mm) cc_final: 0.9032 (mm) REVERT: H 110 LYS cc_start: 0.8405 (mptt) cc_final: 0.8159 (mmtm) REVERT: H 205 GLU cc_start: 0.8165 (pm20) cc_final: 0.7905 (pm20) outliers start: 5 outliers final: 2 residues processed: 120 average time/residue: 0.1158 time to fit residues: 18.5417 Evaluate side-chains 115 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.0270 chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 75 optimal weight: 0.0980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 106 GLN R 97 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.065553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.055277 restraints weight = 35529.433| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.84 r_work: 0.3162 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9270 Z= 0.108 Angle : 0.514 7.468 12560 Z= 0.264 Chirality : 0.039 0.168 1421 Planarity : 0.003 0.038 1609 Dihedral : 3.926 24.106 1252 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.87 % Allowed : 8.19 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.25), residues: 1142 helix: 2.39 (0.21), residues: 652 sheet: -0.80 (0.67), residues: 47 loop : -1.71 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 108 TYR 0.014 0.001 TYR H 59 PHE 0.011 0.001 PHE C 604 TRP 0.013 0.001 TRP G 35 HIS 0.002 0.001 HIS C 566 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9242) covalent geometry : angle 0.49379 (12530) hydrogen bonds : bond 0.03983 ( 512) hydrogen bonds : angle 3.85724 ( 1512) metal coordination : bond 0.00638 ( 28) metal coordination : angle 2.95874 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 5 SER cc_start: 0.7497 (p) cc_final: 0.7206 (p) REVERT: G 8 MET cc_start: 0.7966 (mpp) cc_final: 0.7730 (mpp) REVERT: G 53 ILE cc_start: 0.7627 (mm) cc_final: 0.7293 (mp) REVERT: R 57 VAL cc_start: 0.8730 (p) cc_final: 0.8447 (t) REVERT: R 83 SER cc_start: 0.8330 (p) cc_final: 0.8083 (p) REVERT: C 326 MET cc_start: 0.9033 (mmm) cc_final: 0.8823 (mmm) REVERT: C 513 MET cc_start: 0.8695 (tmm) cc_final: 0.7939 (ttt) REVERT: C 738 LEU cc_start: 0.9305 (mm) cc_final: 0.9021 (mm) REVERT: H 110 LYS cc_start: 0.8471 (mptt) cc_final: 0.8220 (mmtm) REVERT: H 205 GLU cc_start: 0.8082 (pm20) cc_final: 0.7854 (pm20) outliers start: 8 outliers final: 6 residues processed: 120 average time/residue: 0.1196 time to fit residues: 18.8670 Evaluate side-chains 110 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain H residue 209 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 106 GLN R 97 ASN H 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.065226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.055053 restraints weight = 35472.848| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.83 r_work: 0.3155 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9270 Z= 0.112 Angle : 0.507 6.218 12560 Z= 0.261 Chirality : 0.039 0.167 1421 Planarity : 0.003 0.035 1609 Dihedral : 3.863 23.906 1252 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.98 % Allowed : 9.61 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.26), residues: 1142 helix: 2.44 (0.21), residues: 653 sheet: -0.80 (0.66), residues: 47 loop : -1.67 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 463 TYR 0.013 0.001 TYR H 59 PHE 0.012 0.001 PHE G 143 TRP 0.012 0.001 TRP G 35 HIS 0.002 0.001 HIS C 566 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9242) covalent geometry : angle 0.48837 (12530) hydrogen bonds : bond 0.03972 ( 512) hydrogen bonds : angle 3.82202 ( 1512) metal coordination : bond 0.00577 ( 28) metal coordination : angle 2.81492 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 5 SER cc_start: 0.7569 (p) cc_final: 0.6863 (p) REVERT: G 53 ILE cc_start: 0.7606 (mm) cc_final: 0.7251 (mp) REVERT: G 70 PHE cc_start: 0.7461 (m-80) cc_final: 0.7215 (m-80) REVERT: G 102 ASP cc_start: 0.7810 (p0) cc_final: 0.7561 (p0) REVERT: R 83 SER cc_start: 0.8364 (p) cc_final: 0.8134 (p) REVERT: C 326 MET cc_start: 0.9036 (mmm) cc_final: 0.8803 (mmm) REVERT: C 513 MET cc_start: 0.8676 (tmm) cc_final: 0.7965 (ttt) outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 0.1192 time to fit residues: 17.5462 Evaluate side-chains 109 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain H residue 209 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 0.0040 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN G 106 GLN H 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.065762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.055695 restraints weight = 35569.384| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.78 r_work: 0.3170 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9270 Z= 0.105 Angle : 0.510 6.441 12560 Z= 0.264 Chirality : 0.039 0.168 1421 Planarity : 0.003 0.033 1609 Dihedral : 3.841 23.188 1252 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.64 % Allowed : 9.61 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1142 helix: 2.49 (0.21), residues: 652 sheet: -0.00 (0.70), residues: 39 loop : -1.70 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 108 TYR 0.011 0.001 TYR H 59 PHE 0.009 0.001 PHE G 51 TRP 0.012 0.001 TRP G 35 HIS 0.002 0.000 HIS C 566 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9242) covalent geometry : angle 0.49339 (12530) hydrogen bonds : bond 0.03803 ( 512) hydrogen bonds : angle 3.80439 ( 1512) metal coordination : bond 0.00660 ( 28) metal coordination : angle 2.69773 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 53 ILE cc_start: 0.7667 (mm) cc_final: 0.7342 (mp) REVERT: R 83 SER cc_start: 0.8300 (p) cc_final: 0.8068 (p) outliers start: 15 outliers final: 8 residues processed: 118 average time/residue: 0.1175 time to fit residues: 18.7291 Evaluate side-chains 112 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain C residue 660 PHE Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain H residue 209 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN G 106 GLN R 97 ASN H 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.064438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.054310 restraints weight = 35292.416| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.75 r_work: 0.3128 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9270 Z= 0.147 Angle : 0.554 7.199 12560 Z= 0.284 Chirality : 0.040 0.174 1421 Planarity : 0.003 0.034 1609 Dihedral : 4.014 24.301 1252 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.97 % Allowed : 9.39 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.26), residues: 1142 helix: 2.34 (0.21), residues: 654 sheet: -0.41 (0.70), residues: 41 loop : -1.68 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 463 TYR 0.015 0.001 TYR H 223 PHE 0.011 0.001 PHE C 604 TRP 0.015 0.001 TRP G 35 HIS 0.003 0.001 HIS C 566 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9242) covalent geometry : angle 0.53105 (12530) hydrogen bonds : bond 0.04530 ( 512) hydrogen bonds : angle 3.92166 ( 1512) metal coordination : bond 0.00767 ( 28) metal coordination : angle 3.26741 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 53 ILE cc_start: 0.7701 (mm) cc_final: 0.7370 (mp) REVERT: G 70 PHE cc_start: 0.7515 (m-80) cc_final: 0.7312 (m-80) REVERT: G 102 ASP cc_start: 0.7528 (p0) cc_final: 0.7321 (p0) REVERT: R 83 SER cc_start: 0.8376 (p) cc_final: 0.8157 (p) REVERT: R 97 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8194 (t0) REVERT: C 513 MET cc_start: 0.8665 (tmm) cc_final: 0.7906 (ttt) REVERT: H 143 MET cc_start: 0.8613 (mtm) cc_final: 0.8142 (mpp) outliers start: 18 outliers final: 9 residues processed: 115 average time/residue: 0.1163 time to fit residues: 18.0327 Evaluate side-chains 109 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 660 PHE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 206 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN G 106 GLN H 49 GLN H 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.064592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.054354 restraints weight = 35574.785| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.78 r_work: 0.3133 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9270 Z= 0.144 Angle : 0.559 7.515 12560 Z= 0.288 Chirality : 0.040 0.172 1421 Planarity : 0.003 0.036 1609 Dihedral : 4.053 24.618 1252 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.53 % Allowed : 10.04 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.25), residues: 1142 helix: 2.35 (0.21), residues: 652 sheet: -0.46 (0.71), residues: 41 loop : -1.68 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 711 TYR 0.013 0.001 TYR H 223 PHE 0.012 0.001 PHE G 143 TRP 0.015 0.001 TRP G 35 HIS 0.003 0.001 HIS C 566 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9242) covalent geometry : angle 0.53867 (12530) hydrogen bonds : bond 0.04485 ( 512) hydrogen bonds : angle 3.90682 ( 1512) metal coordination : bond 0.00748 ( 28) metal coordination : angle 3.10605 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 53 ILE cc_start: 0.7729 (mm) cc_final: 0.7400 (mp) REVERT: G 70 PHE cc_start: 0.7552 (m-80) cc_final: 0.7345 (m-80) REVERT: R 83 SER cc_start: 0.8396 (p) cc_final: 0.8180 (p) REVERT: C 513 MET cc_start: 0.8683 (tmm) cc_final: 0.7943 (ttt) REVERT: H 143 MET cc_start: 0.8582 (mtm) cc_final: 0.8182 (mpp) outliers start: 14 outliers final: 9 residues processed: 109 average time/residue: 0.1117 time to fit residues: 16.5996 Evaluate side-chains 107 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 632 ARG Chi-restraints excluded: chain C residue 660 PHE Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 206 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.064746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.054513 restraints weight = 35595.237| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.77 r_work: 0.3140 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9270 Z= 0.132 Angle : 0.560 8.423 12560 Z= 0.288 Chirality : 0.040 0.187 1421 Planarity : 0.003 0.035 1609 Dihedral : 4.040 24.274 1252 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.98 % Allowed : 10.81 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.25), residues: 1142 helix: 2.34 (0.21), residues: 652 sheet: -0.42 (0.71), residues: 41 loop : -1.64 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 463 TYR 0.013 0.001 TYR H 59 PHE 0.016 0.001 PHE G 143 TRP 0.014 0.001 TRP G 35 HIS 0.002 0.001 HIS C 566 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9242) covalent geometry : angle 0.54027 (12530) hydrogen bonds : bond 0.04342 ( 512) hydrogen bonds : angle 3.88708 ( 1512) metal coordination : bond 0.00786 ( 28) metal coordination : angle 3.07310 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 53 ILE cc_start: 0.7677 (mm) cc_final: 0.7178 (mp) REVERT: G 70 PHE cc_start: 0.7546 (m-80) cc_final: 0.7336 (m-80) REVERT: R 83 SER cc_start: 0.8385 (p) cc_final: 0.8160 (p) REVERT: C 513 MET cc_start: 0.8663 (tmm) cc_final: 0.7938 (ttt) REVERT: H 143 MET cc_start: 0.8541 (mtm) cc_final: 0.8180 (mpp) outliers start: 9 outliers final: 8 residues processed: 105 average time/residue: 0.1145 time to fit residues: 16.2219 Evaluate side-chains 109 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 632 ARG Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 660 PHE Chi-restraints excluded: chain H residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9990 chunk 113 optimal weight: 0.0010 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 80 optimal weight: 0.0070 chunk 105 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 102 optimal weight: 6.9990 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN H 49 GLN H 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.065640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.055448 restraints weight = 35409.188| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.78 r_work: 0.3168 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9270 Z= 0.107 Angle : 0.542 9.005 12560 Z= 0.282 Chirality : 0.039 0.181 1421 Planarity : 0.003 0.034 1609 Dihedral : 3.916 23.047 1252 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.09 % Allowed : 10.59 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1142 helix: 2.44 (0.21), residues: 651 sheet: -0.04 (0.72), residues: 39 loop : -1.61 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 463 TYR 0.011 0.001 TYR C 340 PHE 0.010 0.001 PHE G 143 TRP 0.012 0.001 TRP G 35 HIS 0.002 0.000 HIS C 566 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9242) covalent geometry : angle 0.52642 (12530) hydrogen bonds : bond 0.03798 ( 512) hydrogen bonds : angle 3.80219 ( 1512) metal coordination : bond 0.00683 ( 28) metal coordination : angle 2.68887 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 53 ILE cc_start: 0.7642 (mm) cc_final: 0.7152 (mp) REVERT: R 83 SER cc_start: 0.8341 (p) cc_final: 0.8119 (p) REVERT: C 326 MET cc_start: 0.9045 (mmm) cc_final: 0.8836 (mmm) REVERT: C 513 MET cc_start: 0.8624 (tmm) cc_final: 0.7920 (ttt) REVERT: H 143 MET cc_start: 0.8506 (mtm) cc_final: 0.8174 (mpp) REVERT: H 463 ARG cc_start: 0.7492 (mpp80) cc_final: 0.7290 (mpp80) outliers start: 10 outliers final: 8 residues processed: 106 average time/residue: 0.1063 time to fit residues: 15.2787 Evaluate side-chains 109 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 632 ARG Chi-restraints excluded: chain C residue 660 PHE Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain H residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 0.1980 chunk 22 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN H 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.065595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.055434 restraints weight = 35209.816| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.77 r_work: 0.3168 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.205 9270 Z= 0.222 Angle : 0.894 59.198 12560 Z= 0.513 Chirality : 0.040 0.288 1421 Planarity : 0.003 0.049 1609 Dihedral : 3.923 23.054 1252 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.98 % Allowed : 11.03 % Favored : 87.99 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.25), residues: 1142 helix: 2.44 (0.21), residues: 651 sheet: -0.02 (0.72), residues: 39 loop : -1.64 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 147 TYR 0.011 0.001 TYR C 340 PHE 0.013 0.001 PHE G 143 TRP 0.012 0.001 TRP G 35 HIS 0.002 0.000 HIS C 566 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9242) covalent geometry : angle 0.88580 (12530) hydrogen bonds : bond 0.03806 ( 512) hydrogen bonds : angle 3.80085 ( 1512) metal coordination : bond 0.00677 ( 28) metal coordination : angle 2.66777 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2518.87 seconds wall clock time: 43 minutes 46.06 seconds (2626.06 seconds total)