Starting phenix.real_space_refine (version: dev) on Wed Feb 22 03:11:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg1_34731/02_2023/8hg1_34731_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg1_34731/02_2023/8hg1_34731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg1_34731/02_2023/8hg1_34731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg1_34731/02_2023/8hg1_34731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg1_34731/02_2023/8hg1_34731_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg1_34731/02_2023/8hg1_34731_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2139 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14155 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 8207 Classifications: {'peptide': 1005} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 37, 'TRANS': 967} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1762 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3418 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 10, 'TRANS': 408} Chain breaks: 1 Chain: "P" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 287 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.37, per 1000 atoms: 0.59 Number of scatterers: 14155 At special positions: 0 Unit cell: (93.5, 119.85, 146.2, 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) S 71 16.00 P 39 15.00 Mg 1 11.99 O 2737 8.00 N 2354 7.00 C 8953 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.92 Conformation dependent library (CDL) restraints added in 1.9 seconds 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3142 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 23 sheets defined 35.5% alpha, 18.3% beta 14 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 4.86 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 109 through 117 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 145 through 148 No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.605A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 449 through 473 removed outlier: 3.738A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 486 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 553 through 561 Processing helix chain 'A' and resid 577 through 590 removed outlier: 3.809A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 642 Processing helix chain 'A' and resid 647 through 671 removed outlier: 3.840A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 702 Processing helix chain 'A' and resid 765 through 781 Processing helix chain 'A' and resid 838 through 856 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 887 through 890 Processing helix chain 'A' and resid 906 through 917 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 968 through 982 removed outlier: 3.574A pdb=" N ASN A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 996 Processing helix chain 'B' and resid 17 through 31 Proline residue: B 21 - end of helix removed outlier: 5.649A pdb=" N SER B 24 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN B 31 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 4.057A pdb=" N ARG B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 87 through 100 Processing helix chain 'B' and resid 134 through 151 removed outlier: 5.555A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 212 through 215 removed outlier: 3.645A pdb=" N GLY B 215 " --> pdb=" O TRP B 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 215' Processing helix chain 'C' and resid 4 through 18 Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'C' and resid 109 through 120 Processing helix chain 'C' and resid 150 through 158 Processing helix chain 'C' and resid 178 through 188 removed outlier: 3.542A pdb=" N PHE C 188 " --> pdb=" O MET C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 256 Processing helix chain 'C' and resid 286 through 297 removed outlier: 3.510A pdb=" N LYS C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 323 removed outlier: 3.675A pdb=" N THR C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 340 removed outlier: 5.712A pdb=" N GLU C 337 " --> pdb=" O LEU C 334 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 338 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN C 339 " --> pdb=" O ASP C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.641A pdb=" N LEU C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 374 Processing helix chain 'C' and resid 393 through 396 Processing helix chain 'C' and resid 398 through 424 removed outlier: 3.993A pdb=" N ASN C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLN C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 124 through 126 removed outlier: 6.837A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 136 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS A 141 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS A 134 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.992A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 327 through 330 removed outlier: 3.815A pdb=" N LEU A 165 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 200 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 285 through 287 Processing sheet with id= E, first strand: chain 'A' and resid 428 through 432 removed outlier: 6.582A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 394 through 397 Processing sheet with id= G, first strand: chain 'A' and resid 789 through 791 removed outlier: 3.778A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 597 through 600 removed outlier: 3.616A pdb=" N SER A 610 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 574 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 711 through 713 Processing sheet with id= J, first strand: chain 'A' and resid 793 through 796 Processing sheet with id= K, first strand: chain 'A' and resid 892 through 895 Processing sheet with id= L, first strand: chain 'A' and resid 933 through 935 Processing sheet with id= M, first strand: chain 'A' and resid 300 through 305 removed outlier: 3.549A pdb=" N ASN A 315 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 799 through 802 removed outlier: 6.663A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 2 through 4 Processing sheet with id= P, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.907A pdb=" N VAL B 62 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N TRP B 119 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 64 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL B 154 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N CYS B 65 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR B 156 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR B 175 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS B 157 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE B 177 " --> pdb=" O CYS B 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 69 through 71 removed outlier: 3.609A pdb=" N ILE C 71 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR C 174 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.660A pdb=" N SER C 196 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C 197 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 85 through 89 removed outlier: 4.287A pdb=" N PHE C 126 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 142 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP C 140 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 130 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N MET C 138 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 214 through 219 removed outlier: 4.145A pdb=" N LYS C 214 " --> pdb=" O LYS C 268 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 268 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 267 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 222 through 227 removed outlier: 3.985A pdb=" N SER C 222 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 238 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 301 through 304 Processing sheet with id= W, first strand: chain 'C' and resid 375 through 380 removed outlier: 3.743A pdb=" N ASN C 386 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 5.15 Time building geometry restraints manager: 6.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2249 1.32 - 1.44: 4117 1.44 - 1.56: 7986 1.56 - 1.69: 76 1.69 - 1.81: 108 Bond restraints: 14536 Sorted by residual: bond pdb=" C PRO A 594 " pdb=" O PRO A 594 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" C PRO A 593 " pdb=" O PRO A 593 " ideal model delta sigma weight residual 1.240 1.204 0.036 1.12e-02 7.97e+03 1.04e+01 bond pdb=" C PRO A 592 " pdb=" O PRO A 592 " ideal model delta sigma weight residual 1.240 1.206 0.034 1.12e-02 7.97e+03 9.18e+00 bond pdb=" C5 TTP A1102 " pdb=" C6 TTP A1102 " ideal model delta sigma weight residual 1.390 1.340 0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" N LYS A 661 " pdb=" CA LYS A 661 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.80e+00 ... (remaining 14531 not shown) Histogram of bond angle deviations from ideal: 98.96 - 107.67: 662 107.67 - 116.37: 9207 116.37 - 125.08: 9661 125.08 - 133.79: 260 133.79 - 142.50: 14 Bond angle restraints: 19804 Sorted by residual: angle pdb=" PA TTP A1102 " pdb=" O3A TTP A1102 " pdb=" PB TTP A1102 " ideal model delta sigma weight residual 120.50 142.50 -22.00 3.00e+00 1.11e-01 5.38e+01 angle pdb=" N PRO A 593 " pdb=" CA PRO A 593 " pdb=" C PRO A 593 " ideal model delta sigma weight residual 110.70 119.47 -8.77 1.22e+00 6.72e-01 5.17e+01 angle pdb=" C PRO A 593 " pdb=" CA PRO A 593 " pdb=" CB PRO A 593 " ideal model delta sigma weight residual 110.92 104.60 6.32 1.22e+00 6.72e-01 2.68e+01 angle pdb=" CA PRO A 593 " pdb=" C PRO A 593 " pdb=" N PRO A 594 " ideal model delta sigma weight residual 117.93 123.76 -5.83 1.20e+00 6.94e-01 2.36e+01 angle pdb=" N LYS A 901 " pdb=" CA LYS A 901 " pdb=" C LYS A 901 " ideal model delta sigma weight residual 110.20 103.75 6.45 1.58e+00 4.01e-01 1.67e+01 ... (remaining 19799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 8413 35.03 - 70.06: 216 70.06 - 105.09: 10 105.09 - 140.12: 2 140.12 - 175.16: 2 Dihedral angle restraints: 8643 sinusoidal: 3770 harmonic: 4873 Sorted by residual: dihedral pdb=" O3B TTP A1102 " pdb=" O3A TTP A1102 " pdb=" PB TTP A1102 " pdb=" PA TTP A1102 " ideal model delta sinusoidal sigma weight residual -180.00 -4.84 -175.16 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C2 TTP A1102 " pdb=" C1' TTP A1102 " pdb=" N1 TTP A1102 " pdb=" O4' TTP A1102 " ideal model delta sinusoidal sigma weight residual 301.68 150.46 151.22 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C5' TTP A1102 " pdb=" O5' TTP A1102 " pdb=" PA TTP A1102 " pdb=" O3A TTP A1102 " ideal model delta sinusoidal sigma weight residual 179.97 48.42 131.55 1 2.00e+01 2.50e-03 3.99e+01 ... (remaining 8640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1598 0.041 - 0.082: 433 0.082 - 0.123: 144 0.123 - 0.164: 10 0.164 - 0.205: 6 Chirality restraints: 2191 Sorted by residual: chirality pdb=" CA LYS A 661 " pdb=" N LYS A 661 " pdb=" C LYS A 661 " pdb=" CB LYS A 661 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU A 341 " pdb=" CB LEU A 341 " pdb=" CD1 LEU A 341 " pdb=" CD2 LEU A 341 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA PRO C 107 " pdb=" N PRO C 107 " pdb=" C PRO C 107 " pdb=" CB PRO C 107 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.41e-01 ... (remaining 2188 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 50 " 0.020 2.00e-02 2.50e+03 3.87e-02 1.49e+01 pdb=" C VAL C 50 " -0.067 2.00e-02 2.50e+03 pdb=" O VAL C 50 " 0.025 2.00e-02 2.50e+03 pdb=" N THR C 51 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 208 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO B 209 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 737 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 738 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " -0.030 5.00e-02 4.00e+02 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 207 2.66 - 3.22: 12657 3.22 - 3.78: 20640 3.78 - 4.34: 28885 4.34 - 4.90: 47511 Nonbonded interactions: 109900 Sorted by model distance: nonbonded pdb=" OD2 ASP A 753 " pdb="MG MG A1101 " model vdw 2.100 2.170 nonbonded pdb=" O TYR A 550 " pdb="MG MG A1101 " model vdw 2.101 2.170 nonbonded pdb=" OG SER B 97 " pdb=" O VAL B 102 " model vdw 2.154 2.440 nonbonded pdb="MG MG A1101 " pdb=" O1B TTP A1102 " model vdw 2.170 2.170 nonbonded pdb=" OD1 ASP A 549 " pdb="MG MG A1101 " model vdw 2.199 2.170 ... (remaining 109895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 39 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 8953 2.51 5 N 2354 2.21 5 O 2737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 8.440 Check model and map are aligned: 0.190 Process input model: 41.000 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 : 0.004 0.050 14536 Z= 0.228 Angle : 0.669 21.996 19804 Z= 0.374 Chirality : 0.042 0.205 2191 Planarity : 0.004 0.054 2388 Dihedral : 15.206 175.155 5501 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.02 % Favored : 94.68 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.19 (0.21), residues: 1634 helix: 1.49 (0.22), residues: 578 sheet: 0.50 (0.28), residues: 376 loop : -1.32 (0.23), residues: 680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 373 time to evaluate : 1.727 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 375 average time/residue: 1.2970 time to fit residues: 531.1136 Evaluate side-chains 331 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 7.9990 chunk 125 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 129 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.0040 chunk 96 optimal weight: 0.2980 chunk 149 optimal weight: 0.0770 overall best weight: 0.2550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 204 ASN ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN B 59 ASN C 386 ASN C 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 14536 Z= 0.149 Angle : 0.535 7.958 19804 Z= 0.283 Chirality : 0.041 0.172 2191 Planarity : 0.004 0.081 2388 Dihedral : 14.375 175.864 2180 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.65 % Favored : 95.04 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.38 (0.22), residues: 1634 helix: 1.52 (0.22), residues: 587 sheet: 0.63 (0.28), residues: 379 loop : -1.13 (0.24), residues: 668 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 346 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 6 residues processed: 352 average time/residue: 1.3112 time to fit residues: 504.4178 Evaluate side-chains 341 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 335 time to evaluate : 1.489 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 4 average time/residue: 0.4138 time to fit residues: 4.1565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 148 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 225 GLN A 413 ASN A 442 GLN A 643 GLN A 825 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN C 94 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 14536 Z= 0.270 Angle : 0.570 9.342 19804 Z= 0.298 Chirality : 0.043 0.165 2191 Planarity : 0.005 0.082 2388 Dihedral : 14.449 165.170 2180 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.96 % Favored : 94.80 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.29 (0.21), residues: 1634 helix: 1.43 (0.22), residues: 590 sheet: 0.63 (0.28), residues: 375 loop : -1.19 (0.23), residues: 669 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 348 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 21 residues processed: 365 average time/residue: 1.2450 time to fit residues: 499.7830 Evaluate side-chains 363 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 342 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 8 residues processed: 14 average time/residue: 0.9237 time to fit residues: 16.8064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 225 GLN A 448 ASN A 467 GLN B 59 ASN C 94 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 14536 Z= 0.281 Angle : 0.574 8.972 19804 Z= 0.301 Chirality : 0.043 0.175 2191 Planarity : 0.005 0.069 2388 Dihedral : 14.300 146.033 2180 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.71 % Favored : 95.10 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.19 (0.21), residues: 1634 helix: 1.35 (0.22), residues: 589 sheet: 0.53 (0.27), residues: 377 loop : -1.23 (0.23), residues: 668 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 358 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 18 residues processed: 370 average time/residue: 1.2768 time to fit residues: 517.9928 Evaluate side-chains 366 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 348 time to evaluate : 1.649 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 10 average time/residue: 0.6299 time to fit residues: 9.7130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 1.9990 chunk 90 optimal weight: 0.0270 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN B 55 GLN B 59 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 14536 Z= 0.309 Angle : 0.595 10.229 19804 Z= 0.311 Chirality : 0.044 0.222 2191 Planarity : 0.005 0.058 2388 Dihedral : 14.197 138.502 2180 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.49 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.08 (0.21), residues: 1634 helix: 1.23 (0.22), residues: 589 sheet: 0.46 (0.28), residues: 363 loop : -1.22 (0.23), residues: 682 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 372 time to evaluate : 1.665 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 26 residues processed: 394 average time/residue: 1.2965 time to fit residues: 560.1438 Evaluate side-chains 378 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 352 time to evaluate : 1.592 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 13 residues processed: 15 average time/residue: 0.6504 time to fit residues: 13.6500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 48 GLN A 643 GLN B 59 ASN B 214 GLN C 94 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14536 Z= 0.199 Angle : 0.550 7.846 19804 Z= 0.288 Chirality : 0.041 0.167 2191 Planarity : 0.004 0.050 2388 Dihedral : 13.968 138.673 2180 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.71 % Favored : 95.10 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.22 (0.21), residues: 1634 helix: 1.33 (0.22), residues: 593 sheet: 0.58 (0.28), residues: 357 loop : -1.15 (0.23), residues: 684 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 351 time to evaluate : 1.710 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 367 average time/residue: 1.3051 time to fit residues: 524.8009 Evaluate side-chains 371 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 346 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 16 residues processed: 12 average time/residue: 0.6171 time to fit residues: 11.0561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 643 GLN B 55 GLN B 59 ASN C 94 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14536 Z= 0.192 Angle : 0.550 7.894 19804 Z= 0.289 Chirality : 0.042 0.235 2191 Planarity : 0.004 0.046 2388 Dihedral : 13.877 137.957 2180 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.02 % Favored : 94.80 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.26 (0.21), residues: 1634 helix: 1.35 (0.22), residues: 594 sheet: 0.61 (0.28), residues: 371 loop : -1.16 (0.23), residues: 669 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 350 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 21 residues processed: 370 average time/residue: 1.3030 time to fit residues: 528.6144 Evaluate side-chains 363 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 342 time to evaluate : 1.709 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 8 average time/residue: 0.9259 time to fit residues: 10.7054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 48 GLN A 467 GLN C 94 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 14536 Z= 0.306 Angle : 0.612 10.757 19804 Z= 0.319 Chirality : 0.044 0.185 2191 Planarity : 0.005 0.047 2388 Dihedral : 14.070 138.470 2180 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.26 % Favored : 94.55 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.10 (0.21), residues: 1634 helix: 1.26 (0.22), residues: 591 sheet: 0.52 (0.28), residues: 371 loop : -1.28 (0.23), residues: 672 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 344 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 22 residues processed: 363 average time/residue: 1.3233 time to fit residues: 526.9824 Evaluate side-chains 361 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 339 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 14 residues processed: 9 average time/residue: 0.6281 time to fit residues: 9.2610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 148 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN C 94 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14536 Z= 0.199 Angle : 0.575 9.891 19804 Z= 0.300 Chirality : 0.042 0.293 2191 Planarity : 0.004 0.047 2388 Dihedral : 13.859 139.078 2180 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.77 % Favored : 95.04 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.27 (0.21), residues: 1634 helix: 1.37 (0.22), residues: 593 sheet: 0.56 (0.28), residues: 357 loop : -1.09 (0.23), residues: 684 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 340 time to evaluate : 1.505 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 353 average time/residue: 1.3250 time to fit residues: 511.7326 Evaluate side-chains 347 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 328 time to evaluate : 1.643 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 7 average time/residue: 0.6699 time to fit residues: 7.8309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 chunk 108 optimal weight: 0.0970 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN C 94 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 14536 Z= 0.232 Angle : 0.605 11.374 19804 Z= 0.313 Chirality : 0.043 0.172 2191 Planarity : 0.004 0.046 2388 Dihedral : 13.894 138.874 2180 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.02 % Favored : 94.80 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.23 (0.21), residues: 1634 helix: 1.36 (0.22), residues: 593 sheet: 0.54 (0.28), residues: 371 loop : -1.19 (0.23), residues: 670 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 329 time to evaluate : 1.668 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 342 average time/residue: 1.2871 time to fit residues: 482.8076 Evaluate side-chains 344 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 326 time to evaluate : 1.675 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 6 average time/residue: 0.6548 time to fit residues: 7.0156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0570 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 54 optimal weight: 0.1980 chunk 134 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 115 optimal weight: 3.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 146 GLN ** C 393 ASN ** 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 = 0.3832 r_free = 0.3832 target = 0.138054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118485 restraints weight = 20400.675| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.03 r_work: 0.3462 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14536 Z= 0.171 Angle : 0.570 10.079 19804 Z= 0.298 Chirality : 0.042 0.286 2191 Planarity : 0.004 0.048 2388 Dihedral : 13.694 138.637 2180 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.71 % Favored : 95.10 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.39 (0.21), residues: 1634 helix: 1.47 (0.22), residues: 595 sheet: 0.60 (0.28), residues: 364 loop : -1.04 (0.23), residues: 675 =============================================================================== Job complete usr+sys time: 7429.45 seconds wall clock time: 131 minutes 13.81 seconds (7873.81 seconds total)