Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 05:25:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2023/6tz1_20586_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2023/6tz1_20586.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2023/6tz1_20586_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2023/6tz1_20586_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2023/6tz1_20586_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2023/6tz1_20586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2023/6tz1_20586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2023/6tz1_20586_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2023/6tz1_20586_updated.pdb" } resolution = 3.4 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= 0.008 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: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 54 5.16 5 C 8949 2.51 5 N 2428 2.21 5 O 2755 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 487": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 738": "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 882": "NH1" <-> "NH2" Residue "A ARG 993": "NH1" <-> "NH2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A ARG 1007": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "A ARG 1146": "NH1" <-> "NH2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 14212 Number of models: 1 Model: "" Number of chains: 5 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: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'RNA': 9} Modifications used: {'rna3p_pyr': 9} Link IDs: {'rna3p': 8} Chain: "N" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'GTA': 1} Classifications: {'RNA': 3, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2, None: 1} Not linked: pdbres="GTA N 1 " pdbres=" G N 2 " Chain: "T" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 242 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 10} Link IDs: {'rna3p': 10} Time building chain proxies: 7.72, per 1000 atoms: 0.54 Number of scatterers: 14212 At special positions: 0 Unit cell: (105.138, 144.432, 87.084, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 26 15.00 O 2755 8.00 N 2428 7.00 C 8949 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.38 Conformation dependent library (CDL) restraints added in 2.2 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: 75 helices and 14 sheets defined 44.8% alpha, 6.8% beta 6 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.687A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 removed outlier: 3.931A pdb=" N HIS A 41 " --> pdb=" O ARG A 37 " (cutoff:3.500A) 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 121 through 134 Processing helix chain 'A' and resid 147 through 160 removed outlier: 3.959A pdb=" N VAL A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 202 through 219 removed outlier: 3.754A pdb=" N VAL A 207 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 3.596A pdb=" N ALA A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 295 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 356 removed outlier: 5.054A pdb=" N ASP A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.937A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.974A pdb=" N LYS A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 440 through 447 removed outlier: 5.094A pdb=" N ASN A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 5.721A pdb=" N ARG A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 494 through 512 removed outlier: 3.545A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Proline residue: A 503 - end of helix removed outlier: 3.653A pdb=" N GLN A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASP A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 534 removed outlier: 3.833A pdb=" N GLY A 530 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU A 531 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 532 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 533 " --> pdb=" O GLY A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'A' and resid 557 through 573 removed outlier: 4.013A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 690 through 706 Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 754 through 766 Processing helix chain 'A' and resid 774 through 787 Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.859A pdb=" N TYR A 801 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASP A 802 " --> pdb=" O LYS A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 838 removed outlier: 3.555A pdb=" N PHE A 838 " --> pdb=" O ALA A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 878 removed outlier: 3.553A pdb=" N LEU A 874 " --> pdb=" O LYS A 871 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 878 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 887 removed outlier: 4.247A pdb=" N GLN A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 899 Processing helix chain 'A' and resid 902 through 911 Processing helix chain 'A' and resid 913 through 924 removed outlier: 4.871A pdb=" N ASP A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 removed outlier: 4.203A pdb=" N GLN A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 958 Processing helix chain 'A' and resid 969 through 981 removed outlier: 4.756A pdb=" N LEU A 973 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1005 removed outlier: 3.689A pdb=" N VAL A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A1004 " --> pdb=" O GLU A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1018 No H-bonds generated for 'chain 'A' and resid 1016 through 1018' Processing helix chain 'A' and resid 1035 through 1037 No H-bonds generated for 'chain 'A' and resid 1035 through 1037' Processing helix chain 'A' and resid 1054 through 1062 Processing helix chain 'A' and resid 1074 through 1080 Processing helix chain 'A' and resid 1091 through 1101 Processing helix chain 'A' and resid 1104 through 1113 removed outlier: 3.818A pdb=" N ASN A1108 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE A1111 " --> pdb=" O ASN A1108 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1112 " --> pdb=" O ASP A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1132 Processing helix chain 'A' and resid 1155 through 1161 removed outlier: 3.589A pdb=" N ALA A1158 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG A1160 " --> pdb=" O SER A1157 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A1161 " --> pdb=" O ALA A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1168 No H-bonds generated for 'chain 'A' and resid 1166 through 1168' Processing helix chain 'A' and resid 1174 through 1188 Processing helix chain 'A' and resid 1204 through 1211 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 41 through 62 removed outlier: 3.588A pdb=" N LYS B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 162 through 165 No H-bonds generated for 'chain 'B' and resid 162 through 165' Processing helix chain 'B' and resid 170 through 178 removed outlier: 4.166A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TYR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 359 through 374 removed outlier: 3.843A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 4.067A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.584A pdb=" N LEU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 428 Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 442 through 459 removed outlier: 3.599A pdb=" N MET B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 4.786A 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: 3.880A pdb=" N ALA B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 516 No H-bonds generated for 'chain 'B' and resid 513 through 516' Processing helix chain 'B' and resid 524 through 536 Processing helix chain 'B' and resid 547 through 556 removed outlier: 3.854A pdb=" N ILE B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 54 through 58 Processing sheet with id= B, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.511A pdb=" N LYS A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 475 through 477 Processing sheet with id= D, first strand: chain 'A' and resid 541 through 544 removed outlier: 3.653A pdb=" N THR A 674 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN A 687 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU A 672 " --> pdb=" O GLN A 687 " (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 719 through 721 Processing sheet with id= G, first strand: chain 'A' and resid 794 through 796 Processing sheet with id= H, first strand: chain 'A' and resid 1023 through 1026 Processing sheet with id= I, first strand: chain 'A' and resid 267 through 272 removed outlier: 3.520A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 370 through 373 removed outlier: 6.412A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 157 through 159 removed outlier: 5.794A pdb=" N HIS B 182 " --> pdb=" O ILE B 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 204 through 208 Processing sheet with id= M, first strand: chain 'B' and resid 266 through 271 removed outlier: 3.637A pdb=" N LYS B 315 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR B 261 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE B 313 " --> pdb=" O THR B 261 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 543 through 546 removed outlier: 4.306A pdb=" N THR B 543 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL B 505 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 350 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU B 507 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR B 352 " --> pdb=" O LEU B 507 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2264 1.31 - 1.43: 4093 1.43 - 1.56: 8062 1.56 - 1.68: 52 1.68 - 1.81: 96 Bond restraints: 14567 Sorted by residual: bond pdb=" C1A GTA N 1 " pdb=" O4A GTA N 1 " ideal model delta sigma weight residual 1.591 1.298 0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C3B GTA N 1 " pdb=" C4B GTA N 1 " ideal model delta sigma weight residual 1.275 1.542 -0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C4B GTA N 1 " pdb=" O4B GTA N 1 " ideal model delta sigma weight residual 1.556 1.305 0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C1A GTA N 1 " pdb=" C2A GTA N 1 " ideal model delta sigma weight residual 1.325 1.576 -0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C3B GTA N 1 " pdb=" O3B GTA N 1 " ideal model delta sigma weight residual 1.482 1.357 0.125 2.00e-02 2.50e+03 3.89e+01 ... (remaining 14562 not shown) Histogram of bond angle deviations from ideal: 97.53 - 106.46: 468 106.46 - 115.39: 8813 115.39 - 124.32: 10202 124.32 - 133.25: 339 133.25 - 142.17: 21 Bond angle restraints: 19843 Sorted by residual: angle pdb=" C1B GTA N 1 " pdb=" N9C GTA N 1 " pdb=" C4C GTA N 1 " ideal model delta sigma weight residual 121.43 140.98 -19.55 3.00e+00 1.11e-01 4.25e+01 angle pdb=" C1A GTA N 1 " pdb=" N9 GTA N 1 " pdb=" C4 GTA N 1 " ideal model delta sigma weight residual 114.98 133.92 -18.94 3.00e+00 1.11e-01 3.98e+01 angle pdb=" C1A GTA N 1 " pdb=" N9 GTA N 1 " pdb=" C8 GTA N 1 " ideal model delta sigma weight residual 133.44 115.23 18.21 3.00e+00 1.11e-01 3.68e+01 angle pdb=" C1B GTA N 1 " pdb=" N9C GTA N 1 " pdb=" C8C GTA N 1 " ideal model delta sigma weight residual 127.97 110.87 17.10 3.00e+00 1.11e-01 3.25e+01 angle pdb=" C ASP A 749 " pdb=" N ILE A 750 " pdb=" CA ILE A 750 " ideal model delta sigma weight residual 120.69 128.03 -7.34 1.46e+00 4.69e-01 2.53e+01 ... (remaining 19838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 8220 16.06 - 32.13: 329 32.13 - 48.19: 90 48.19 - 64.26: 6 64.26 - 80.32: 6 Dihedral angle restraints: 8651 sinusoidal: 3619 harmonic: 5032 Sorted by residual: dihedral pdb=" CA LEU A1045 " pdb=" C LEU A1045 " pdb=" N ALA A1046 " pdb=" CA ALA A1046 " ideal model delta harmonic sigma weight residual 180.00 154.43 25.57 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA VAL A 989 " pdb=" C VAL A 989 " pdb=" N GLN A 990 " pdb=" CA GLN A 990 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLU A 986 " pdb=" C GLU A 986 " pdb=" N THR A 987 " pdb=" CA THR A 987 " ideal model delta harmonic sigma weight residual -180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 8648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1723 0.060 - 0.119: 435 0.119 - 0.179: 61 0.179 - 0.239: 15 0.239 - 0.299: 1 Chirality restraints: 2235 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 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB VAL A 199 " pdb=" CA VAL A 199 " pdb=" CG1 VAL A 199 " pdb=" CG2 VAL A 199 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE A 450 " pdb=" CA ILE A 450 " pdb=" CG1 ILE A 450 " pdb=" CG2 ILE A 450 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2232 not shown) Planarity restraints: 2442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " -0.028 2.00e-02 2.50e+03 2.34e-02 1.37e+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 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " -0.003 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 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 203 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.69e+00 pdb=" N PRO A 204 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A1014 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO A1015 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A1015 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1015 " -0.036 5.00e-02 4.00e+02 ... (remaining 2439 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1489 2.75 - 3.28: 13469 3.28 - 3.82: 23493 3.82 - 4.36: 28650 4.36 - 4.90: 48807 Nonbonded interactions: 115908 Sorted by model distance: nonbonded pdb=" OD2 ASP A 766 " pdb=" O2' U M 6 " model vdw 2.207 2.440 nonbonded pdb=" OD1 ASP A1075 " pdb=" OH TYR A1130 " model vdw 2.282 2.440 nonbonded pdb=" O LYS A 778 " pdb=" OH TYR A 845 " model vdw 2.288 2.440 nonbonded pdb=" OE2 GLU A 947 " pdb=" OH TYR B 135 " model vdw 2.306 2.440 nonbonded pdb=" OH TYR B 352 " pdb=" OD1 ASP B 495 " model vdw 2.308 2.440 ... (remaining 115903 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 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: 0.820 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: 4.850 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 41.590 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 : 0.008 0.293 14567 Z= 0.522 Angle : 0.921 19.549 19843 Z= 0.478 Chirality : 0.054 0.299 2235 Planarity : 0.006 0.069 2442 Dihedral : 10.155 80.321 5417 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % 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: -3.92 (0.15), residues: 1701 helix: -2.75 (0.12), residues: 821 sheet: -2.30 (0.36), residues: 149 loop : -2.30 (0.19), residues: 731 *********************** 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 393 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 386 time to evaluate : 1.604 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 390 average time/residue: 0.3340 time to fit residues: 180.1880 Evaluate side-chains 226 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 274 GLN A 412 HIS A 413 HIS A 447 ASN A 522 GLN A 653 GLN A 696 HIS A 887 GLN A 888 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 ASN ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 HIS A1108 ASN A1121 GLN B 182 HIS B 511 ASN B 542 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 14567 Z= 0.260 Angle : 0.565 8.029 19843 Z= 0.294 Chirality : 0.041 0.156 2235 Planarity : 0.005 0.052 2442 Dihedral : 6.238 84.017 2166 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 2.15 % 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: -2.41 (0.18), residues: 1701 helix: -1.20 (0.16), residues: 833 sheet: -2.10 (0.34), residues: 163 loop : -1.82 (0.21), residues: 705 *********************** 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 263 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 1.784 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 252 average time/residue: 0.3075 time to fit residues: 110.2599 Evaluate side-chains 220 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 204 time to evaluate : 1.654 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1363 time to fit residues: 6.2674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 GLN B 429 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 14567 Z= 0.446 Angle : 0.659 10.750 19843 Z= 0.335 Chirality : 0.045 0.196 2235 Planarity : 0.005 0.043 2442 Dihedral : 6.421 90.808 2166 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -1.86 (0.19), residues: 1701 helix: -0.68 (0.17), residues: 828 sheet: -1.85 (0.34), residues: 173 loop : -1.61 (0.22), residues: 700 *********************** 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 253 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 213 time to evaluate : 1.627 Fit side-chains outliers start: 40 outliers final: 27 residues processed: 238 average time/residue: 0.3132 time to fit residues: 105.5009 Evaluate side-chains 227 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 1.634 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1508 time to fit residues: 9.5201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 81 optimal weight: 0.0570 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 14567 Z= 0.241 Angle : 0.535 10.185 19843 Z= 0.273 Chirality : 0.041 0.161 2235 Planarity : 0.004 0.041 2442 Dihedral : 6.078 88.814 2166 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.75 % 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: -1.29 (0.20), residues: 1701 helix: -0.18 (0.18), residues: 830 sheet: -1.62 (0.36), residues: 156 loop : -1.38 (0.22), residues: 715 *********************** 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 242 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 1.605 Fit side-chains outliers start: 26 outliers final: 14 residues processed: 235 average time/residue: 0.3171 time to fit residues: 106.2400 Evaluate side-chains 215 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 1.667 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1351 time to fit residues: 5.8476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 41 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 522 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 14567 Z= 0.384 Angle : 0.599 9.895 19843 Z= 0.304 Chirality : 0.044 0.193 2235 Planarity : 0.004 0.039 2442 Dihedral : 6.243 92.187 2166 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 1.68 % 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: -1.27 (0.20), residues: 1701 helix: -0.11 (0.18), residues: 828 sheet: -1.68 (0.35), residues: 170 loop : -1.39 (0.22), residues: 703 *********************** 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 234 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 209 time to evaluate : 1.583 Fit side-chains outliers start: 25 outliers final: 15 residues processed: 221 average time/residue: 0.3166 time to fit residues: 98.7159 Evaluate side-chains 216 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 1.808 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1599 time to fit residues: 6.5920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 137 optimal weight: 20.0000 chunk 76 optimal weight: 0.1980 chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 14567 Z= 0.166 Angle : 0.495 11.713 19843 Z= 0.251 Chirality : 0.039 0.171 2235 Planarity : 0.003 0.040 2442 Dihedral : 5.839 87.747 2166 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 1.14 % 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: -0.80 (0.20), residues: 1701 helix: 0.32 (0.18), residues: 823 sheet: -1.50 (0.35), residues: 168 loop : -1.21 (0.22), residues: 710 *********************** 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 235 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 218 time to evaluate : 1.746 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 229 average time/residue: 0.3192 time to fit residues: 102.9866 Evaluate side-chains 214 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1413 time to fit residues: 4.3733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 100 optimal weight: 0.4980 chunk 76 optimal weight: 0.0170 overall best weight: 3.9024 ------------------------------------------------------------------------------- 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** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14567 Z= 0.218 Angle : 0.520 11.450 19843 Z= 0.262 Chirality : 0.040 0.159 2235 Planarity : 0.003 0.039 2442 Dihedral : 5.817 88.556 2166 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 1.01 % 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: -0.67 (0.20), residues: 1701 helix: 0.41 (0.18), residues: 824 sheet: -1.34 (0.35), residues: 168 loop : -1.15 (0.23), residues: 709 *********************** 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 224 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 1.552 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 213 average time/residue: 0.3475 time to fit residues: 103.6493 Evaluate side-chains 210 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 200 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1794 time to fit residues: 5.3723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 14567 Z= 0.347 Angle : 0.586 12.054 19843 Z= 0.295 Chirality : 0.043 0.165 2235 Planarity : 0.004 0.038 2442 Dihedral : 6.044 90.983 2166 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.74 % 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: -0.80 (0.20), residues: 1701 helix: 0.30 (0.18), residues: 820 sheet: -1.51 (0.35), residues: 172 loop : -1.16 (0.23), residues: 709 *********************** 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 213 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 202 time to evaluate : 1.619 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 208 average time/residue: 0.3273 time to fit residues: 96.1409 Evaluate side-chains 202 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 199 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1262 time to fit residues: 2.9521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 145 optimal weight: 0.1980 chunk 100 optimal weight: 20.0000 overall best weight: 4.6388 ------------------------------------------------------------------------------- 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** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 14567 Z= 0.250 Angle : 0.544 13.188 19843 Z= 0.275 Chirality : 0.041 0.153 2235 Planarity : 0.003 0.039 2442 Dihedral : 5.916 89.529 2166 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.34 % 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: -0.60 (0.20), residues: 1701 helix: 0.48 (0.18), residues: 814 sheet: -1.44 (0.35), residues: 172 loop : -1.06 (0.23), residues: 715 *********************** 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 214 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 209 time to evaluate : 1.771 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 210 average time/residue: 0.3421 time to fit residues: 101.6672 Evaluate side-chains 205 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 202 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1611 time to fit residues: 3.3900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.0570 chunk 99 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 170 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 14567 Z= 0.145 Angle : 0.502 13.204 19843 Z= 0.254 Chirality : 0.038 0.128 2235 Planarity : 0.003 0.040 2442 Dihedral : 5.610 85.945 2166 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.27 % 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: -0.26 (0.20), residues: 1701 helix: 0.77 (0.19), residues: 808 sheet: -1.20 (0.36), residues: 171 loop : -0.92 (0.23), residues: 722 ********************** 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 222 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 218 time to evaluate : 1.643 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 220 average time/residue: 0.3278 time to fit residues: 101.9385 Evaluate side-chains 207 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1611 time to fit residues: 2.9127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.114932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.096808 restraints weight = 20631.894| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.56 r_work: 0.2858 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 14567 Z= 0.199 Angle : 0.532 12.637 19843 Z= 0.268 Chirality : 0.039 0.148 2235 Planarity : 0.003 0.041 2442 Dihedral : 5.640 86.992 2166 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.40 % 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: -0.27 (0.20), residues: 1701 helix: 0.74 (0.19), residues: 813 sheet: -1.15 (0.36), residues: 171 loop : -0.92 (0.23), residues: 717 =============================================================================== Job complete usr+sys time: 2964.64 seconds wall clock time: 54 minutes 49.31 seconds (3289.31 seconds total)