Starting phenix.real_space_refine on Fri Jul 3 06:33:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7b5m_12040/07_2026/7b5m_12040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5m_12040/07_2026/7b5m_12040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7b5m_12040/07_2026/7b5m_12040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5m_12040/07_2026/7b5m_12040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b5m_12040/07_2026/7b5m_12040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5m_12040/07_2026/7b5m_12040.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7b5m_12040/07_2026/7b5m_12040.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7b5m_12040/07_2026/7b5m_12040.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 5 6.06 5 P 1 5.49 5 S 77 5.16 5 C 7934 2.51 5 N 2165 2.21 5 O 2348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12530 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 5171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5171 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 623} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1753 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "T" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2535 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 598 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 5, 'TRANS': 63} Chain: "S" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1112 Classifications: {'peptide': 140} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 677 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'DHA:plan-1': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5383 SG CYS H 344 124.834 27.487 42.162 1.00187.92 S ATOM 5401 SG CYS H 347 124.269 24.043 44.127 1.00184.84 S ATOM 5512 SG CYS H 362 123.783 27.327 45.755 1.00183.12 S ATOM 5548 SG CYS H 367 127.110 26.277 44.967 1.00193.28 S ATOM 5584 SG CYS H 372 123.440 39.235 41.178 1.00198.39 S ATOM 5611 SG CYS H 375 126.387 39.421 38.980 1.00203.22 S ATOM 5705 SG CYS H 389 123.621 41.887 38.172 1.00185.76 S ATOM 11951 SG CYS R 42 70.704 48.988 30.551 1.00 63.26 S ATOM 11970 SG CYS R 45 70.096 47.638 34.273 1.00 71.18 S ATOM 12218 SG CYS R 83 72.706 50.193 33.564 1.00 93.25 S ATOM 12147 SG CYS R 75 74.570 51.227 16.962 1.00111.39 S ATOM 12314 SG CYS R 94 75.900 49.930 20.422 1.00 97.58 S ATOM 12037 SG CYS R 53 70.792 52.218 37.790 1.00112.66 S ATOM 12060 SG CYS R 56 68.791 55.270 38.874 1.00126.06 S ATOM 12097 SG CYS R 68 68.319 53.615 35.339 1.00134.19 S Time building chain proxies: 2.38, per 1000 atoms: 0.19 Number of scatterers: 12530 At special positions: 0 Unit cell: (153.69, 86.11, 159.14, 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 5 29.99 S 77 16.00 P 1 15.00 O 2348 8.00 N 2165 7.00 C 7934 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: 0.94 Conformation dependent library (CDL) restraints added in 596.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 601 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 367 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 362 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 347 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 344 " pdb=" ZN H 602 " pdb="ZN ZN H 602 " - pdb=" NE2 HIS H 382 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 375 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 372 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 389 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " Number of angles added : 15 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB DHA P 163 " Number of C-beta restraints generated: 3004 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 54.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 38 through 54 removed outlier: 3.681A pdb=" N CYS C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 106 removed outlier: 3.884A pdb=" N ASP C 106 " --> pdb=" O ASN C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 137 removed outlier: 3.846A pdb=" N GLN C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.887A pdb=" N ASN C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 172 removed outlier: 3.527A pdb=" N ASP C 169 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 188 removed outlier: 4.628A pdb=" N THR C 180 " --> pdb=" O ASN C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 211 Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 232 through 252 removed outlier: 4.179A pdb=" N THR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 276 removed outlier: 4.083A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN C 276 " --> pdb=" O GLN C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.917A pdb=" N ASN C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 329 removed outlier: 3.822A pdb=" N ILE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 356 removed outlier: 4.010A pdb=" N CYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 360 Processing helix chain 'C' and resid 362 through 382 removed outlier: 3.607A pdb=" N TYR C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 404 Processing helix chain 'C' and resid 406 through 412 Processing helix chain 'C' and resid 416 through 431 removed outlier: 3.712A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 455 removed outlier: 4.332A pdb=" N ASP C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 476 removed outlier: 3.552A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 501 removed outlier: 7.653A pdb=" N PHE C 498 " --> pdb=" O GLN C 494 " (cutoff:3.500A) removed outlier: 9.724A pdb=" N GLU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR C 501 " --> pdb=" O GLY C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 525 removed outlier: 3.964A pdb=" N ILE C 511 " --> pdb=" O MET C 507 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN C 520 " --> pdb=" O ASP C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 528 No H-bonds generated for 'chain 'C' and resid 526 through 528' Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 559 through 574 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 614 through 616 No H-bonds generated for 'chain 'C' and resid 614 through 616' Processing helix chain 'C' and resid 621 through 630 Processing helix chain 'C' and resid 632 through 646 removed outlier: 3.961A pdb=" N SER C 646 " --> pdb=" O ILE C 642 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 325 Processing helix chain 'H' and resid 331 through 341 Processing helix chain 'H' and resid 404 through 430 removed outlier: 3.741A pdb=" N ALA H 409 " --> pdb=" O GLU H 405 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA H 410 " --> pdb=" O ARG H 406 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU H 411 " --> pdb=" O SER H 407 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA H 430 " --> pdb=" O GLN H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 448 Processing helix chain 'H' and resid 452 through 481 removed outlier: 4.383A pdb=" N TYR H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR H 481 " --> pdb=" O VAL H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 512 Processing helix chain 'H' and resid 517 through 550 Processing helix chain 'T' and resid 96 through 100 removed outlier: 3.538A pdb=" N SER T 99 " --> pdb=" O SER T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 110 Processing helix chain 'T' and resid 113 through 121 Processing helix chain 'T' and resid 124 through 131 Processing helix chain 'T' and resid 148 through 158 Processing helix chain 'T' and resid 194 through 203 Processing helix chain 'T' and resid 219 through 227 Processing helix chain 'T' and resid 244 through 255 Processing helix chain 'T' and resid 270 through 281 Processing helix chain 'T' and resid 298 through 309 Processing helix chain 'T' and resid 324 through 334 removed outlier: 3.919A pdb=" N PHE T 328 " --> pdb=" O LYS T 324 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN T 329 " --> pdb=" O ASN T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 353 through 358 removed outlier: 3.612A pdb=" N GLY T 357 " --> pdb=" O LEU T 353 " (cutoff:3.500A) Processing helix chain 'T' and resid 375 through 383 Processing helix chain 'K' and resid 25 through 30 Processing helix chain 'K' and resid 39 through 47 Processing helix chain 'S' and resid 24 through 31 Processing helix chain 'S' and resid 45 through 59 Processing helix chain 'S' and resid 86 through 91 removed outlier: 4.165A pdb=" N GLN S 90 " --> pdb=" O PRO S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 111 Processing helix chain 'S' and resid 112 through 128 removed outlier: 3.747A pdb=" N LYS S 128 " --> pdb=" O ALA S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 139 Processing helix chain 'S' and resid 149 through 157 Processing helix chain 'U' and resid 22 through 35 Processing helix chain 'R' and resid 53 through 58 Processing helix chain 'R' and resid 83 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541 removed outlier: 5.367A pdb=" N ASP C 534 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA R 29 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP R 33 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU C 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS R 26 " --> pdb=" O GLU C 589 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 587 " --> pdb=" O ASN R 28 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 601 " --> pdb=" O LEU C 590 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 649 through 650 Processing sheet with id=AA3, first strand: chain 'T' and resid 139 through 141 removed outlier: 6.521A pdb=" N LEU T 140 " --> pdb=" O ARG T 164 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP T 187 " --> pdb=" O PHE T 163 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU T 235 " --> pdb=" O ASN T 262 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU T 340 " --> pdb=" O GLN T 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 55 through 60 removed outlier: 4.017A pdb=" N TYR K 57 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU K 68 " --> pdb=" O TYR K 57 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE K 59 " --> pdb=" O ILE K 66 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ILE K 66 " --> pdb=" O ILE K 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 13 through 16 removed outlier: 3.556A pdb=" N PHE S 14 " --> pdb=" O LEU S 6 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU S 6 " --> pdb=" O PHE S 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'U' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'U' and resid 48 through 50 removed outlier: 4.245A pdb=" N LEU U 43 " --> pdb=" O LEU U 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 78 through 79 removed outlier: 3.714A pdb=" N LYS R 105 " --> pdb=" O TRP R 72 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1779 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: 1.45 Time building geometry restraints manager: 1.27 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: 4107 1.34 - 1.46: 2570 1.46 - 1.58: 5977 1.58 - 1.70: 3 1.70 - 1.82: 105 Bond restraints: 12762 Sorted by residual: bond pdb=" CA DHA P 163 " pdb=" CB DHA P 163 " ideal model delta sigma weight residual 1.530 1.350 0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" OG1 TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O1P TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O3P TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N DHA P 163 " pdb=" CA DHA P 163 " ideal model delta sigma weight residual 1.458 1.406 0.052 1.90e-02 2.77e+03 7.58e+00 ... (remaining 12757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 16961 2.74 - 5.47: 246 5.47 - 8.21: 37 8.21 - 10.95: 6 10.95 - 13.69: 2 Bond angle restraints: 17252 Sorted by residual: angle pdb=" N DHA P 163 " pdb=" CA DHA P 163 " pdb=" CB DHA P 163 " ideal model delta sigma weight residual 110.50 123.21 -12.71 1.70e+00 3.46e-01 5.59e+01 angle pdb=" N PRO S 2 " pdb=" CA PRO S 2 " pdb=" CB PRO S 2 " ideal model delta sigma weight residual 103.00 110.39 -7.39 1.10e+00 8.26e-01 4.52e+01 angle pdb=" N GLU C 335 " pdb=" CA GLU C 335 " pdb=" C GLU C 335 " ideal model delta sigma weight residual 114.62 107.55 7.07 1.14e+00 7.69e-01 3.85e+01 angle pdb=" N VAL C 591 " pdb=" CA VAL C 591 " pdb=" C VAL C 591 " ideal model delta sigma weight residual 113.53 108.35 5.18 9.80e-01 1.04e+00 2.79e+01 angle pdb=" C DHA P 163 " pdb=" CA DHA P 163 " pdb=" CB DHA P 163 " ideal model delta sigma weight residual 110.10 120.10 -10.00 1.90e+00 2.77e-01 2.77e+01 ... (remaining 17247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6829 17.94 - 35.87: 706 35.87 - 53.80: 147 53.80 - 71.74: 28 71.74 - 89.67: 14 Dihedral angle restraints: 7724 sinusoidal: 3120 harmonic: 4604 Sorted by residual: dihedral pdb=" CA ASP S 33 " pdb=" C ASP S 33 " pdb=" N LEU S 34 " pdb=" CA LEU S 34 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ASP S 96 " pdb=" C ASP S 96 " pdb=" N GLN S 97 " pdb=" CA GLN S 97 " ideal model delta harmonic sigma weight residual 180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PHE C 385 " pdb=" C PHE C 385 " pdb=" N ASN C 386 " pdb=" CA ASN C 386 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 7721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1389 0.047 - 0.094: 427 0.094 - 0.141: 100 0.141 - 0.188: 15 0.188 - 0.235: 4 Chirality restraints: 1935 Sorted by residual: chirality pdb=" CA PRO S 2 " pdb=" N PRO S 2 " pdb=" C PRO S 2 " pdb=" CB PRO S 2 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU T 100 " pdb=" CB LEU T 100 " pdb=" CD1 LEU T 100 " pdb=" CD2 LEU T 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE C 684 " pdb=" CA ILE C 684 " pdb=" CG1 ILE C 684 " pdb=" CG2 ILE C 684 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1932 not shown) Planarity restraints: 2204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 385 " 0.016 2.00e-02 2.50e+03 2.25e-02 8.86e+00 pdb=" CG PHE C 385 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE C 385 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE C 385 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE C 385 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 385 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 385 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 27 " -0.021 2.00e-02 2.50e+03 1.69e-02 7.16e+00 pdb=" CG TRP R 27 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP R 27 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP R 27 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 27 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 27 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 27 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 27 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 27 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 27 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 173 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO C 174 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 174 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 174 " -0.036 5.00e-02 4.00e+02 ... (remaining 2201 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 151 2.58 - 3.16: 11005 3.16 - 3.74: 19734 3.74 - 4.32: 25637 4.32 - 4.90: 41089 Nonbonded interactions: 97616 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 2.001 2.230 nonbonded pdb=" O VAL C 227 " pdb=" OG SER C 231 " model vdw 2.210 3.040 nonbonded pdb=" OG SER C 481 " pdb=" OD1 ASP C 483 " model vdw 2.212 3.040 nonbonded pdb=" NH2 ARG T 294 " pdb=" OE1 GLU P 185 " model vdw 2.236 3.120 nonbonded pdb=" O SER H 331 " pdb=" OG SER H 334 " model vdw 2.246 3.040 ... (remaining 97611 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 group one per residue 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.730 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.006 0.271 12783 Z= 0.269 Angle : 0.880 13.687 17267 Z= 0.487 Chirality : 0.048 0.235 1935 Planarity : 0.005 0.081 2204 Dihedral : 15.580 89.674 4720 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 0.22 % Allowed : 0.58 % Favored : 99.20 % Cbeta Deviations : 0.07 % 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: -2.61 (0.20), residues: 1527 helix: -0.54 (0.18), residues: 803 sheet: -2.63 (0.60), residues: 72 loop : -3.23 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 86 TYR 0.026 0.002 TYR C 278 PHE 0.051 0.002 PHE C 385 TRP 0.046 0.003 TRP R 27 HIS 0.010 0.002 HIS H 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.23 (12762) covalent geometry : angle 0.86626 / 0.49 (17252) hydrogen bonds : bond 0.13982 / 9.35 ( 603) hydrogen bonds : angle 6.50408 / 4.64 ( 1779) metal coordination : bond 0.06617 / 3.49 ( 19) metal coordination : angle 5.41758 / 2.40 ( 15) Misc. bond : bond 0.08590 / 4.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 173 ARG cc_start: 0.5463 (mmm-85) cc_final: 0.5023 (mmm-85) REVERT: C 261 MET cc_start: 0.8469 (mpp) cc_final: 0.8129 (mtm) REVERT: C 537 ILE cc_start: 0.8384 (tt) cc_final: 0.8164 (tp) REVERT: C 672 TYR cc_start: 0.8405 (t80) cc_final: 0.8123 (t80) REVERT: C 675 TYR cc_start: 0.6480 (t80) cc_final: 0.5839 (t80) REVERT: T 97 TRP cc_start: 0.3785 (m100) cc_final: 0.3156 (m100) REVERT: K 38 MET cc_start: 0.6698 (mtt) cc_final: 0.6311 (mtt) REVERT: K 58 MET cc_start: 0.6429 (ptm) cc_final: 0.6075 (ptm) REVERT: U 39 ASP cc_start: 0.8380 (m-30) cc_final: 0.7945 (p0) REVERT: U 61 ILE cc_start: 0.8931 (mp) cc_final: 0.8617 (mp) outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.1024 time to fit residues: 19.9443 Evaluate side-chains 98 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain T residue 238 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0010 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 404 ASN C 447 ASN C 685 ASN ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 542 HIS T 138 GLN T 190 ASN ** T 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.094315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.065726 restraints weight = 42697.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.066516 restraints weight = 30177.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.066815 restraints weight = 22932.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.067122 restraints weight = 22496.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.067239 restraints weight = 18998.942| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12783 Z= 0.166 Angle : 0.685 15.436 17267 Z= 0.362 Chirality : 0.043 0.202 1935 Planarity : 0.005 0.060 2204 Dihedral : 5.902 47.837 1678 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.09 % Allowed : 8.83 % Favored : 90.08 % Cbeta Deviations : 0.07 % 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: -2.13 (0.21), residues: 1527 helix: -0.03 (0.18), residues: 822 sheet: -2.56 (0.64), residues: 69 loop : -3.24 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 274 TYR 0.027 0.002 TYR H 529 PHE 0.028 0.002 PHE H 457 TRP 0.015 0.002 TRP R 27 HIS 0.008 0.001 HIS R 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (12762) covalent geometry : angle 0.67932 / 0.36 (17252) hydrogen bonds : bond 0.05473 / 3.47 ( 603) hydrogen bonds : angle 5.10132 / 3.59 ( 1779) metal coordination : bond 0.01156 / 0.65 ( 19) metal coordination : angle 2.97057 / 1.45 ( 15) Misc. bond : bond 0.00014 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 173 ARG cc_start: 0.5814 (mmm-85) cc_final: 0.5523 (mmm-85) REVERT: C 233 GLU cc_start: 0.7518 (tt0) cc_final: 0.7280 (tm-30) REVERT: C 585 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8737 (pp) REVERT: C 614 TYR cc_start: 0.6585 (m-80) cc_final: 0.6338 (m-80) REVERT: C 675 TYR cc_start: 0.6504 (t80) cc_final: 0.5426 (t80) REVERT: H 473 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7968 (mtp) REVERT: T 97 TRP cc_start: 0.4219 (m100) cc_final: 0.3207 (m100) REVERT: T 170 MET cc_start: 0.7243 (mmt) cc_final: 0.6846 (tpp) REVERT: T 186 MET cc_start: 0.7524 (tpp) cc_final: 0.7321 (tpp) REVERT: K 38 MET cc_start: 0.7089 (mtt) cc_final: 0.6694 (mtt) REVERT: K 58 MET cc_start: 0.6232 (ptm) cc_final: 0.5969 (ptm) REVERT: U 11 LYS cc_start: 0.7345 (tttm) cc_final: 0.6867 (mttp) REVERT: U 39 ASP cc_start: 0.8562 (m-30) cc_final: 0.7903 (p0) outliers start: 15 outliers final: 10 residues processed: 115 average time/residue: 0.1024 time to fit residues: 17.4730 Evaluate side-chains 108 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 128 optimal weight: 0.0050 chunk 103 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 199 HIS ** T 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.096397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.071512 restraints weight = 41529.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.071578 restraints weight = 35013.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072076 restraints weight = 34588.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.071980 restraints weight = 24575.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072177 restraints weight = 22195.546| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12783 Z= 0.120 Angle : 0.606 15.537 17267 Z= 0.318 Chirality : 0.041 0.169 1935 Planarity : 0.004 0.058 2204 Dihedral : 5.295 46.387 1675 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.75 % Allowed : 11.89 % Favored : 86.36 % Cbeta Deviations : 0.07 % 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: -1.56 (0.22), residues: 1527 helix: 0.53 (0.18), residues: 822 sheet: -2.72 (0.56), residues: 88 loop : -3.05 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 70 TYR 0.023 0.001 TYR H 529 PHE 0.021 0.001 PHE H 457 TRP 0.018 0.001 TRP K 43 HIS 0.005 0.001 HIS C 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (12762) covalent geometry : angle 0.60227 / 0.32 (17252) hydrogen bonds : bond 0.04339 / 2.73 ( 603) hydrogen bonds : angle 4.54546 / 3.19 ( 1779) metal coordination : bond 0.00581 / 0.34 ( 19) metal coordination : angle 2.43632 / 1.18 ( 15) Misc. bond : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 GLU cc_start: 0.7609 (mp0) cc_final: 0.7395 (mp0) REVERT: C 478 ASN cc_start: 0.8684 (t0) cc_final: 0.8461 (t0) REVERT: C 585 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8592 (pp) REVERT: C 587 LYS cc_start: 0.8031 (pttp) cc_final: 0.7777 (mtmt) REVERT: C 614 TYR cc_start: 0.6771 (m-80) cc_final: 0.6515 (m-80) REVERT: H 422 MET cc_start: 0.8194 (tpp) cc_final: 0.7978 (mmt) REVERT: T 97 TRP cc_start: 0.4035 (m100) cc_final: 0.3257 (m100) REVERT: T 170 MET cc_start: 0.7190 (mmt) cc_final: 0.6901 (tpp) REVERT: K 38 MET cc_start: 0.6413 (mtt) cc_final: 0.6158 (mtt) REVERT: U 11 LYS cc_start: 0.7161 (tttm) cc_final: 0.6708 (mttp) REVERT: U 39 ASP cc_start: 0.8296 (m-30) cc_final: 0.7762 (p0) outliers start: 24 outliers final: 12 residues processed: 138 average time/residue: 0.0966 time to fit residues: 19.7029 Evaluate side-chains 112 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 360 MET Chi-restraints excluded: chain T residue 199 HIS Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 90 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 chunk 124 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 59 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 262 ASN T 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.095057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.067841 restraints weight = 41193.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.067036 restraints weight = 30996.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067228 restraints weight = 25783.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.067526 restraints weight = 23841.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.067665 restraints weight = 22184.657| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12783 Z= 0.145 Angle : 0.625 15.585 17267 Z= 0.325 Chirality : 0.041 0.159 1935 Planarity : 0.004 0.054 2204 Dihedral : 5.255 49.548 1675 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.97 % Allowed : 15.03 % Favored : 83.01 % Cbeta Deviations : 0.07 % 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: -1.43 (0.22), residues: 1527 helix: 0.60 (0.18), residues: 825 sheet: -2.73 (0.56), residues: 88 loop : -2.93 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 274 TYR 0.023 0.001 TYR H 529 PHE 0.024 0.002 PHE H 457 TRP 0.016 0.001 TRP K 43 HIS 0.011 0.001 HIS T 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (12762) covalent geometry : angle 0.62007 / 0.32 (17252) hydrogen bonds : bond 0.04623 / 2.92 ( 603) hydrogen bonds : angle 4.51057 / 3.17 ( 1779) metal coordination : bond 0.01109 / 0.59 ( 19) metal coordination : angle 2.68692 / 1.34 ( 15) Misc. bond : bond 0.00027 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 GLU cc_start: 0.7685 (mp0) cc_final: 0.7397 (mp0) REVERT: C 585 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8628 (pp) REVERT: C 587 LYS cc_start: 0.8068 (pttp) cc_final: 0.7725 (mtmt) REVERT: C 614 TYR cc_start: 0.6607 (m-80) cc_final: 0.6373 (m-80) REVERT: H 422 MET cc_start: 0.8247 (tpp) cc_final: 0.7997 (mmt) REVERT: T 97 TRP cc_start: 0.4087 (m100) cc_final: 0.3061 (m100) REVERT: T 170 MET cc_start: 0.7265 (mmt) cc_final: 0.6911 (tpp) REVERT: K 38 MET cc_start: 0.6431 (mtt) cc_final: 0.6209 (mtt) REVERT: S 91 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: U 11 LYS cc_start: 0.7149 (tttm) cc_final: 0.6649 (mttp) REVERT: U 39 ASP cc_start: 0.8445 (m-30) cc_final: 0.7804 (p0) outliers start: 27 outliers final: 16 residues processed: 123 average time/residue: 0.1026 time to fit residues: 18.2010 Evaluate side-chains 111 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain P residue 184 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 134 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** 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 = 0.3878 r_free = 0.3878 target = 0.095408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.066294 restraints weight = 41688.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066271 restraints weight = 29657.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067235 restraints weight = 23491.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.067716 restraints weight = 19090.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067768 restraints weight = 16768.726| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12783 Z= 0.132 Angle : 0.604 15.593 17267 Z= 0.314 Chirality : 0.041 0.156 1935 Planarity : 0.004 0.053 2204 Dihedral : 5.146 53.687 1675 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.19 % Allowed : 15.17 % Favored : 82.64 % Cbeta Deviations : 0.07 % 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: -1.33 (0.22), residues: 1527 helix: 0.71 (0.18), residues: 829 sheet: -2.45 (0.66), residues: 68 loop : -3.01 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 86 TYR 0.022 0.001 TYR H 529 PHE 0.022 0.001 PHE C 402 TRP 0.012 0.001 TRP C 144 HIS 0.005 0.001 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (12762) covalent geometry : angle 0.60018 / 0.31 (17252) hydrogen bonds : bond 0.04406 / 2.76 ( 603) hydrogen bonds : angle 4.35351 / 3.05 ( 1779) metal coordination : bond 0.00833 / 0.45 ( 19) metal coordination : angle 2.46660 / 1.24 ( 15) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 GLU cc_start: 0.7633 (mp0) cc_final: 0.7409 (mp0) REVERT: C 261 MET cc_start: 0.8610 (mtm) cc_final: 0.8308 (mtm) REVERT: C 585 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8651 (pp) REVERT: C 587 LYS cc_start: 0.7997 (pttp) cc_final: 0.7665 (mtmt) REVERT: H 422 MET cc_start: 0.8172 (tpp) cc_final: 0.7940 (mmt) REVERT: T 97 TRP cc_start: 0.4195 (m100) cc_final: 0.3176 (m100) REVERT: T 170 MET cc_start: 0.7277 (mmt) cc_final: 0.6913 (tpp) REVERT: K 11 LYS cc_start: 0.6654 (mttt) cc_final: 0.6338 (mmmt) REVERT: K 38 MET cc_start: 0.6439 (mtt) cc_final: 0.6201 (mtt) REVERT: K 70 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7183 (mtp85) REVERT: S 91 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: S 147 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: U 11 LYS cc_start: 0.7046 (tttm) cc_final: 0.6523 (mttp) REVERT: U 39 ASP cc_start: 0.8464 (m-30) cc_final: 0.7791 (p0) REVERT: P 186 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7484 (tm-30) outliers start: 30 outliers final: 19 residues processed: 127 average time/residue: 0.0902 time to fit residues: 17.2497 Evaluate side-chains 116 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 375 CYS Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain P residue 184 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 138 GLN ** T 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.095210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.065909 restraints weight = 41668.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066178 restraints weight = 29990.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.067205 restraints weight = 22263.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067406 restraints weight = 19430.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.067519 restraints weight = 17497.715| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12783 Z= 0.134 Angle : 0.606 15.596 17267 Z= 0.315 Chirality : 0.041 0.174 1935 Planarity : 0.004 0.050 2204 Dihedral : 5.033 51.748 1675 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.19 % Allowed : 16.19 % Favored : 81.62 % Cbeta Deviations : 0.07 % 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: -1.21 (0.22), residues: 1527 helix: 0.78 (0.18), residues: 832 sheet: -2.69 (0.56), residues: 86 loop : -2.86 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 86 TYR 0.022 0.001 TYR H 529 PHE 0.027 0.001 PHE T 331 TRP 0.014 0.001 TRP K 43 HIS 0.005 0.001 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (12762) covalent geometry : angle 0.60263 / 0.31 (17252) hydrogen bonds : bond 0.04390 / 2.77 ( 603) hydrogen bonds : angle 4.30782 / 3.01 ( 1779) metal coordination : bond 0.00873 / 0.48 ( 19) metal coordination : angle 2.35037 / 1.19 ( 15) Misc. bond : bond 0.00019 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.8579 (mtm) cc_final: 0.8274 (mtp) REVERT: C 585 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8676 (pp) REVERT: C 587 LYS cc_start: 0.7984 (pttp) cc_final: 0.7650 (mtmt) REVERT: H 422 MET cc_start: 0.8213 (tpp) cc_final: 0.7980 (mmt) REVERT: T 97 TRP cc_start: 0.4329 (m100) cc_final: 0.3369 (m100) REVERT: T 170 MET cc_start: 0.7270 (mmt) cc_final: 0.6982 (tpp) REVERT: K 11 LYS cc_start: 0.6739 (mttt) cc_final: 0.6391 (mmmt) REVERT: K 38 MET cc_start: 0.6332 (mtt) cc_final: 0.6108 (mtt) REVERT: K 70 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7202 (mtt180) REVERT: S 147 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: U 11 LYS cc_start: 0.7000 (tttm) cc_final: 0.6477 (mttp) REVERT: U 25 ASN cc_start: 0.8475 (m110) cc_final: 0.8245 (m110) REVERT: U 39 ASP cc_start: 0.8303 (m-30) cc_final: 0.7687 (p0) REVERT: U 52 ASP cc_start: 0.5923 (t0) cc_final: 0.5213 (p0) outliers start: 30 outliers final: 21 residues processed: 124 average time/residue: 0.0994 time to fit residues: 18.3584 Evaluate side-chains 116 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 375 CYS Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain P residue 184 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 50 optimal weight: 8.9990 chunk 144 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 68 optimal weight: 0.0970 chunk 129 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 84 optimal weight: 0.4980 chunk 64 optimal weight: 8.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** 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 = 0.3905 r_free = 0.3905 target = 0.097503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.068076 restraints weight = 41127.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.069634 restraints weight = 26419.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.070878 restraints weight = 19349.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.071642 restraints weight = 15592.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.072210 restraints weight = 13429.627| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12783 Z= 0.112 Angle : 0.597 15.585 17267 Z= 0.308 Chirality : 0.040 0.242 1935 Planarity : 0.003 0.051 2204 Dihedral : 4.822 46.479 1675 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.19 % Allowed : 16.05 % Favored : 81.77 % Cbeta Deviations : 0.07 % 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: -0.95 (0.22), residues: 1527 helix: 0.99 (0.18), residues: 831 sheet: -2.67 (0.57), residues: 86 loop : -2.73 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 86 TYR 0.019 0.001 TYR H 529 PHE 0.029 0.001 PHE T 331 TRP 0.016 0.001 TRP K 43 HIS 0.005 0.001 HIS C 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (12762) covalent geometry : angle 0.59374 / 0.31 (17252) hydrogen bonds : bond 0.03919 / 2.47 ( 603) hydrogen bonds : angle 4.16459 / 2.92 ( 1779) metal coordination : bond 0.00475 / 0.26 ( 19) metal coordination : angle 2.19407 / 1.14 ( 15) Misc. bond : bond 0.00012 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 126 TYR cc_start: 0.9030 (t80) cc_final: 0.8166 (t80) REVERT: C 261 MET cc_start: 0.8539 (mtm) cc_final: 0.8261 (mtp) REVERT: C 478 ASN cc_start: 0.8688 (t0) cc_final: 0.8452 (t0) REVERT: C 587 LYS cc_start: 0.8000 (pttp) cc_final: 0.7661 (mtmt) REVERT: H 422 MET cc_start: 0.8070 (tpp) cc_final: 0.7838 (mmt) REVERT: T 97 TRP cc_start: 0.4269 (m100) cc_final: 0.3764 (m100) REVERT: T 186 MET cc_start: 0.7809 (tpt) cc_final: 0.7429 (tpp) REVERT: K 11 LYS cc_start: 0.6777 (mttt) cc_final: 0.6439 (mmmt) REVERT: K 38 MET cc_start: 0.6068 (mtt) cc_final: 0.5797 (mtt) REVERT: K 70 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7082 (mtt180) REVERT: S 147 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: U 11 LYS cc_start: 0.6961 (tttm) cc_final: 0.6478 (mttp) REVERT: U 25 ASN cc_start: 0.8445 (m110) cc_final: 0.8237 (m110) REVERT: U 39 ASP cc_start: 0.8434 (m-30) cc_final: 0.7788 (p0) REVERT: U 52 ASP cc_start: 0.5544 (t0) cc_final: 0.4831 (p0) outliers start: 30 outliers final: 20 residues processed: 128 average time/residue: 0.1122 time to fit residues: 21.2780 Evaluate side-chains 120 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 375 CYS Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.0570 chunk 2 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 122 optimal weight: 0.9980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** 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 = 0.3897 r_free = 0.3897 target = 0.096869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.069094 restraints weight = 40483.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.069746 restraints weight = 26807.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.070403 restraints weight = 19410.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.070792 restraints weight = 17675.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070857 restraints weight = 15226.160| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12783 Z= 0.127 Angle : 0.621 15.596 17267 Z= 0.319 Chirality : 0.041 0.187 1935 Planarity : 0.004 0.050 2204 Dihedral : 4.808 45.578 1675 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 1.82 % Allowed : 16.56 % Favored : 81.62 % Cbeta Deviations : 0.07 % 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: -0.95 (0.22), residues: 1527 helix: 1.01 (0.18), residues: 832 sheet: -2.64 (0.57), residues: 86 loop : -2.76 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 99 TYR 0.020 0.001 TYR H 529 PHE 0.029 0.001 PHE T 331 TRP 0.017 0.001 TRP C 545 HIS 0.005 0.001 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (12762) covalent geometry : angle 0.61819 / 0.32 (17252) hydrogen bonds : bond 0.04142 / 2.63 ( 603) hydrogen bonds : angle 4.19890 / 2.95 ( 1779) metal coordination : bond 0.00704 / 0.38 ( 19) metal coordination : angle 2.23377 / 1.18 ( 15) Misc. bond : bond 0.00013 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.8556 (mtm) cc_final: 0.8293 (mtp) REVERT: C 478 ASN cc_start: 0.8716 (t0) cc_final: 0.8475 (t0) REVERT: C 587 LYS cc_start: 0.8060 (pttp) cc_final: 0.7707 (mtmt) REVERT: H 422 MET cc_start: 0.8260 (tpp) cc_final: 0.8018 (mmt) REVERT: T 97 TRP cc_start: 0.4390 (m100) cc_final: 0.3688 (m100) REVERT: T 186 MET cc_start: 0.7754 (tpt) cc_final: 0.7286 (tpp) REVERT: K 11 LYS cc_start: 0.6815 (mttt) cc_final: 0.6455 (mmmt) REVERT: K 38 MET cc_start: 0.6022 (mtt) cc_final: 0.5740 (mtt) REVERT: K 70 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7011 (mtt180) REVERT: S 147 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: U 11 LYS cc_start: 0.6972 (tttm) cc_final: 0.6464 (mttp) REVERT: U 25 ASN cc_start: 0.8526 (m110) cc_final: 0.8281 (m-40) REVERT: U 39 ASP cc_start: 0.8275 (m-30) cc_final: 0.7653 (p0) outliers start: 25 outliers final: 20 residues processed: 125 average time/residue: 0.1011 time to fit residues: 18.4671 Evaluate side-chains 118 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 375 CYS Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 25 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 42 optimal weight: 0.0050 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 0.0010 chunk 106 optimal weight: 20.0000 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** 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 = 0.3955 r_free = 0.3955 target = 0.101576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071877 restraints weight = 43179.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.072804 restraints weight = 29887.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073605 restraints weight = 22079.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.074070 restraints weight = 18731.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074345 restraints weight = 16410.804| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12783 Z= 0.113 Angle : 0.609 15.589 17267 Z= 0.312 Chirality : 0.040 0.176 1935 Planarity : 0.004 0.051 2204 Dihedral : 4.708 45.641 1675 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.53 % Allowed : 17.29 % Favored : 81.18 % Cbeta Deviations : 0.07 % 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: -0.83 (0.22), residues: 1527 helix: 1.14 (0.18), residues: 831 sheet: -2.67 (0.57), residues: 86 loop : -2.74 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 99 TYR 0.018 0.001 TYR H 529 PHE 0.028 0.001 PHE T 331 TRP 0.017 0.001 TRP T 265 HIS 0.005 0.001 HIS C 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (12762) covalent geometry : angle 0.60666 / 0.31 (17252) hydrogen bonds : bond 0.03756 / 2.38 ( 603) hydrogen bonds : angle 4.09746 / 2.87 ( 1779) metal coordination : bond 0.00468 / 0.25 ( 19) metal coordination : angle 2.07044 / 1.12 ( 15) Misc. bond : bond 0.00010 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 126 TYR cc_start: 0.9045 (t80) cc_final: 0.8229 (t80) REVERT: C 261 MET cc_start: 0.8464 (mtm) cc_final: 0.8186 (mtp) REVERT: C 478 ASN cc_start: 0.8654 (t0) cc_final: 0.8407 (t0) REVERT: C 587 LYS cc_start: 0.8130 (pttp) cc_final: 0.7825 (mtmt) REVERT: C 608 MET cc_start: 0.7281 (mmt) cc_final: 0.6836 (mmm) REVERT: T 97 TRP cc_start: 0.4181 (m100) cc_final: 0.3803 (m100) REVERT: T 186 MET cc_start: 0.7728 (tpt) cc_final: 0.7284 (tpp) REVERT: K 11 LYS cc_start: 0.6836 (mttt) cc_final: 0.6494 (mmmt) REVERT: K 38 MET cc_start: 0.5910 (mtt) cc_final: 0.5645 (mtt) REVERT: K 70 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7185 (mtt180) REVERT: S 147 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: U 11 LYS cc_start: 0.6954 (tttm) cc_final: 0.6472 (mttp) REVERT: U 39 ASP cc_start: 0.8530 (m-30) cc_final: 0.7799 (p0) REVERT: U 52 ASP cc_start: 0.5812 (t0) cc_final: 0.4849 (p0) outliers start: 21 outliers final: 17 residues processed: 119 average time/residue: 0.0883 time to fit residues: 15.8403 Evaluate side-chains 116 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 375 CYS Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 143 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 106 optimal weight: 30.0000 chunk 121 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 0.0470 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.097621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.068347 restraints weight = 41042.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.069417 restraints weight = 31381.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070051 restraints weight = 22368.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.070683 restraints weight = 19258.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.071070 restraints weight = 16505.711| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12783 Z= 0.118 Angle : 0.615 15.600 17267 Z= 0.315 Chirality : 0.041 0.239 1935 Planarity : 0.004 0.051 2204 Dihedral : 4.681 45.166 1675 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 1.46 % Allowed : 17.87 % Favored : 80.67 % Cbeta Deviations : 0.07 % 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: -0.77 (0.22), residues: 1527 helix: 1.18 (0.18), residues: 832 sheet: -2.88 (0.53), residues: 98 loop : -2.64 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 99 TYR 0.019 0.001 TYR H 529 PHE 0.027 0.001 PHE T 331 TRP 0.016 0.001 TRP K 43 HIS 0.004 0.001 HIS C 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12762) covalent geometry : angle 0.61214 / 0.31 (17252) hydrogen bonds : bond 0.03889 / 2.47 ( 603) hydrogen bonds : angle 4.09586 / 2.87 ( 1779) metal coordination : bond 0.00589 / 0.31 ( 19) metal coordination : angle 2.20563 / 1.16 ( 15) Misc. bond : bond 0.00011 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 126 TYR cc_start: 0.9017 (t80) cc_final: 0.8188 (t80) REVERT: C 261 MET cc_start: 0.8524 (mtm) cc_final: 0.8239 (mtp) REVERT: C 478 ASN cc_start: 0.8736 (t0) cc_final: 0.8465 (t0) REVERT: C 587 LYS cc_start: 0.8110 (pttp) cc_final: 0.7762 (mtmt) REVERT: C 608 MET cc_start: 0.7174 (mmt) cc_final: 0.6754 (mmm) REVERT: C 675 TYR cc_start: 0.6978 (t80) cc_final: 0.6528 (t80) REVERT: H 422 MET cc_start: 0.7937 (mmt) cc_final: 0.7611 (mmp) REVERT: T 97 TRP cc_start: 0.4301 (m100) cc_final: 0.3853 (m100) REVERT: T 170 MET cc_start: 0.7295 (tpp) cc_final: 0.6971 (tpp) REVERT: T 186 MET cc_start: 0.7823 (tpt) cc_final: 0.7372 (tpp) REVERT: K 11 LYS cc_start: 0.6922 (mttt) cc_final: 0.6562 (mmmt) REVERT: K 38 MET cc_start: 0.5809 (mtt) cc_final: 0.5509 (mtt) REVERT: S 147 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: U 11 LYS cc_start: 0.6922 (tttm) cc_final: 0.6451 (mttp) REVERT: U 39 ASP cc_start: 0.8536 (m-30) cc_final: 0.7841 (p0) REVERT: U 52 ASP cc_start: 0.5864 (t0) cc_final: 0.4897 (p0) REVERT: U 61 ILE cc_start: 0.8764 (mp) cc_final: 0.8180 (mp) outliers start: 20 outliers final: 17 residues processed: 114 average time/residue: 0.1129 time to fit residues: 19.1789 Evaluate side-chains 115 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 375 CYS Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 152 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 110 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 17 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** 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 = 0.3963 r_free = 0.3963 target = 0.101749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.074455 restraints weight = 43135.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.074077 restraints weight = 33688.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.074192 restraints weight = 25744.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.074733 restraints weight = 22892.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.074964 restraints weight = 19527.462| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12783 Z= 0.114 Angle : 0.621 15.625 17267 Z= 0.316 Chirality : 0.040 0.235 1935 Planarity : 0.003 0.051 2204 Dihedral : 4.643 44.947 1675 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.39 % Allowed : 17.80 % Favored : 80.82 % Cbeta Deviations : 0.07 % 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: -0.67 (0.22), residues: 1527 helix: 1.26 (0.19), residues: 820 sheet: -2.93 (0.52), residues: 98 loop : -2.49 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 70 TYR 0.018 0.001 TYR H 529 PHE 0.027 0.001 PHE T 331 TRP 0.016 0.001 TRP K 43 HIS 0.005 0.001 HIS C 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (12762) covalent geometry : angle 0.61770 / 0.32 (17252) hydrogen bonds : bond 0.03750 / 2.38 ( 603) hydrogen bonds : angle 4.05162 / 2.83 ( 1779) metal coordination : bond 0.00540 / 0.29 ( 19) metal coordination : angle 2.09774 / 1.13 ( 15) Misc. bond : bond 0.00008 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2102.82 seconds wall clock time: 37 minutes 12.53 seconds (2232.53 seconds total)