Starting phenix.real_space_refine on Wed Jul 30 17:54:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b5m_12040/07_2025/7b5m_12040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5m_12040/07_2025/7b5m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7b5m_12040/07_2025/7b5m_12040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5m_12040/07_2025/7b5m_12040.map" model { file = "/net/cci-nas-00/data/ceres_data/7b5m_12040/07_2025/7b5m_12040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5m_12040/07_2025/7b5m_12040.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG: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, 'GLU:plan': 2, 'ASP:plan': 1} 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: {'TPO:plan-1': 1, 'DHA: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: 7.47, per 1000 atoms: 0.60 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: 3.04 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.14 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: 3.45 Time building geometry restraints manager: 3.63 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.790 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.130 ------------------------------------------------------------------------------- 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 : 15.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.046 0.003 TRP R 27 HIS 0.010 0.002 HIS H 382 PHE 0.051 0.002 PHE C 385 TYR 0.026 0.002 TYR C 278 ARG 0.014 0.001 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.13982 ( 603) hydrogen bonds : angle 6.50408 ( 1779) metal coordination : bond 0.06617 ( 19) metal coordination : angle 5.41758 ( 15) covalent geometry : bond 0.00448 (12762) covalent geometry : angle 0.85659 (17252) 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 : 1.599 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: 0.8163 (tp) REVERT: C 672 TYR cc_start: 0.8404 (t80) cc_final: 0.8122 (t80) REVERT: C 675 TYR cc_start: 0.6480 (t80) cc_final: 0.5836 (t80) REVERT: T 97 TRP cc_start: 0.3785 (m100) cc_final: 0.3157 (m100) REVERT: K 38 MET cc_start: 0.6698 (mtt) cc_final: 0.6310 (mtt) REVERT: K 58 MET cc_start: 0.6429 (ptm) cc_final: 0.6074 (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: 0.8616 (mp) outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.2605 time to fit residues: 50.1082 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 : 1.578 ------------------------------------------------------------------------------- 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 129 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 119 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 190 ASN T 199 HIS ** 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 = 0.3894 r_free = 0.3894 target = 0.096191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.067486 restraints weight = 41065.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067896 restraints weight = 28861.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.068930 restraints weight = 23172.471| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12783 Z= 0.130 Angle : 0.631 6.871 17267 Z= 0.335 Chirality : 0.042 0.211 1935 Planarity : 0.004 0.056 2204 Dihedral : 5.679 49.114 1678 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 1.09 % Allowed : 8.10 % Favored : 90.81 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.21), residues: 1527 helix: 0.17 (0.18), residues: 826 sheet: -2.67 (0.60), residues: 79 loop : -3.14 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 97 HIS 0.006 0.001 HIS R 48 PHE 0.026 0.002 PHE C 385 TYR 0.025 0.001 TYR H 529 ARG 0.004 0.000 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 603) hydrogen bonds : angle 4.81770 ( 1779) metal coordination : bond 0.00690 ( 19) metal coordination : angle 2.92399 ( 15) covalent geometry : bond 0.00273 (12762) covalent geometry : angle 0.62517 (17252) Misc. bond : bond 0.00021 ( 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 140 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 233 GLU cc_start: 0.7411 (tt0) cc_final: 0.7195 (tm-30) REVERT: C 478 ASN cc_start: 0.8706 (t0) cc_final: 0.8474 (t0) REVERT: C 515 LYS cc_start: 0.8718 (mttt) cc_final: 0.8462 (mtmm) REVERT: C 585 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8561 (pp) REVERT: C 587 LYS cc_start: 0.8009 (pttp) cc_final: 0.7630 (mtmt) REVERT: C 614 TYR cc_start: 0.6740 (m-80) cc_final: 0.6528 (m-80) REVERT: C 675 TYR cc_start: 0.6446 (t80) cc_final: 0.5430 (t80) REVERT: T 97 TRP cc_start: 0.4126 (m100) cc_final: 0.3347 (m100) REVERT: T 170 MET cc_start: 0.7260 (mmt) cc_final: 0.6794 (tpp) REVERT: K 11 LYS cc_start: 0.6712 (mttt) cc_final: 0.6459 (mmmt) REVERT: K 38 MET cc_start: 0.7012 (mtt) cc_final: 0.6653 (mtt) REVERT: K 58 MET cc_start: 0.6062 (ptm) cc_final: 0.5851 (ptm) REVERT: U 11 LYS cc_start: 0.7330 (tttm) cc_final: 0.6735 (mttp) REVERT: U 39 ASP cc_start: 0.8537 (m-30) cc_final: 0.7949 (p0) outliers start: 15 outliers final: 9 residues processed: 134 average time/residue: 0.2556 time to fit residues: 50.4045 Evaluate side-chains 111 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 T residue 199 HIS Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 21 optimal weight: 0.8980 chunk 59 optimal weight: 0.0030 chunk 65 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 116 optimal weight: 0.0000 chunk 123 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 142 optimal weight: 0.0040 chunk 51 optimal weight: 6.9990 overall best weight: 0.3206 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.100962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.075070 restraints weight = 43813.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.074146 restraints weight = 32889.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.074458 restraints weight = 26531.918| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12783 Z= 0.113 Angle : 0.579 6.838 17267 Z= 0.305 Chirality : 0.040 0.165 1935 Planarity : 0.004 0.052 2204 Dihedral : 5.157 48.042 1675 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 1.53 % Allowed : 11.38 % Favored : 87.09 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1527 helix: 0.64 (0.18), residues: 823 sheet: -2.51 (0.58), residues: 86 loop : -3.01 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 43 HIS 0.016 0.001 HIS T 199 PHE 0.022 0.001 PHE H 457 TYR 0.021 0.001 TYR H 529 ARG 0.004 0.000 ARG R 86 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 603) hydrogen bonds : angle 4.42758 ( 1779) metal coordination : bond 0.00620 ( 19) metal coordination : angle 2.43933 ( 15) covalent geometry : bond 0.00230 (12762) covalent geometry : angle 0.57442 (17252) Misc. bond : bond 0.00014 ( 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 136 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7238 (tpp) cc_final: 0.7007 (tpp) REVERT: C 478 ASN cc_start: 0.8639 (t0) cc_final: 0.8411 (t0) REVERT: C 585 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8570 (pp) REVERT: C 587 LYS cc_start: 0.7988 (pttp) cc_final: 0.7693 (mtmt) REVERT: C 614 TYR cc_start: 0.6673 (m-80) cc_final: 0.6282 (m-80) REVERT: H 422 MET cc_start: 0.8209 (tpp) cc_final: 0.7977 (mmt) REVERT: H 511 ARG cc_start: 0.6999 (ptt90) cc_final: 0.5420 (ptt90) REVERT: T 97 TRP cc_start: 0.3724 (m100) cc_final: 0.3342 (m100) REVERT: T 170 MET cc_start: 0.7205 (mmt) cc_final: 0.6839 (tpp) REVERT: T 322 MET cc_start: 0.5969 (mmp) cc_final: 0.5719 (ttt) REVERT: K 11 LYS cc_start: 0.6631 (mttt) cc_final: 0.6390 (mmmt) REVERT: K 38 MET cc_start: 0.6419 (mtt) cc_final: 0.6187 (mtt) REVERT: U 11 LYS cc_start: 0.7049 (tttm) cc_final: 0.6573 (mttp) REVERT: U 39 ASP cc_start: 0.8411 (m-30) cc_final: 0.7881 (p0) outliers start: 21 outliers final: 10 residues processed: 129 average time/residue: 0.2618 time to fit residues: 49.0395 Evaluate side-chains 110 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL 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 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 18 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.095773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.071126 restraints weight = 42058.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070178 restraints weight = 36100.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.070744 restraints weight = 37479.463| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2221 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= 0.124 Angle : 0.577 6.363 17267 Z= 0.304 Chirality : 0.041 0.175 1935 Planarity : 0.004 0.049 2204 Dihedral : 5.066 51.530 1675 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 1.60 % Allowed : 14.73 % Favored : 83.66 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1527 helix: 0.81 (0.18), residues: 822 sheet: -2.66 (0.56), residues: 88 loop : -2.83 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 43 HIS 0.005 0.001 HIS C 343 PHE 0.022 0.001 PHE H 457 TYR 0.021 0.001 TYR H 529 ARG 0.004 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 603) hydrogen bonds : angle 4.31904 ( 1779) metal coordination : bond 0.00820 ( 19) metal coordination : angle 2.36380 ( 15) covalent geometry : bond 0.00271 (12762) covalent geometry : angle 0.57264 (17252) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.575 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: 0.5224 (mmm-85) cc_final: 0.5002 (mmm-85) REVERT: C 478 ASN cc_start: 0.8717 (t0) cc_final: 0.8454 (t0) REVERT: C 585 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8639 (pp) REVERT: C 587 LYS cc_start: 0.8013 (pttp) cc_final: 0.7681 (mtmt) REVERT: H 422 MET cc_start: 0.8067 (tpp) cc_final: 0.7846 (mmt) REVERT: T 170 MET cc_start: 0.7239 (mmt) cc_final: 0.6947 (tpp) REVERT: T 186 MET cc_start: 0.7397 (tpp) cc_final: 0.7143 (tpp) REVERT: S 91 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: U 11 LYS cc_start: 0.7062 (tttm) cc_final: 0.6618 (mttp) REVERT: U 39 ASP cc_start: 0.8350 (m-30) cc_final: 0.7795 (p0) outliers start: 22 outliers final: 12 residues processed: 125 average time/residue: 0.2623 time to fit residues: 47.4820 Evaluate side-chains 112 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 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 S residue 91 GLU Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 70 VAL 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 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 116 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** ** 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 = 0.3948 r_free = 0.3948 target = 0.100077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.073225 restraints weight = 43123.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.071989 restraints weight = 35788.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072060 restraints weight = 30359.868| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12783 Z= 0.116 Angle : 0.565 7.071 17267 Z= 0.296 Chirality : 0.040 0.170 1935 Planarity : 0.004 0.047 2204 Dihedral : 4.952 54.930 1675 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.75 % Allowed : 15.24 % Favored : 83.01 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1527 helix: 0.97 (0.18), residues: 825 sheet: -2.55 (0.57), residues: 86 loop : -2.82 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 545 HIS 0.004 0.001 HIS C 343 PHE 0.019 0.001 PHE H 457 TYR 0.020 0.001 TYR H 529 ARG 0.005 0.000 ARG R 99 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 603) hydrogen bonds : angle 4.21052 ( 1779) metal coordination : bond 0.00606 ( 19) metal coordination : angle 2.26280 ( 15) covalent geometry : bond 0.00251 (12762) covalent geometry : angle 0.56106 (17252) Misc. bond : bond 0.00016 ( 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 129 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.454 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: 0.5256 (mmm-85) cc_final: 0.5045 (mmm-85) REVERT: C 478 ASN cc_start: 0.8689 (t0) cc_final: 0.8454 (t0) REVERT: C 585 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8726 (pp) REVERT: C 587 LYS cc_start: 0.8019 (pttp) cc_final: 0.7648 (mtmt) REVERT: H 422 MET cc_start: 0.8254 (tpp) cc_final: 0.8040 (mmt) REVERT: T 170 MET cc_start: 0.7201 (mmt) cc_final: 0.6885 (tpp) REVERT: K 11 LYS cc_start: 0.6700 (mttt) cc_final: 0.6409 (mmmt) REVERT: S 147 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: U 11 LYS cc_start: 0.6984 (tttm) cc_final: 0.6511 (mttp) REVERT: U 39 ASP cc_start: 0.8487 (m-30) cc_final: 0.7871 (p0) outliers start: 24 outliers final: 13 residues processed: 124 average time/residue: 0.2433 time to fit residues: 44.7562 Evaluate side-chains 111 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.625 ------------------------------------------------------------------------------- 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 510 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 146 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 ASN ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 199 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** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.093294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.064096 restraints weight = 42012.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064674 restraints weight = 30603.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.064767 restraints weight = 24144.864| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12783 Z= 0.220 Angle : 0.675 9.264 17267 Z= 0.354 Chirality : 0.043 0.167 1935 Planarity : 0.004 0.051 2204 Dihedral : 5.352 53.652 1675 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 1.82 % Allowed : 16.85 % Favored : 81.33 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.22), residues: 1527 helix: 0.59 (0.18), residues: 831 sheet: -2.67 (0.59), residues: 78 loop : -2.89 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 144 HIS 0.007 0.001 HIS C 343 PHE 0.033 0.002 PHE H 457 TYR 0.029 0.002 TYR C 278 ARG 0.009 0.001 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.05434 ( 603) hydrogen bonds : angle 4.73184 ( 1779) metal coordination : bond 0.02006 ( 19) metal coordination : angle 3.18350 ( 15) covalent geometry : bond 0.00497 (12762) covalent geometry : angle 0.66913 (17252) Misc. bond : bond 0.00042 ( 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 128 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: C 585 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8669 (pp) REVERT: C 587 LYS cc_start: 0.8048 (pttp) cc_final: 0.7714 (mtmt) REVERT: H 422 MET cc_start: 0.8365 (tpp) cc_final: 0.8125 (mmt) REVERT: T 97 TRP cc_start: 0.4690 (m100) cc_final: 0.3382 (m100) REVERT: T 170 MET cc_start: 0.7313 (mmt) cc_final: 0.6997 (tpp) REVERT: K 11 LYS cc_start: 0.6814 (mttt) cc_final: 0.6428 (mmmt) REVERT: S 147 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7426 (pm20) REVERT: U 11 LYS cc_start: 0.7078 (tttm) cc_final: 0.6517 (mttp) REVERT: U 39 ASP cc_start: 0.8568 (m-30) cc_final: 0.7844 (p0) REVERT: P 186 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7574 (tm-30) outliers start: 25 outliers final: 17 residues processed: 123 average time/residue: 0.2653 time to fit residues: 48.0294 Evaluate side-chains 115 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 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 66 THR 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 82 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 143 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.096194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.065803 restraints weight = 41071.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.067350 restraints weight = 27174.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.068343 restraints weight = 20490.968| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12783 Z= 0.117 Angle : 0.588 8.642 17267 Z= 0.308 Chirality : 0.040 0.154 1935 Planarity : 0.003 0.050 2204 Dihedral : 5.016 52.953 1675 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 1.53 % Allowed : 18.02 % Favored : 80.45 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.22), residues: 1527 helix: 1.03 (0.19), residues: 822 sheet: -2.73 (0.55), residues: 88 loop : -2.71 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 43 HIS 0.005 0.001 HIS C 345 PHE 0.019 0.001 PHE C 402 TYR 0.021 0.001 TYR H 529 ARG 0.007 0.000 ARG R 99 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 603) hydrogen bonds : angle 4.28864 ( 1779) metal coordination : bond 0.00502 ( 19) metal coordination : angle 2.33773 ( 15) covalent geometry : bond 0.00252 (12762) covalent geometry : angle 0.58401 (17252) Misc. bond : bond 0.00017 ( 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 127 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7141 (tpp) cc_final: 0.6939 (tpp) REVERT: C 478 ASN cc_start: 0.8737 (t0) cc_final: 0.8514 (t0) REVERT: C 587 LYS cc_start: 0.7990 (pttp) cc_final: 0.7644 (mtmt) REVERT: H 422 MET cc_start: 0.8155 (tpp) cc_final: 0.7933 (mmt) REVERT: T 186 MET cc_start: 0.7632 (tpt) cc_final: 0.7203 (tpp) REVERT: K 11 LYS cc_start: 0.6779 (mttt) cc_final: 0.6471 (mmmt) REVERT: K 58 MET cc_start: 0.6189 (ptm) cc_final: 0.4623 (ttt) REVERT: S 147 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: U 11 LYS cc_start: 0.7060 (tttm) cc_final: 0.6565 (mttp) REVERT: U 25 ASN cc_start: 0.8460 (m110) cc_final: 0.8209 (m-40) REVERT: U 39 ASP cc_start: 0.8367 (m-30) cc_final: 0.7723 (p0) REVERT: U 52 ASP cc_start: 0.5696 (t0) cc_final: 0.5140 (p0) REVERT: P 186 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7525 (tm-30) outliers start: 21 outliers final: 13 residues processed: 124 average time/residue: 0.2547 time to fit residues: 46.7565 Evaluate side-chains 108 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 510 ASP 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 66 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 27 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 33 optimal weight: 0.0050 chunk 19 optimal weight: 0.0980 chunk 142 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.097891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.069892 restraints weight = 41661.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.069854 restraints weight = 30645.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.070878 restraints weight = 22976.250| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12783 Z= 0.109 Angle : 0.588 12.457 17267 Z= 0.302 Chirality : 0.040 0.204 1935 Planarity : 0.004 0.050 2204 Dihedral : 4.768 52.001 1675 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.24 % Allowed : 18.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1527 helix: 1.16 (0.18), residues: 829 sheet: -2.62 (0.57), residues: 86 loop : -2.71 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 43 HIS 0.005 0.001 HIS C 345 PHE 0.043 0.001 PHE T 331 TYR 0.017 0.001 TYR H 529 ARG 0.007 0.000 ARG R 99 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 603) hydrogen bonds : angle 4.10827 ( 1779) metal coordination : bond 0.00420 ( 19) metal coordination : angle 2.15508 ( 15) covalent geometry : bond 0.00234 (12762) covalent geometry : angle 0.58490 (17252) Misc. bond : bond 0.00010 ( 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 123 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 587 LYS cc_start: 0.7969 (pttp) cc_final: 0.7580 (mtmt) REVERT: C 675 TYR cc_start: 0.6967 (t80) cc_final: 0.6383 (t80) REVERT: T 97 TRP cc_start: 0.4344 (m100) cc_final: 0.4127 (m100) REVERT: T 186 MET cc_start: 0.7754 (tpt) cc_final: 0.7326 (tpp) REVERT: K 11 LYS cc_start: 0.6865 (mttt) cc_final: 0.6539 (mmmt) REVERT: K 23 MET cc_start: 0.5897 (mtt) cc_final: 0.4922 (ttt) REVERT: K 58 MET cc_start: 0.5982 (ptm) cc_final: 0.4693 (ttt) REVERT: S 91 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: S 147 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: U 11 LYS cc_start: 0.6873 (tttm) cc_final: 0.6393 (mttp) REVERT: U 25 ASN cc_start: 0.8482 (m110) cc_final: 0.8269 (m-40) REVERT: U 39 ASP cc_start: 0.8480 (m-30) cc_final: 0.7833 (p0) REVERT: U 52 ASP cc_start: 0.6035 (t0) cc_final: 0.5328 (p0) REVERT: U 61 ILE cc_start: 0.8809 (mp) cc_final: 0.8583 (mp) REVERT: P 186 GLN cc_start: 0.7747 (tm-30) cc_final: 0.7480 (tm-30) outliers start: 17 outliers final: 12 residues processed: 120 average time/residue: 0.2470 time to fit residues: 43.9671 Evaluate side-chains 112 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 585 LEU 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 91 GLU Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain P residue 184 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.101103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074275 restraints weight = 42993.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073299 restraints weight = 35557.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.073748 restraints weight = 25801.299| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12783 Z= 0.121 Angle : 0.592 9.357 17267 Z= 0.308 Chirality : 0.040 0.156 1935 Planarity : 0.003 0.051 2204 Dihedral : 4.742 52.057 1675 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 1.31 % Allowed : 18.96 % Favored : 79.72 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1527 helix: 1.21 (0.18), residues: 826 sheet: -2.62 (0.56), residues: 86 loop : -2.70 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP T 265 HIS 0.005 0.001 HIS C 343 PHE 0.020 0.001 PHE H 457 TYR 0.019 0.001 TYR H 529 ARG 0.007 0.000 ARG R 99 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 603) hydrogen bonds : angle 4.17176 ( 1779) metal coordination : bond 0.00626 ( 19) metal coordination : angle 2.20792 ( 15) covalent geometry : bond 0.00268 (12762) covalent geometry : angle 0.58828 (17252) Misc. bond : bond 0.00013 ( 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 116 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 587 LYS cc_start: 0.7918 (pttp) cc_final: 0.7555 (mtmt) REVERT: T 97 TRP cc_start: 0.4498 (m100) cc_final: 0.4040 (m100) REVERT: K 11 LYS cc_start: 0.6863 (mttt) cc_final: 0.6532 (mmmt) REVERT: K 23 MET cc_start: 0.6162 (mtt) cc_final: 0.5152 (ttt) REVERT: K 58 MET cc_start: 0.6009 (ptm) cc_final: 0.4731 (ttt) REVERT: S 147 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: U 11 LYS cc_start: 0.6931 (tttm) cc_final: 0.6436 (mttp) REVERT: U 39 ASP cc_start: 0.8479 (m-30) cc_final: 0.7837 (p0) REVERT: U 52 ASP cc_start: 0.5921 (t0) cc_final: 0.5154 (p0) REVERT: U 61 ILE cc_start: 0.8835 (mp) cc_final: 0.8417 (mp) REVERT: P 186 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7483 (tm-30) outliers start: 18 outliers final: 14 residues processed: 112 average time/residue: 0.2568 time to fit residues: 42.4192 Evaluate side-chains 110 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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 585 LEU 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 66 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain P residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.095022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.066639 restraints weight = 40958.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.066204 restraints weight = 30351.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066817 restraints weight = 25878.347| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12783 Z= 0.163 Angle : 0.631 8.686 17267 Z= 0.330 Chirality : 0.042 0.157 1935 Planarity : 0.004 0.052 2204 Dihedral : 4.956 51.951 1675 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.24 % Allowed : 18.89 % Favored : 79.87 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.22), residues: 1527 helix: 1.05 (0.18), residues: 826 sheet: -2.48 (0.60), residues: 74 loop : -2.73 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 43 HIS 0.006 0.001 HIS C 343 PHE 0.024 0.002 PHE H 457 TYR 0.024 0.002 TYR H 529 ARG 0.007 0.001 ARG R 99 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 603) hydrogen bonds : angle 4.38287 ( 1779) metal coordination : bond 0.01270 ( 19) metal coordination : angle 2.45406 ( 15) covalent geometry : bond 0.00368 (12762) covalent geometry : angle 0.62757 (17252) Misc. bond : bond 0.00020 ( 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 121 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 587 LYS cc_start: 0.7944 (pttp) cc_final: 0.7589 (mtmt) REVERT: C 675 TYR cc_start: 0.7027 (t80) cc_final: 0.6610 (t80) REVERT: T 97 TRP cc_start: 0.4711 (m100) cc_final: 0.3916 (m100) REVERT: T 170 MET cc_start: 0.7050 (tpp) cc_final: 0.6752 (tpp) REVERT: T 186 MET cc_start: 0.7623 (tpt) cc_final: 0.7128 (tpp) REVERT: K 11 LYS cc_start: 0.6859 (mttt) cc_final: 0.6436 (mmmt) REVERT: K 58 MET cc_start: 0.5725 (ptm) cc_final: 0.4693 (ttt) REVERT: S 91 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: S 147 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: U 11 LYS cc_start: 0.7052 (tttm) cc_final: 0.6564 (mttp) REVERT: U 39 ASP cc_start: 0.8393 (m-30) cc_final: 0.7712 (p0) REVERT: U 52 ASP cc_start: 0.6057 (t0) cc_final: 0.5122 (p0) REVERT: U 61 ILE cc_start: 0.8906 (mp) cc_final: 0.8663 (mp) outliers start: 17 outliers final: 15 residues processed: 118 average time/residue: 0.2617 time to fit residues: 45.2985 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 : 1.530 ------------------------------------------------------------------------------- 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 585 LEU Chi-restraints excluded: chain H residue 375 CYS Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain P residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 9 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.096202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.068437 restraints weight = 40632.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068706 restraints weight = 28682.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068743 restraints weight = 21643.045| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2992 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= 0.139 Angle : 0.625 9.066 17267 Z= 0.326 Chirality : 0.041 0.198 1935 Planarity : 0.004 0.051 2204 Dihedral : 4.918 49.003 1675 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 1.46 % Allowed : 18.82 % Favored : 79.72 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1527 helix: 1.08 (0.18), residues: 821 sheet: -2.17 (0.56), residues: 84 loop : -2.71 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 43 HIS 0.005 0.001 HIS C 343 PHE 0.021 0.002 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.007 0.000 ARG R 99 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 603) hydrogen bonds : angle 4.29312 ( 1779) metal coordination : bond 0.00897 ( 19) metal coordination : angle 2.27185 ( 15) covalent geometry : bond 0.00313 (12762) covalent geometry : angle 0.62145 (17252) Misc. bond : bond 0.00017 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4534.65 seconds wall clock time: 79 minutes 13.08 seconds (4753.08 seconds total)