Starting phenix.real_space_refine (version: dev) on Tue Apr 5 15:15:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2022/6tz1_20586_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2022/6tz1_20586.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2022/6tz1_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_2022/6tz1_20586_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2022/6tz1_20586_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2022/6tz1_20586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2022/6tz1_20586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2022/6tz1_20586_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/04_2022/6tz1_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 Convert atoms to be neutral 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-dev-4553/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: {'PTRANS': 17, 'TRANS': 482, 'PCIS': 1} 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: {'undetermined': 1, 'RNA': 3} Modifications used: {'rna3p_pyr': 1, 'rna3p_pur': 2} Link IDs: {None: 1, 'rna3p': 2} 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: 8.11, per 1000 atoms: 0.57 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: 5.72 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: 5.57 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: 4.79 Time building geometry restraints manager: 6.17 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=" C1B GTA N 1 " pdb=" C2B GTA N 1 " ideal model delta sigma weight residual 1.648 1.303 0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" C1B GTA N 1 " pdb=" O4B GTA N 1 " ideal model delta sigma weight residual 1.318 1.617 -0.299 2.00e-02 2.50e+03 2.23e+02 bond pdb=" C2B GTA N 1 " pdb=" C3B GTA N 1 " ideal model delta sigma weight residual 1.250 1.538 -0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C4B GTA N 1 " pdb=" O4B GTA N 1 " ideal model delta sigma weight residual 1.504 1.305 0.199 2.00e-02 2.50e+03 9.91e+01 bond pdb=" C4B GTA N 1 " pdb=" C5B GTA N 1 " ideal model delta sigma weight residual 1.373 1.553 -0.180 2.00e-02 2.50e+03 8.10e+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=" C1A GTA N 1 " pdb=" N9 GTA N 1 " pdb=" C8 GTA N 1 " ideal model delta sigma weight residual 144.86 115.23 29.63 3.00e+00 1.11e-01 9.76e+01 angle pdb=" C1A GTA N 1 " pdb=" N9 GTA N 1 " pdb=" C4 GTA N 1 " ideal model delta sigma weight residual 104.75 133.92 -29.17 3.00e+00 1.11e-01 9.45e+01 angle pdb=" C1B GTA N 1 " pdb=" N9C GTA N 1 " pdb=" C4C GTA N 1 " ideal model delta sigma weight residual 112.29 140.98 -28.69 3.00e+00 1.11e-01 9.15e+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 angle pdb=" CB MET A 779 " pdb=" CG MET A 779 " pdb=" SD MET A 779 " ideal model delta sigma weight residual 112.70 100.50 12.20 3.00e+00 1.11e-01 1.65e+01 ... (remaining 19838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 8221 16.06 - 32.13: 330 32.13 - 48.19: 89 48.19 - 64.26: 6 64.26 - 80.32: 5 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: 1726 0.060 - 0.119: 431 0.119 - 0.179: 62 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 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. 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: 0.940 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: 5.060 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.120 Process input model: 41.450 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 0.345 14567 Z= 0.550 Angle : 0.948 29.631 19843 Z= 0.484 Chirality : 0.054 0.299 2235 Planarity : 0.006 0.069 2442 Dihedral : 10.101 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 : 1.756 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 390 average time/residue: 0.3133 time to fit residues: 171.6864 Evaluate side-chains 226 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.685 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2964 ------------------------------------------------------------------------------- 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 14567 Z= 0.258 Angle : 0.574 9.858 19843 Z= 0.295 Chirality : 0.041 0.150 2235 Planarity : 0.005 0.053 2442 Dihedral : 5.990 84.454 2166 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 2.22 % 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: -2.38 (0.18), residues: 1701 helix: -1.19 (0.16), residues: 833 sheet: -2.13 (0.35), residues: 153 loop : -1.77 (0.21), residues: 715 *********************** 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 266 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 233 time to evaluate : 1.759 Fit side-chains outliers start: 33 outliers final: 17 residues processed: 255 average time/residue: 0.2865 time to fit residues: 104.9757 Evaluate side-chains 218 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 1.774 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1334 time to fit residues: 6.4217 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 155 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 14567 Z= 0.368 Angle : 0.614 10.516 19843 Z= 0.309 Chirality : 0.043 0.187 2235 Planarity : 0.004 0.044 2442 Dihedral : 5.969 88.234 2166 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 2.35 % 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: -1.77 (0.19), residues: 1701 helix: -0.61 (0.17), residues: 834 sheet: -1.72 (0.36), residues: 161 loop : -1.60 (0.22), residues: 706 *********************** 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 244 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 1.509 Fit side-chains outliers start: 35 outliers final: 21 residues processed: 231 average time/residue: 0.2979 time to fit residues: 97.8256 Evaluate side-chains 220 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1310 time to fit residues: 7.3318 ------------------------------------------------------------------------------- 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: 0.6980 chunk 80 optimal weight: 0.3980 chunk 17 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 165 optimal weight: 0.0970 chunk 81 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 14567 Z= 0.115 Angle : 0.485 9.893 19843 Z= 0.243 Chirality : 0.038 0.126 2235 Planarity : 0.003 0.039 2442 Dihedral : 5.410 83.006 2166 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: -0.91 (0.20), residues: 1701 helix: 0.16 (0.18), residues: 826 sheet: -1.23 (0.37), residues: 148 loop : -1.28 (0.22), residues: 727 *********************** 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 264 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 249 time to evaluate : 1.693 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 258 average time/residue: 0.3096 time to fit residues: 113.1456 Evaluate side-chains 219 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 213 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1901 time to fit residues: 4.0364 ------------------------------------------------------------------------------- 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: 10.0000 chunk 2 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 14567 Z= 0.371 Angle : 0.608 10.533 19843 Z= 0.303 Chirality : 0.044 0.180 2235 Planarity : 0.004 0.064 2442 Dihedral : 5.800 89.782 2166 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 2.02 % 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: -1.06 (0.20), residues: 1701 helix: 0.04 (0.18), residues: 837 sheet: -1.48 (0.35), residues: 168 loop : -1.32 (0.23), residues: 696 *********************** 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 239 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 209 time to evaluate : 1.646 Fit side-chains outliers start: 30 outliers final: 18 residues processed: 228 average time/residue: 0.3041 time to fit residues: 98.9224 Evaluate side-chains 216 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 1.712 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1531 time to fit residues: 7.3103 ------------------------------------------------------------------------------- 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: 9.9990 chunk 148 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3134 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= 0.348 Angle : 0.594 10.724 19843 Z= 0.297 Chirality : 0.043 0.178 2235 Planarity : 0.004 0.043 2442 Dihedral : 5.828 90.653 2166 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.55 % 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: -1.00 (0.20), residues: 1701 helix: 0.12 (0.18), residues: 829 sheet: -1.48 (0.35), residues: 170 loop : -1.31 (0.23), residues: 702 *********************** 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 232 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 209 time to evaluate : 1.632 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 224 average time/residue: 0.3040 time to fit residues: 96.9072 Evaluate side-chains 217 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 203 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1531 time to fit residues: 5.9821 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 14567 Z= 0.210 Angle : 0.531 12.034 19843 Z= 0.263 Chirality : 0.040 0.151 2235 Planarity : 0.003 0.040 2442 Dihedral : 5.572 88.231 2166 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: -0.60 (0.20), residues: 1701 helix: 0.47 (0.19), residues: 818 sheet: -1.38 (0.35), residues: 170 loop : -1.09 (0.23), residues: 713 *********************** 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 227 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 216 time to evaluate : 1.626 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 220 average time/residue: 0.3177 time to fit residues: 99.1702 Evaluate side-chains 205 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 201 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1438 time to fit residues: 3.2788 ------------------------------------------------------------------------------- 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: 3.9990 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 14567 Z= 0.313 Angle : 0.585 12.184 19843 Z= 0.292 Chirality : 0.042 0.143 2235 Planarity : 0.004 0.042 2442 Dihedral : 5.691 90.132 2166 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: -0.66 (0.20), residues: 1701 helix: 0.40 (0.18), residues: 815 sheet: -1.38 (0.35), residues: 170 loop : -1.09 (0.23), residues: 716 *********************** 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 : 1.673 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 208 average time/residue: 0.3135 time to fit residues: 92.6808 Evaluate side-chains 209 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 201 time to evaluate : 1.654 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1871 time to fit residues: 4.6421 ------------------------------------------------------------------------------- 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: 7.9990 chunk 157 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 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 522 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8696 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 14567 Z= 0.346 Angle : 0.610 13.176 19843 Z= 0.305 Chirality : 0.043 0.138 2235 Planarity : 0.004 0.040 2442 Dihedral : 5.796 91.754 2166 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.81 % 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: -0.70 (0.20), residues: 1701 helix: 0.33 (0.18), residues: 813 sheet: -1.46 (0.35), residues: 172 loop : -1.03 (0.23), residues: 716 *********************** 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 208 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 196 time to evaluate : 1.819 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 201 average time/residue: 0.3505 time to fit residues: 101.2468 Evaluate side-chains 200 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 194 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1376 time to fit residues: 3.6514 ------------------------------------------------------------------------------- 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: 0.0070 chunk 99 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 170 optimal weight: 30.0000 chunk 156 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 14567 Z= 0.227 Angle : 0.560 13.825 19843 Z= 0.281 Chirality : 0.040 0.133 2235 Planarity : 0.004 0.041 2442 Dihedral : 5.611 89.860 2166 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: -0.49 (0.20), residues: 1701 helix: 0.54 (0.19), residues: 812 sheet: -1.34 (0.35), residues: 173 loop : -0.98 (0.23), residues: 716 ********************** 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 204 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 200 time to evaluate : 1.686 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 202 average time/residue: 0.2975 time to fit residues: 85.9062 Evaluate side-chains 198 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1350 time to fit residues: 2.7900 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.096007 restraints weight = 20743.288| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.57 r_work: 0.2928 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.2905 rms_B_bonded: 1.45 restraints_weight: 0.1250 r_work: 0.2893 rms_B_bonded: 1.57 restraints_weight: 0.0625 r_work: 0.2879 rms_B_bonded: 1.73 restraints_weight: 0.0312 r_work: 0.2863 rms_B_bonded: 1.95 restraints_weight: 0.0156 r_work: 0.2845 rms_B_bonded: 2.21 restraints_weight: 0.0078 r_work: 0.2825 rms_B_bonded: 2.53 restraints_weight: 0.0039 r_work: 0.2803 rms_B_bonded: 2.92 restraints_weight: 0.0020 r_work: 0.2777 rms_B_bonded: 3.38 restraints_weight: 0.0010 r_work: 0.2748 rms_B_bonded: 3.93 restraints_weight: 0.0005 r_work: 0.2714 rms_B_bonded: 4.59 restraints_weight: 0.0002 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14567 Z= 0.193 Angle : 0.536 13.745 19843 Z= 0.268 Chirality : 0.039 0.135 2235 Planarity : 0.003 0.041 2442 Dihedral : 5.457 88.455 2166 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % 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: -0.26 (0.20), residues: 1701 helix: 0.71 (0.19), residues: 807 sheet: -1.16 (0.36), residues: 171 loop : -0.85 (0.23), residues: 723 =============================================================================== Job complete usr+sys time: 2775.79 seconds wall clock time: 51 minutes 36.51 seconds (3096.51 seconds total)