Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 18:32:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/04_2023/6tz2_20587_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/04_2023/6tz2_20587.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/04_2023/6tz2_20587_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/04_2023/6tz2_20587_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/04_2023/6tz2_20587_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/04_2023/6tz2_20587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/04_2023/6tz2_20587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/04_2023/6tz2_20587_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz2_20587/04_2023/6tz2_20587_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.006 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 P 96 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 9573 2.51 5 N 2628 2.21 5 O 3255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 738": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 752": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 867": "NH1" <-> "NH2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A ARG 1007": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "A TYR 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1146": "NH1" <-> "NH2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 520": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15608 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9667 Classifications: {'peptide': 1208} Link IDs: {'PTRANS': 38, 'TRANS': 1169} Chain: "B" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 4007 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 482} Chain breaks: 2 Chain: "M" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'RNA': 18} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 15} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "N" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'RNA': 36} Modifications used: {'rna2p_pyr': 5, 'rna3p_pyr': 31} Link IDs: {'rna2p': 5, 'rna3p': 30} Chain: "T" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 792 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 34} Link IDs: {'rna2p': 2, 'rna3p': 33} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.53, per 1000 atoms: 0.55 Number of scatterers: 15608 At special positions: 0 Unit cell: (119.68, 145.52, 115.6, 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 54 16.00 P 96 15.00 Mg 2 11.99 O 3255 8.00 N 2628 7.00 C 9573 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: 6.44 Conformation dependent library (CDL) restraints added in 1.9 seconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 13 sheets defined 43.8% alpha, 6.8% beta 21 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 12 through 15 No H-bonds generated for 'chain 'A' and resid 12 through 15' Processing helix chain 'A' and resid 20 through 35 removed outlier: 4.023A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 145 through 160 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 201 through 219 Proline residue: A 204 - end of helix removed outlier: 3.509A pdb=" N GLY A 214 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET A 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.742A pdb=" N ILE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.756A pdb=" N LYS A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 296 through 306 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 349 through 357 removed outlier: 4.538A pdb=" N ASP A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 409 removed outlier: 3.787A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.546A pdb=" N ILE A 466 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.599A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N MET A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Proline residue: A 503 - end of helix removed outlier: 3.878A pdb=" N GLN A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TYR A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 537 removed outlier: 3.838A pdb=" N SER A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 573 removed outlier: 3.949A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 690 through 706 Processing helix chain 'A' and resid 753 through 767 removed outlier: 3.539A pdb=" N ASP A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 786 Processing helix chain 'A' and resid 801 through 808 Processing helix chain 'A' and resid 834 through 838 Processing helix chain 'A' and resid 869 through 878 removed outlier: 4.381A pdb=" N LEU A 874 " --> pdb=" O TYR A 870 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 886 Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 902 through 911 Processing helix chain 'A' and resid 927 through 937 Processing helix chain 'A' and resid 946 through 958 Processing helix chain 'A' and resid 972 through 984 removed outlier: 3.504A pdb=" N ALA A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 984 " --> pdb=" O SER A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 Processing helix chain 'A' and resid 1017 through 1019 No H-bonds generated for 'chain 'A' and resid 1017 through 1019' Processing helix chain 'A' and resid 1035 through 1041 removed outlier: 3.951A pdb=" N THR A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A1041 " --> pdb=" O LYS A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1061 Processing helix chain 'A' and resid 1076 through 1080 Processing helix chain 'A' and resid 1091 through 1101 Processing helix chain 'A' and resid 1104 through 1114 removed outlier: 4.752A pdb=" N ASN A1108 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A1109 " --> pdb=" O LEU A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1132 Processing helix chain 'A' and resid 1155 through 1158 removed outlier: 3.504A pdb=" N ALA A1158 " --> pdb=" O PRO A1155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1155 through 1158' Processing helix chain 'A' and resid 1174 through 1188 removed outlier: 3.627A pdb=" N ASN A1179 " --> pdb=" O ARG A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1211 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 41 through 62 removed outlier: 3.517A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 133 through 148 removed outlier: 3.546A pdb=" N LYS B 136 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA B 137 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 140 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.931A pdb=" N LEU B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 4.222A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 360 through 374 removed outlier: 4.324A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 4.233A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.541A pdb=" N LEU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 429 removed outlier: 3.937A pdb=" N HIS B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 437 No H-bonds generated for 'chain 'B' and resid 434 through 437' Processing helix chain 'B' and resid 442 through 459 removed outlier: 3.878A pdb=" N VAL B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 492 through 496 removed outlier: 3.699A pdb=" N ALA B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.767A pdb=" N ARG B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 537 Processing helix chain 'B' and resid 547 through 555 Processing sheet with id= A, first strand: chain 'A' and resid 54 through 58 removed outlier: 3.675A pdb=" N TYR A 55 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.852A pdb=" N LYS A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 476 through 478 Processing sheet with id= D, first strand: chain 'A' and resid 711 through 716 removed outlier: 3.769A pdb=" N GLU A 714 " --> pdb=" O SER A 545 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 585 through 590 Processing sheet with id= F, first strand: chain 'A' and resid 720 through 722 Processing sheet with id= G, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 3.682A pdb=" N GLU A1023 " --> pdb=" O VAL A1201 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.620A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 370 through 373 removed outlier: 6.450A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 157 through 159 removed outlier: 6.058A pdb=" N HIS B 182 " --> pdb=" O ILE B 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 269 through 271 Processing sheet with id= L, first strand: chain 'B' and resid 543 through 546 removed outlier: 4.598A pdb=" N THR B 543 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL B 505 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL B 350 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU B 507 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR B 352 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU B 488 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 255 through 260 removed outlier: 4.075A pdb=" N LYS B 315 " --> pdb=" O THR B 259 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 5.68 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2353 1.30 - 1.43: 4828 1.43 - 1.55: 8648 1.55 - 1.68: 190 1.68 - 1.81: 97 Bond restraints: 16116 Sorted by residual: bond pdb=" C2' ATP A1301 " pdb=" C3' ATP A1301 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.79e+02 bond pdb=" C3' UTP A1302 " pdb=" C4' UTP A1302 " ideal model delta sigma weight residual 1.654 1.296 0.358 2.00e-02 2.50e+03 3.20e+02 bond pdb=" C2' UTP A1302 " pdb=" C3' UTP A1302 " ideal model delta sigma weight residual 1.301 1.621 -0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" C1' UTP A1302 " pdb=" C2' UTP A1302 " ideal model delta sigma weight residual 1.585 1.326 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C4' UTP A1302 " pdb=" O4' UTP A1302 " ideal model delta sigma weight residual 1.320 1.568 -0.248 2.00e-02 2.50e+03 1.53e+02 ... (remaining 16111 not shown) Histogram of bond angle deviations from ideal: 95.84 - 105.16: 608 105.16 - 114.48: 9727 114.48 - 123.79: 11196 123.79 - 133.11: 692 133.11 - 142.43: 22 Bond angle restraints: 22245 Sorted by residual: angle pdb=" C5 ATP A1301 " pdb=" C6 ATP A1301 " pdb=" N6 ATP A1301 " ideal model delta sigma weight residual 123.59 142.43 -18.84 1.08e+00 8.64e-01 3.07e+02 angle pdb=" N1 ATP A1301 " pdb=" C6 ATP A1301 " pdb=" N6 ATP A1301 " ideal model delta sigma weight residual 118.11 97.49 20.62 1.23e+00 6.64e-01 2.82e+02 angle pdb=" PB ATP A1301 " pdb=" O3B ATP A1301 " pdb=" PG ATP A1301 " ideal model delta sigma weight residual 139.87 123.37 16.50 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP A1301 " pdb=" O3A ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 136.83 123.36 13.47 1.00e+00 1.00e+00 1.81e+02 angle pdb=" C1' ATP A1301 " pdb=" N9 ATP A1301 " pdb=" C4 ATP A1301 " ideal model delta sigma weight residual 126.88 108.64 18.24 1.80e+00 3.09e-01 1.03e+02 ... (remaining 22240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 9312 34.55 - 69.10: 134 69.10 - 103.65: 10 103.65 - 138.19: 0 138.19 - 172.74: 1 Dihedral angle restraints: 9457 sinusoidal: 4425 harmonic: 5032 Sorted by residual: dihedral pdb=" O4' U N 19 " pdb=" C1' U N 19 " pdb=" N1 U N 19 " pdb=" C2 U N 19 " ideal model delta sinusoidal sigma weight residual -128.00 44.74 -172.74 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA LYS A 921 " pdb=" C LYS A 921 " pdb=" N LYS A 922 " pdb=" CA LYS A 922 " ideal model delta harmonic sigma weight residual -180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" O4' U N 20 " pdb=" C1' U N 20 " pdb=" N1 U N 20 " pdb=" C2 U N 20 " ideal model delta sinusoidal sigma weight residual -160.00 -103.19 -56.81 1 1.50e+01 4.44e-03 1.93e+01 ... (remaining 9454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2036 0.060 - 0.121: 453 0.121 - 0.181: 63 0.181 - 0.241: 14 0.241 - 0.301: 4 Chirality restraints: 2570 Sorted by residual: chirality pdb=" CB ILE A 881 " pdb=" CA ILE A 881 " pdb=" CG1 ILE A 881 " pdb=" CG2 ILE A 881 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1' UTP A1302 " pdb=" C2' UTP A1302 " pdb=" N1 UTP A1302 " pdb=" O4' UTP A1302 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE A 546 " pdb=" CA ILE A 546 " pdb=" CG1 ILE A 546 " pdb=" CG2 ILE A 546 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2567 not shown) Planarity restraints: 2509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " 0.028 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP A 606 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 996 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C SER A 996 " 0.050 2.00e-02 2.50e+03 pdb=" O SER A 996 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG A 997 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 538 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.69e+00 pdb=" N PRO B 539 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 539 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 539 " 0.035 5.00e-02 4.00e+02 ... (remaining 2506 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 209 2.64 - 3.20: 13561 3.20 - 3.77: 24380 3.77 - 4.33: 33098 4.33 - 4.90: 52461 Nonbonded interactions: 123709 Sorted by model distance: nonbonded pdb=" O2A UTP A1302 " pdb="MG MG A1303 " model vdw 2.073 2.170 nonbonded pdb=" OD2 ASP A 680 " pdb="MG MG A1303 " model vdw 2.095 2.170 nonbonded pdb=" O3A UTP A1302 " pdb="MG MG A1304 " model vdw 2.100 2.170 nonbonded pdb=" OD1 ASP A 681 " pdb="MG MG A1303 " model vdw 2.112 2.170 nonbonded pdb=" O3G UTP A1302 " pdb="MG MG A1304 " model vdw 2.156 2.170 ... (remaining 123704 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 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: 0.570 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: 3.270 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 42.860 Find NCS groups from input model: 0.400 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.009 0.358 16116 Z= 0.574 Angle : 0.951 20.615 22245 Z= 0.546 Chirality : 0.053 0.301 2570 Planarity : 0.007 0.065 2509 Dihedral : 11.669 172.742 6223 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.35 % Favored : 94.59 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -3.55 (0.16), residues: 1701 helix: -2.42 (0.14), residues: 764 sheet: -1.85 (0.39), residues: 150 loop : -2.29 (0.18), residues: 787 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 506 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 512 average time/residue: 0.3099 time to fit residues: 224.1905 Evaluate side-chains 309 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 307 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1270 time to fit residues: 2.6079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 691 ASN A 694 HIS A 696 HIS A 820 ASN ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 HIS A1140 HIS ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 180 GLN B 272 ASN B 414 ASN B 542 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 16116 Z= 0.250 Angle : 0.584 11.333 22245 Z= 0.297 Chirality : 0.040 0.161 2570 Planarity : 0.005 0.055 2509 Dihedral : 10.546 167.717 2972 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 3.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.98 (0.18), residues: 1701 helix: -0.77 (0.17), residues: 775 sheet: -1.61 (0.39), residues: 150 loop : -1.74 (0.21), residues: 776 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 322 time to evaluate : 1.778 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 37 residues processed: 355 average time/residue: 0.2939 time to fit residues: 152.3443 Evaluate side-chains 311 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 274 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1695 time to fit residues: 13.3964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 173 optimal weight: 50.0000 chunk 143 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 126 HIS A 629 GLN A 888 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 453 ASN B 492 ASN B 542 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 16116 Z= 0.325 Angle : 0.590 9.589 22245 Z= 0.300 Chirality : 0.041 0.155 2570 Planarity : 0.004 0.047 2509 Dihedral : 10.547 163.313 2972 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.21 (0.20), residues: 1701 helix: 0.04 (0.18), residues: 767 sheet: -1.45 (0.39), residues: 152 loop : -1.47 (0.21), residues: 782 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 284 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 25 residues processed: 306 average time/residue: 0.2954 time to fit residues: 132.7619 Evaluate side-chains 280 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 255 time to evaluate : 1.762 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1505 time to fit residues: 9.3652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 171 optimal weight: 50.0000 chunk 84 optimal weight: 20.0000 chunk 153 optimal weight: 0.0870 chunk 46 optimal weight: 8.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN B 494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 16116 Z= 0.223 Angle : 0.535 10.015 22245 Z= 0.268 Chirality : 0.039 0.152 2570 Planarity : 0.004 0.039 2509 Dihedral : 10.455 163.093 2972 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.83 (0.20), residues: 1701 helix: 0.43 (0.19), residues: 774 sheet: -1.22 (0.40), residues: 155 loop : -1.40 (0.22), residues: 772 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 289 time to evaluate : 1.800 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 20 residues processed: 310 average time/residue: 0.2959 time to fit residues: 134.0020 Evaluate side-chains 287 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 267 time to evaluate : 1.650 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1442 time to fit residues: 7.7497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 153 optimal weight: 0.4980 chunk 43 optimal weight: 20.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN A1095 GLN ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16116 Z= 0.213 Angle : 0.525 9.581 22245 Z= 0.262 Chirality : 0.039 0.159 2570 Planarity : 0.004 0.041 2509 Dihedral : 10.440 162.981 2972 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.54 (0.20), residues: 1701 helix: 0.68 (0.19), residues: 766 sheet: -1.11 (0.40), residues: 155 loop : -1.22 (0.22), residues: 780 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 290 time to evaluate : 1.737 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 17 residues processed: 310 average time/residue: 0.3010 time to fit residues: 136.7842 Evaluate side-chains 283 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 266 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1638 time to fit residues: 7.2425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 9.9990 chunk 154 optimal weight: 0.0770 chunk 33 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 171 optimal weight: 50.0000 chunk 142 optimal weight: 0.5980 chunk 79 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 overall best weight: 5.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 16116 Z= 0.243 Angle : 0.533 9.146 22245 Z= 0.267 Chirality : 0.039 0.165 2570 Planarity : 0.004 0.039 2509 Dihedral : 10.475 162.056 2972 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.45 (0.20), residues: 1701 helix: 0.77 (0.19), residues: 767 sheet: -1.06 (0.39), residues: 155 loop : -1.19 (0.22), residues: 779 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 275 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 11 residues processed: 292 average time/residue: 0.3102 time to fit residues: 132.5604 Evaluate side-chains 274 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 263 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1476 time to fit residues: 5.2954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 170 optimal weight: 40.0000 chunk 106 optimal weight: 0.1980 chunk 104 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 16116 Z= 0.165 Angle : 0.509 9.904 22245 Z= 0.251 Chirality : 0.038 0.188 2570 Planarity : 0.003 0.041 2509 Dihedral : 10.368 163.071 2972 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.28 (0.21), residues: 1701 helix: 0.90 (0.19), residues: 766 sheet: -0.98 (0.39), residues: 165 loop : -1.08 (0.22), residues: 770 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 290 time to evaluate : 1.830 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 297 average time/residue: 0.3033 time to fit residues: 131.9445 Evaluate side-chains 278 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 266 time to evaluate : 1.614 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.1590 time to fit residues: 5.5372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 116 optimal weight: 0.0980 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 164 ASN ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 165 GLN B 494 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 16116 Z= 0.269 Angle : 0.553 9.451 22245 Z= 0.275 Chirality : 0.040 0.176 2570 Planarity : 0.004 0.041 2509 Dihedral : 10.453 161.897 2972 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.28 (0.21), residues: 1701 helix: 0.92 (0.20), residues: 762 sheet: -1.16 (0.37), residues: 174 loop : -1.05 (0.22), residues: 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 268 time to evaluate : 1.668 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 279 average time/residue: 0.3022 time to fit residues: 123.5072 Evaluate side-chains 270 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 263 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1446 time to fit residues: 4.1258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 0.0770 chunk 149 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 168 optimal weight: 0.0470 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 GLN ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 16116 Z= 0.124 Angle : 0.529 16.161 22245 Z= 0.254 Chirality : 0.037 0.190 2570 Planarity : 0.003 0.041 2509 Dihedral : 10.286 165.312 2972 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.13 (0.21), residues: 1701 helix: 1.00 (0.19), residues: 766 sheet: -0.85 (0.39), residues: 165 loop : -0.99 (0.22), residues: 770 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 311 time to evaluate : 1.805 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 316 average time/residue: 0.3102 time to fit residues: 144.5174 Evaluate side-chains 286 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 1.692 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1478 time to fit residues: 3.0239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.0870 chunk 79 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 176 optimal weight: 50.0000 chunk 162 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 413 HIS ** A1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 63 HIS B 165 GLN B 453 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 16116 Z= 0.198 Angle : 0.549 10.633 22245 Z= 0.269 Chirality : 0.039 0.211 2570 Planarity : 0.004 0.041 2509 Dihedral : 10.328 165.461 2972 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.13 (0.21), residues: 1701 helix: 1.08 (0.20), residues: 762 sheet: -1.07 (0.38), residues: 170 loop : -1.01 (0.22), residues: 769 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 279 time to evaluate : 1.827 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 283 average time/residue: 0.3031 time to fit residues: 125.9624 Evaluate side-chains 265 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 260 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1402 time to fit residues: 3.5055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.135736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.100783 restraints weight = 27868.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103206 restraints weight = 13913.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104721 restraints weight = 8950.582| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16116 Z= 0.211 Angle : 0.563 10.755 22245 Z= 0.276 Chirality : 0.039 0.166 2570 Planarity : 0.004 0.040 2509 Dihedral : 10.376 165.490 2972 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.02 (0.21), residues: 1701 helix: 1.15 (0.20), residues: 754 sheet: -0.93 (0.39), residues: 161 loop : -0.94 (0.22), residues: 786 =============================================================================== Job complete usr+sys time: 3128.37 seconds wall clock time: 57 minutes 55.29 seconds (3475.29 seconds total)