Starting phenix.real_space_refine on Wed Mar 4 09:42:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b5m_12040/03_2026/7b5m_12040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5m_12040/03_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_12040/03_2026/7b5m_12040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5m_12040/03_2026/7b5m_12040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b5m_12040/03_2026/7b5m_12040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5m_12040/03_2026/7b5m_12040.map" } 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-5986/lib/python3.9/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: 2.96, per 1000 atoms: 0.24 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: 0.93 Conformation dependent library (CDL) restraints added in 548.4 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: 0.28 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: 1.69 Time building geometry restraints manager: 1.25 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=" 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 THR C 526 " pdb=" CA THR C 526 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.30e-02 5.92e+03 7.45e+00 bond pdb=" C SER C 541 " pdb=" O SER C 541 " ideal model delta sigma weight residual 1.234 1.268 -0.034 1.36e-02 5.41e+03 6.26e+00 ... (remaining 12757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 16964 2.74 - 5.47: 246 5.47 - 8.21: 36 8.21 - 10.95: 5 10.95 - 13.69: 1 Bond angle restraints: 17252 Sorted by residual: 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=" N ASP H 512 " pdb=" CA ASP H 512 " pdb=" C ASP H 512 " ideal model delta sigma weight residual 110.44 116.35 -5.91 1.20e+00 6.94e-01 2.43e+01 angle pdb=" N ASP C 388 " pdb=" CA ASP C 388 " pdb=" C ASP C 388 " ideal model delta sigma weight residual 110.33 116.25 -5.92 1.29e+00 6.01e-01 2.10e+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: 2.270 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 12.630 Find NCS groups from input model: 0.060 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.005 0.271 12783 Z= 0.256 Angle : 0.871 13.687 17267 Z= 0.481 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 covalent geometry : bond 0.00448 (12762) covalent geometry : angle 0.85659 (17252) hydrogen bonds : bond 0.13982 ( 603) hydrogen bonds : angle 6.50408 ( 1779) metal coordination : bond 0.06617 ( 19) metal coordination : angle 5.41758 ( 15) Misc. bond : bond 0.08590 ( 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 : 0.506 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: 0.1068 time to fit residues: 20.5583 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 : 0.483 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.094312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.065564 restraints weight = 42778.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.065870 restraints weight = 29837.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.066513 restraints weight = 23990.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.067031 restraints weight = 20627.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.067158 restraints weight = 17475.765| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12783 Z= 0.165 Angle : 0.667 6.614 17267 Z= 0.355 Chirality : 0.043 0.202 1935 Planarity : 0.005 0.059 2204 Dihedral : 5.872 48.892 1678 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 1.09 % Allowed : 9.04 % Favored : 89.86 % 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: -2.11 (0.21), residues: 1527 helix: -0.01 (0.18), residues: 825 sheet: -2.55 (0.64), residues: 69 loop : -3.25 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 274 TYR 0.027 0.002 TYR H 529 PHE 0.029 0.002 PHE C 385 TRP 0.014 0.002 TRP R 27 HIS 0.007 0.001 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00365 (12762) covalent geometry : angle 0.66055 (17252) hydrogen bonds : bond 0.05371 ( 603) hydrogen bonds : angle 5.03333 ( 1779) metal coordination : bond 0.01121 ( 19) metal coordination : angle 3.16064 ( 15) Misc. bond : bond 0.00037 ( 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 125 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.520 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: 0.5784 (mmm-85) cc_final: 0.5505 (mmm-85) REVERT: C 233 GLU cc_start: 0.7565 (tt0) cc_final: 0.7244 (tm-30) REVERT: C 585 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8564 (pp) REVERT: C 587 LYS cc_start: 0.8041 (pttp) cc_final: 0.7707 (mtmt) REVERT: C 614 TYR cc_start: 0.6761 (m-80) cc_final: 0.6542 (m-80) REVERT: C 675 TYR cc_start: 0.6521 (t80) cc_final: 0.5452 (t80) REVERT: T 97 TRP cc_start: 0.4199 (m100) cc_final: 0.3137 (m100) REVERT: T 170 MET cc_start: 0.7258 (mmt) cc_final: 0.6861 (tpp) REVERT: K 38 MET cc_start: 0.7093 (mtt) cc_final: 0.6688 (mtt) REVERT: K 58 MET cc_start: 0.6228 (ptm) cc_final: 0.5951 (ptm) REVERT: U 11 LYS cc_start: 0.7267 (tttm) cc_final: 0.6735 (mttp) REVERT: U 39 ASP cc_start: 0.8557 (m-30) cc_final: 0.7897 (p0) outliers start: 15 outliers final: 8 residues processed: 119 average time/residue: 0.1104 time to fit residues: 19.3618 Evaluate side-chains 108 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 539 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL 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: 0.6980 chunk 88 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 128 optimal weight: 0.3980 chunk 103 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.0030 chunk 130 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** T 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 289 ASN ** T 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.096383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.071496 restraints weight = 41499.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.071734 restraints weight = 34750.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.071989 restraints weight = 34962.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072039 restraints weight = 24663.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.072215 restraints weight = 21971.095| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12783 Z= 0.119 Angle : 0.588 8.140 17267 Z= 0.312 Chirality : 0.040 0.167 1935 Planarity : 0.004 0.054 2204 Dihedral : 5.289 46.834 1675 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.75 % Allowed : 12.04 % Favored : 86.21 % 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: -1.55 (0.22), residues: 1527 helix: 0.53 (0.18), residues: 822 sheet: -2.73 (0.56), residues: 88 loop : -3.04 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 86 TYR 0.022 0.001 TYR H 529 PHE 0.020 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 covalent geometry : bond 0.00248 (12762) covalent geometry : angle 0.58307 (17252) hydrogen bonds : bond 0.04331 ( 603) hydrogen bonds : angle 4.52366 ( 1779) metal coordination : bond 0.00616 ( 19) metal coordination : angle 2.57383 ( 15) Misc. bond : bond 0.00021 ( 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 : 0.514 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: 0.7605 (mp0) cc_final: 0.7392 (mp0) REVERT: C 478 ASN cc_start: 0.8686 (t0) cc_final: 0.8469 (t0) REVERT: C 535 PHE cc_start: 0.7527 (t80) cc_final: 0.7123 (t80) REVERT: C 585 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8605 (pp) REVERT: C 587 LYS cc_start: 0.8017 (pttp) cc_final: 0.7761 (mtmt) REVERT: C 614 TYR cc_start: 0.6772 (m-80) cc_final: 0.6508 (m-80) REVERT: H 422 MET cc_start: 0.8237 (tpp) cc_final: 0.7998 (mmt) REVERT: T 97 TRP cc_start: 0.4060 (m100) cc_final: 0.3276 (m100) REVERT: T 170 MET cc_start: 0.7192 (mmt) cc_final: 0.6902 (tpp) REVERT: K 38 MET cc_start: 0.6356 (mtt) cc_final: 0.6152 (mtt) REVERT: K 58 MET cc_start: 0.6096 (ptm) cc_final: 0.5764 (ptm) REVERT: U 11 LYS cc_start: 0.7150 (tttm) cc_final: 0.6701 (mttp) REVERT: U 39 ASP cc_start: 0.8297 (m-30) cc_final: 0.7759 (p0) outliers start: 24 outliers final: 13 residues processed: 138 average time/residue: 0.1018 time to fit residues: 20.5941 Evaluate side-chains 113 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 90 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 135 optimal weight: 0.0170 chunk 109 optimal weight: 0.0040 chunk 120 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 overall best weight: 0.9032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 314 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 = 0.095816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.065094 restraints weight = 42514.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.066579 restraints weight = 28261.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.067602 restraints weight = 21389.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.068397 restraints weight = 17608.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.068893 restraints weight = 15364.321| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2103 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= 0.127 Angle : 0.593 9.515 17267 Z= 0.311 Chirality : 0.041 0.160 1935 Planarity : 0.004 0.052 2204 Dihedral : 5.190 50.198 1675 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 1.97 % Allowed : 14.73 % Favored : 83.30 % 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: 0.70 (0.18), residues: 823 sheet: -2.72 (0.56), residues: 88 loop : -2.91 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 99 TYR 0.022 0.001 TYR H 529 PHE 0.021 0.001 PHE H 457 TRP 0.017 0.001 TRP K 43 HIS 0.012 0.001 HIS T 199 Details of bonding type rmsd covalent geometry : bond 0.00280 (12762) covalent geometry : angle 0.58865 (17252) hydrogen bonds : bond 0.04373 ( 603) hydrogen bonds : angle 4.41312 ( 1779) metal coordination : bond 0.00880 ( 19) metal coordination : angle 2.60129 ( 15) Misc. bond : bond 0.00020 ( 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 133 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.8454 (mtm) cc_final: 0.8249 (mtm) REVERT: C 478 ASN cc_start: 0.8643 (t0) cc_final: 0.8409 (t0) REVERT: C 585 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8659 (pp) REVERT: C 587 LYS cc_start: 0.8050 (pttp) cc_final: 0.7683 (mtmt) REVERT: H 422 MET cc_start: 0.8169 (tpp) cc_final: 0.7936 (mmt) REVERT: H 511 ARG cc_start: 0.6768 (ptt90) cc_final: 0.5237 (ptt90) REVERT: T 97 TRP cc_start: 0.4156 (m100) cc_final: 0.3326 (m100) REVERT: T 170 MET cc_start: 0.7234 (mmt) cc_final: 0.6879 (tpp) REVERT: T 186 MET cc_start: 0.7502 (tpp) cc_final: 0.7189 (tpp) REVERT: S 91 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: U 11 LYS cc_start: 0.7065 (tttm) cc_final: 0.6566 (mttp) REVERT: U 39 ASP cc_start: 0.8339 (m-30) cc_final: 0.7753 (p0) outliers start: 27 outliers final: 17 residues processed: 128 average time/residue: 0.1193 time to fit residues: 21.9182 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 : 0.513 ------------------------------------------------------------------------------- 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 131 THR 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: 0.6980 chunk 147 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 1 optimal weight: 0.0970 chunk 43 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3900 r_free = 0.3900 target = 0.095952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.065289 restraints weight = 42238.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.066734 restraints weight = 28164.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.067796 restraints weight = 21389.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.068518 restraints weight = 17590.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.069095 restraints weight = 15335.192| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2305 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= 0.124 Angle : 0.581 6.778 17267 Z= 0.305 Chirality : 0.040 0.155 1935 Planarity : 0.004 0.057 2204 Dihedral : 5.081 53.321 1675 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 2.19 % Allowed : 15.61 % Favored : 82.20 % 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: -1.23 (0.22), residues: 1527 helix: 0.77 (0.18), residues: 828 sheet: -2.65 (0.56), residues: 86 loop : -2.88 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 99 TYR 0.021 0.001 TYR H 529 PHE 0.020 0.001 PHE H 457 TRP 0.011 0.001 TRP K 43 HIS 0.005 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00274 (12762) covalent geometry : angle 0.57615 (17252) hydrogen bonds : bond 0.04242 ( 603) hydrogen bonds : angle 4.30081 ( 1779) metal coordination : bond 0.00738 ( 19) metal coordination : angle 2.47860 ( 15) Misc. bond : bond 0.00019 ( 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 134 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.8554 (mtt) cc_final: 0.8271 (mtm) REVERT: C 478 ASN cc_start: 0.8701 (t0) cc_final: 0.8466 (t0) REVERT: C 585 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8662 (pp) REVERT: C 587 LYS cc_start: 0.7985 (pttp) cc_final: 0.7621 (mtmt) REVERT: H 422 MET cc_start: 0.8142 (tpp) cc_final: 0.7912 (mmt) REVERT: T 97 TRP cc_start: 0.4211 (m100) cc_final: 0.3400 (m100) REVERT: T 170 MET cc_start: 0.7285 (mmt) cc_final: 0.6954 (tpp) REVERT: K 11 LYS cc_start: 0.6726 (mttt) cc_final: 0.6422 (mmmt) REVERT: S 91 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: S 147 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: U 11 LYS cc_start: 0.7021 (tttm) cc_final: 0.6521 (mttp) REVERT: U 39 ASP cc_start: 0.8429 (m-30) cc_final: 0.7788 (p0) outliers start: 30 outliers final: 20 residues processed: 129 average time/residue: 0.1086 time to fit residues: 20.6634 Evaluate side-chains 120 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 540 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain S residue 131 THR 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: 2.9990 chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.093970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.063374 restraints weight = 41962.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.064687 restraints weight = 29228.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.065603 restraints weight = 22719.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.066216 restraints weight = 19119.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.066731 restraints weight = 16980.511| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12783 Z= 0.183 Angle : 0.641 9.822 17267 Z= 0.335 Chirality : 0.042 0.172 1935 Planarity : 0.004 0.060 2204 Dihedral : 5.241 52.981 1675 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 2.19 % Allowed : 16.70 % Favored : 81.11 % 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: -1.38 (0.22), residues: 1527 helix: 0.60 (0.18), residues: 833 sheet: -2.67 (0.59), residues: 78 loop : -2.91 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 274 TYR 0.025 0.002 TYR H 529 PHE 0.028 0.002 PHE H 457 TRP 0.015 0.002 TRP C 144 HIS 0.006 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00415 (12762) covalent geometry : angle 0.63588 (17252) hydrogen bonds : bond 0.04955 ( 603) hydrogen bonds : angle 4.52557 ( 1779) metal coordination : bond 0.01508 ( 19) metal coordination : angle 2.81820 ( 15) Misc. bond : bond 0.00033 ( 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 131 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.8587 (mtt) cc_final: 0.8182 (mtp) REVERT: C 382 MET cc_start: 0.7237 (tpp) cc_final: 0.6998 (tpp) REVERT: C 585 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8625 (pp) REVERT: C 587 LYS cc_start: 0.8076 (pttp) cc_final: 0.7706 (mtmt) REVERT: H 422 MET cc_start: 0.8232 (tpp) cc_final: 0.7983 (mmt) REVERT: T 97 TRP cc_start: 0.4399 (m100) cc_final: 0.3323 (m100) REVERT: T 170 MET cc_start: 0.7320 (mmt) cc_final: 0.7051 (tpp) REVERT: K 11 LYS cc_start: 0.6792 (mttt) cc_final: 0.6482 (mmmt) REVERT: S 147 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7402 (pm20) REVERT: U 11 LYS cc_start: 0.7091 (tttm) cc_final: 0.6551 (mttp) REVERT: U 25 ASN cc_start: 0.8413 (m110) cc_final: 0.8187 (m110) REVERT: U 39 ASP cc_start: 0.8268 (m-30) cc_final: 0.7656 (p0) outliers start: 30 outliers final: 21 residues processed: 126 average time/residue: 0.1024 time to fit residues: 19.3086 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 : 0.428 ------------------------------------------------------------------------------- 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 540 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain S residue 131 THR 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: 0.8980 chunk 144 optimal weight: 0.0020 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 68 optimal weight: 0.0980 chunk 129 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.100153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.072713 restraints weight = 43655.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072412 restraints weight = 34418.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072539 restraints weight = 25082.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.072824 restraints weight = 23088.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072976 restraints weight = 21737.400| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12783 Z= 0.111 Angle : 0.589 7.791 17267 Z= 0.307 Chirality : 0.040 0.216 1935 Planarity : 0.004 0.058 2204 Dihedral : 4.880 47.117 1675 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.12 % Allowed : 17.07 % 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: -0.94 (0.22), residues: 1527 helix: 1.01 (0.18), residues: 828 sheet: -2.61 (0.57), residues: 86 loop : -2.72 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 99 TYR 0.018 0.001 TYR H 529 PHE 0.016 0.001 PHE H 457 TRP 0.016 0.001 TRP T 97 HIS 0.006 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00233 (12762) covalent geometry : angle 0.58574 (17252) hydrogen bonds : bond 0.03860 ( 603) hydrogen bonds : angle 4.18323 ( 1779) metal coordination : bond 0.00392 ( 19) metal coordination : angle 2.28346 ( 15) Misc. bond : bond 0.00012 ( 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 138 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 126 TYR cc_start: 0.9053 (t80) cc_final: 0.8209 (t80) REVERT: C 261 MET cc_start: 0.8547 (mtt) cc_final: 0.8133 (mtp) REVERT: C 478 ASN cc_start: 0.8749 (t0) cc_final: 0.8539 (t0) REVERT: C 510 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7861 (t0) REVERT: C 587 LYS cc_start: 0.8092 (pttp) cc_final: 0.7745 (mtmt) REVERT: T 97 TRP cc_start: 0.4203 (m100) cc_final: 0.3743 (m100) REVERT: T 186 MET cc_start: 0.7899 (tpt) cc_final: 0.7470 (tpp) REVERT: K 11 LYS cc_start: 0.6867 (mttt) cc_final: 0.6567 (mmmt) REVERT: S 147 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: U 11 LYS cc_start: 0.7018 (tttm) cc_final: 0.6515 (mttp) REVERT: U 25 ASN cc_start: 0.8478 (m110) cc_final: 0.8264 (m110) REVERT: U 39 ASP cc_start: 0.8426 (m-30) cc_final: 0.7773 (p0) REVERT: U 52 ASP cc_start: 0.5800 (t0) cc_final: 0.4996 (p0) outliers start: 29 outliers final: 13 residues processed: 134 average time/residue: 0.1061 time to fit residues: 20.9873 Evaluate side-chains 115 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL 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 H residue 331 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 122 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3902 r_free = 0.3902 target = 0.096540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068112 restraints weight = 41371.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069088 restraints weight = 30390.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.068865 restraints weight = 21311.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069047 restraints weight = 21532.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.069139 restraints weight = 21361.037| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12783 Z= 0.113 Angle : 0.597 11.805 17267 Z= 0.308 Chirality : 0.040 0.189 1935 Planarity : 0.004 0.057 2204 Dihedral : 4.754 44.572 1675 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.39 % Allowed : 17.94 % 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: -0.91 (0.22), residues: 1527 helix: 1.08 (0.18), residues: 828 sheet: -2.56 (0.58), residues: 86 loop : -2.79 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 99 TYR 0.018 0.001 TYR H 529 PHE 0.037 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 covalent geometry : bond 0.00246 (12762) covalent geometry : angle 0.59397 (17252) hydrogen bonds : bond 0.03853 ( 603) hydrogen bonds : angle 4.13597 ( 1779) metal coordination : bond 0.00480 ( 19) metal coordination : angle 2.12024 ( 15) Misc. bond : bond 0.00011 ( 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 121 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 126 TYR cc_start: 0.9095 (t80) cc_final: 0.8147 (t80) REVERT: C 261 MET cc_start: 0.8522 (mtt) cc_final: 0.8115 (mtp) REVERT: C 478 ASN cc_start: 0.8700 (t0) cc_final: 0.8475 (t0) REVERT: C 587 LYS cc_start: 0.7992 (pttp) cc_final: 0.7596 (mtmt) REVERT: C 608 MET cc_start: 0.7809 (mtp) cc_final: 0.7591 (mmm) REVERT: T 97 TRP cc_start: 0.4234 (m100) cc_final: 0.3758 (m100) REVERT: T 186 MET cc_start: 0.7733 (tpt) cc_final: 0.7314 (tpp) REVERT: K 11 LYS cc_start: 0.6846 (mttt) cc_final: 0.6524 (mmmt) REVERT: S 147 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: U 11 LYS cc_start: 0.6913 (tttm) cc_final: 0.6426 (mttp) REVERT: U 25 ASN cc_start: 0.8473 (m110) cc_final: 0.8236 (m-40) REVERT: U 39 ASP cc_start: 0.8547 (m-30) cc_final: 0.7864 (p0) REVERT: U 52 ASP cc_start: 0.6036 (t0) cc_final: 0.5128 (p0) REVERT: U 61 ILE cc_start: 0.8713 (mp) cc_final: 0.8313 (mp) outliers start: 19 outliers final: 16 residues processed: 116 average time/residue: 0.1115 time to fit residues: 19.1748 Evaluate side-chains 116 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL 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 585 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 25 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 42 optimal weight: 0.0050 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3948 r_free = 0.3948 target = 0.100549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.075507 restraints weight = 44186.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.073684 restraints weight = 31953.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.074387 restraints weight = 30046.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.074693 restraints weight = 23576.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.074837 restraints weight = 21733.253| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12783 Z= 0.115 Angle : 0.593 9.407 17267 Z= 0.308 Chirality : 0.040 0.173 1935 Planarity : 0.004 0.057 2204 Dihedral : 4.689 44.975 1675 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 1.46 % Allowed : 18.23 % Favored : 80.31 % 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: -0.85 (0.22), residues: 1527 helix: 1.14 (0.18), residues: 822 sheet: -2.61 (0.57), residues: 86 loop : -2.75 (0.23), residues: 619 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 0.025 0.001 PHE T 331 TRP 0.018 0.001 TRP T 265 HIS 0.004 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00254 (12762) covalent geometry : angle 0.59007 (17252) hydrogen bonds : bond 0.03850 ( 603) hydrogen bonds : angle 4.12177 ( 1779) metal coordination : bond 0.00566 ( 19) metal coordination : angle 2.22777 ( 15) Misc. bond : bond 0.00011 ( 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: 20 poor density : 103 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 126 TYR cc_start: 0.9085 (t80) cc_final: 0.8203 (t80) REVERT: C 261 MET cc_start: 0.8575 (mtt) cc_final: 0.8177 (mtp) REVERT: C 478 ASN cc_start: 0.8813 (t0) cc_final: 0.8557 (t0) REVERT: C 587 LYS cc_start: 0.8086 (pttp) cc_final: 0.7684 (mtmt) REVERT: T 97 TRP cc_start: 0.4336 (m100) cc_final: 0.3887 (m100) REVERT: T 186 MET cc_start: 0.7892 (tpt) cc_final: 0.7408 (tpp) REVERT: K 11 LYS cc_start: 0.6916 (mttt) cc_final: 0.6587 (mmmt) REVERT: S 147 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: U 11 LYS cc_start: 0.6941 (tttm) cc_final: 0.6499 (mttp) REVERT: U 39 ASP cc_start: 0.8390 (m-30) cc_final: 0.7810 (p0) REVERT: U 61 ILE cc_start: 0.8679 (mp) cc_final: 0.8475 (mp) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.1072 time to fit residues: 18.7875 Evaluate side-chains 118 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL 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 585 LEU 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 33 TRP 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: 5.9990 chunk 64 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.094431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063321 restraints weight = 42459.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.064753 restraints weight = 28745.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.065781 restraints weight = 21943.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.066522 restraints weight = 18140.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.066949 restraints weight = 15956.440| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12783 Z= 0.178 Angle : 0.659 9.600 17267 Z= 0.343 Chirality : 0.042 0.243 1935 Planarity : 0.004 0.058 2204 Dihedral : 5.006 45.170 1675 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.39 % Allowed : 18.60 % Favored : 80.01 % 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: -1.09 (0.22), residues: 1527 helix: 0.90 (0.18), residues: 824 sheet: -2.61 (0.59), residues: 78 loop : -2.81 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 99 TYR 0.025 0.002 TYR H 529 PHE 0.034 0.002 PHE H 457 TRP 0.015 0.002 TRP R 33 HIS 0.006 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00405 (12762) covalent geometry : angle 0.65466 (17252) hydrogen bonds : bond 0.04872 ( 603) hydrogen bonds : angle 4.43452 ( 1779) metal coordination : bond 0.01482 ( 19) metal coordination : angle 2.58589 ( 15) Misc. bond : bond 0.00023 ( 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 122 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.8533 (mtt) cc_final: 0.8158 (mtp) REVERT: C 478 ASN cc_start: 0.8690 (t0) cc_final: 0.8449 (t0) REVERT: C 587 LYS cc_start: 0.8052 (pttp) cc_final: 0.7687 (mtmt) REVERT: C 675 TYR cc_start: 0.7088 (t80) cc_final: 0.6444 (t80) REVERT: T 97 TRP cc_start: 0.4708 (m100) cc_final: 0.3877 (m100) REVERT: T 170 MET cc_start: 0.7226 (tpp) cc_final: 0.6922 (tpp) REVERT: T 186 MET cc_start: 0.7719 (tpt) cc_final: 0.7277 (tpp) REVERT: K 11 LYS cc_start: 0.6820 (mttt) cc_final: 0.6424 (mmmt) REVERT: S 147 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: U 11 LYS cc_start: 0.7030 (tttm) cc_final: 0.6514 (mttp) REVERT: U 39 ASP cc_start: 0.8248 (m-30) cc_final: 0.7600 (p0) outliers start: 19 outliers final: 16 residues processed: 117 average time/residue: 0.1125 time to fit residues: 19.3965 Evaluate side-chains 118 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL 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 513 VAL Chi-restraints excluded: chain C residue 585 LEU 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 33 TRP 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: 9.9990 chunk 96 optimal weight: 4.9990 chunk 49 optimal weight: 0.0000 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 125 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3887 r_free = 0.3887 target = 0.095598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.067527 restraints weight = 42413.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.067232 restraints weight = 34277.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067383 restraints weight = 27483.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067617 restraints weight = 25622.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.067784 restraints weight = 23437.098| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12783 Z= 0.127 Angle : 0.620 9.223 17267 Z= 0.321 Chirality : 0.041 0.242 1935 Planarity : 0.003 0.055 2204 Dihedral : 4.832 44.251 1675 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 1.31 % Allowed : 18.45 % Favored : 80.23 % 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: -0.90 (0.22), residues: 1527 helix: 1.06 (0.18), residues: 822 sheet: -2.43 (0.59), residues: 82 loop : -2.74 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 99 TYR 0.020 0.001 TYR H 529 PHE 0.026 0.001 PHE H 457 TRP 0.016 0.001 TRP K 43 HIS 0.005 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00284 (12762) covalent geometry : angle 0.61690 (17252) hydrogen bonds : bond 0.04197 ( 603) hydrogen bonds : angle 4.23596 ( 1779) metal coordination : bond 0.00727 ( 19) metal coordination : angle 2.28699 ( 15) Misc. bond : bond 0.00014 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.57 seconds wall clock time: 41 minutes 26.65 seconds (2486.65 seconds total)