Starting phenix.real_space_refine on Sat Mar 16 08:52:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/03_2024/6tz1_20586_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/03_2024/6tz1_20586.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/03_2024/6tz1_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_20586/03_2024/6tz1_20586_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/03_2024/6tz1_20586_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/03_2024/6tz1_20586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/03_2024/6tz1_20586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/03_2024/6tz1_20586_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz1_20586/03_2024/6tz1_20586_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-dev-5265/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: 7.64, 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: 4.89 Conformation dependent library (CDL) restraints added in 2.3 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: 7.00 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: 5.08 Time building geometry restraints manager: 5.36 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: 8235 16.06 - 32.13: 339 32.13 - 48.19: 104 48.19 - 64.26: 25 64.26 - 80.32: 6 Dihedral angle restraints: 8709 sinusoidal: 3677 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 8706 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: 0.930 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: 4.380 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 44.520 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.530 ------------------------------------------------------------------------------- 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 : 10.922 80.321 5475 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 % Allowed : 4.10 % Favored : 95.43 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP A 606 HIS 0.018 0.002 HIS B 59 PHE 0.028 0.003 PHE A 234 TYR 0.035 0.003 TYR A 331 ARG 0.011 0.001 ARG A 336 *********************** 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 : 1.629 Fit side-chains revert: symmetry clash REVERT: A 430 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6889 (mp) REVERT: A 478 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7371 (mt-10) REVERT: A 483 ASP cc_start: 0.7554 (t0) cc_final: 0.6839 (t0) REVERT: A 528 ASP cc_start: 0.7508 (m-30) cc_final: 0.7208 (m-30) REVERT: A 884 MET cc_start: 0.8469 (mtt) cc_final: 0.8176 (mtt) REVERT: A 899 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6548 (mm-30) REVERT: A 906 LEU cc_start: 0.9037 (mt) cc_final: 0.8630 (mp) REVERT: A 955 ASP cc_start: 0.7155 (t0) cc_final: 0.6657 (t0) REVERT: A 1080 ARG cc_start: 0.7475 (ttt180) cc_final: 0.7147 (ttt-90) REVERT: A 1173 GLN cc_start: 0.8333 (pt0) cc_final: 0.8111 (pt0) REVERT: A 1207 ILE cc_start: 0.9122 (mm) cc_final: 0.8875 (mm) REVERT: B 400 SER cc_start: 0.9111 (t) cc_final: 0.8843 (p) REVERT: B 427 ILE cc_start: 0.8789 (mm) cc_final: 0.8509 (mt) REVERT: B 453 ASN cc_start: 0.8866 (m-40) cc_final: 0.8637 (m-40) outliers start: 7 outliers final: 0 residues processed: 390 average time/residue: 0.3170 time to fit residues: 170.0988 Evaluate side-chains 230 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 LEU 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: 0.8980 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 overall best weight: 4.7586 ------------------------------------------------------------------------------- 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 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14567 Z= 0.263 Angle : 0.574 7.867 19843 Z= 0.297 Chirality : 0.042 0.154 2235 Planarity : 0.005 0.053 2442 Dihedral : 8.811 84.663 2226 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.22 % Allowed : 8.67 % Favored : 89.11 % 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: -2.46 (0.18), residues: 1701 helix: -1.27 (0.16), residues: 834 sheet: -2.11 (0.36), residues: 153 loop : -1.81 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 606 HIS 0.005 0.001 HIS B 59 PHE 0.014 0.002 PHE A 206 TYR 0.019 0.001 TYR A 969 ARG 0.008 0.001 ARG B 252 *********************** 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 271 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 238 time to evaluate : 1.617 Fit side-chains REVERT: A 114 ASN cc_start: 0.7804 (t0) cc_final: 0.7195 (p0) REVERT: A 249 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8872 (pp) REVERT: A 341 ASP cc_start: 0.8227 (t70) cc_final: 0.7940 (t0) REVERT: A 483 ASP cc_start: 0.7653 (t0) cc_final: 0.6707 (t0) REVERT: A 528 ASP cc_start: 0.7608 (m-30) cc_final: 0.7293 (m-30) REVERT: A 768 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8094 (tt) REVERT: A 899 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6514 (mm-30) REVERT: A 908 LEU cc_start: 0.8197 (tp) cc_final: 0.7982 (tt) REVERT: A 1080 ARG cc_start: 0.7639 (ttt180) cc_final: 0.7346 (ttt-90) REVERT: B 400 SER cc_start: 0.9177 (t) cc_final: 0.8906 (p) REVERT: B 427 ILE cc_start: 0.8856 (mm) cc_final: 0.8581 (mt) outliers start: 33 outliers final: 18 residues processed: 258 average time/residue: 0.3064 time to fit residues: 112.0518 Evaluate side-chains 233 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 213 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1028 ASP Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 501 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14567 Z= 0.390 Angle : 0.621 10.845 19843 Z= 0.316 Chirality : 0.044 0.188 2235 Planarity : 0.005 0.043 2442 Dihedral : 8.735 91.187 2224 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.36 % Allowed : 9.81 % Favored : 86.83 % 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: -1.83 (0.19), residues: 1701 helix: -0.69 (0.17), residues: 839 sheet: -1.81 (0.35), residues: 168 loop : -1.56 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 606 HIS 0.006 0.001 HIS A1036 PHE 0.017 0.002 PHE A 206 TYR 0.021 0.002 TYR A 969 ARG 0.008 0.001 ARG B 252 *********************** 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 259 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 209 time to evaluate : 1.646 Fit side-chains REVERT: A 114 ASN cc_start: 0.7776 (t0) cc_final: 0.7179 (p0) REVERT: A 382 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8666 (mtpp) REVERT: A 450 ILE cc_start: 0.9220 (tp) cc_final: 0.9020 (tt) REVERT: A 483 ASP cc_start: 0.7728 (t0) cc_final: 0.6895 (t0) REVERT: A 623 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7371 (tm-30) REVERT: A 768 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8360 (tp) REVERT: A 899 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6632 (mm-30) REVERT: A 908 LEU cc_start: 0.8315 (tp) cc_final: 0.8102 (tt) REVERT: A 1080 ARG cc_start: 0.7809 (ttt180) cc_final: 0.7479 (ttt-90) REVERT: A 1130 TYR cc_start: 0.8172 (t80) cc_final: 0.7925 (t80) REVERT: B 400 SER cc_start: 0.9161 (t) cc_final: 0.8910 (p) REVERT: B 427 ILE cc_start: 0.8906 (mm) cc_final: 0.8632 (mt) outliers start: 50 outliers final: 38 residues processed: 243 average time/residue: 0.3299 time to fit residues: 113.9675 Evaluate side-chains 240 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 201 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1028 ASP Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 81 optimal weight: 0.3980 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14567 Z= 0.176 Angle : 0.500 9.615 19843 Z= 0.255 Chirality : 0.039 0.146 2235 Planarity : 0.004 0.039 2442 Dihedral : 8.418 89.689 2224 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.09 % Allowed : 11.09 % Favored : 85.82 % 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: -1.19 (0.20), residues: 1701 helix: -0.13 (0.18), residues: 839 sheet: -1.44 (0.37), residues: 150 loop : -1.34 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 606 HIS 0.003 0.001 HIS B 59 PHE 0.009 0.001 PHE A1086 TYR 0.022 0.001 TYR A 969 ARG 0.007 0.000 ARG B 252 *********************** 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 273 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 227 time to evaluate : 1.641 Fit side-chains REVERT: A 100 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8399 (ptmt) REVERT: A 101 TYR cc_start: 0.8375 (m-80) cc_final: 0.8107 (m-80) REVERT: A 114 ASN cc_start: 0.7719 (t0) cc_final: 0.7123 (p0) REVERT: A 240 ASP cc_start: 0.7466 (t0) cc_final: 0.7183 (t0) REVERT: A 249 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8898 (pp) REVERT: A 382 LYS cc_start: 0.8983 (ttmt) cc_final: 0.8713 (mtpp) REVERT: A 483 ASP cc_start: 0.7603 (t0) cc_final: 0.6585 (t0) REVERT: A 623 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7292 (tm-30) REVERT: A 768 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8349 (tp) REVERT: A 899 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6639 (mm-30) REVERT: A 1080 ARG cc_start: 0.7814 (ttt180) cc_final: 0.7510 (ttt-90) REVERT: A 1130 TYR cc_start: 0.8073 (t80) cc_final: 0.7828 (t80) REVERT: B 201 TYR cc_start: 0.8673 (m-10) cc_final: 0.8438 (m-10) REVERT: B 427 ILE cc_start: 0.8890 (mm) cc_final: 0.8599 (mt) REVERT: B 550 MET cc_start: 0.8807 (mtp) cc_final: 0.8489 (mtm) outliers start: 46 outliers final: 25 residues processed: 259 average time/residue: 0.2953 time to fit residues: 106.8398 Evaluate side-chains 236 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1028 ASP Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 514 THR 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: 4.9990 chunk 2 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.8457 moved from start: 0.2870 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= 0.285 Angle : 0.543 9.904 19843 Z= 0.275 Chirality : 0.042 0.174 2235 Planarity : 0.004 0.038 2442 Dihedral : 8.435 92.793 2224 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.49 % Allowed : 11.42 % Favored : 85.08 % 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: -1.04 (0.20), residues: 1701 helix: 0.06 (0.18), residues: 833 sheet: -1.53 (0.35), residues: 166 loop : -1.28 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 606 HIS 0.005 0.001 HIS B 542 PHE 0.011 0.001 PHE A 566 TYR 0.020 0.001 TYR A 969 ARG 0.003 0.000 ARG A1163 *********************** 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 264 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 212 time to evaluate : 1.609 Fit side-chains REVERT: A 100 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8417 (ptmt) REVERT: A 101 TYR cc_start: 0.8388 (m-80) cc_final: 0.8182 (m-80) REVERT: A 114 ASN cc_start: 0.7743 (t0) cc_final: 0.7144 (p0) REVERT: A 240 ASP cc_start: 0.7675 (t0) cc_final: 0.7255 (t0) REVERT: A 249 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8886 (pp) REVERT: A 382 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8690 (mtpp) REVERT: A 483 ASP cc_start: 0.7608 (t0) cc_final: 0.6571 (t0) REVERT: A 623 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 768 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8430 (tp) REVERT: A 812 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6072 (pmt) REVERT: A 899 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6638 (mm-30) REVERT: A 922 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7794 (mmmt) REVERT: A 1080 ARG cc_start: 0.7956 (ttt180) cc_final: 0.7658 (ttt-90) REVERT: B 427 ILE cc_start: 0.8927 (mm) cc_final: 0.8627 (mt) REVERT: B 550 MET cc_start: 0.8911 (mtp) cc_final: 0.8584 (mtm) outliers start: 52 outliers final: 39 residues processed: 246 average time/residue: 0.2987 time to fit residues: 104.4460 Evaluate side-chains 250 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 207 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1028 ASP Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 40 optimal weight: 0.2980 chunk 165 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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: 0.8422 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14567 Z= 0.168 Angle : 0.489 10.809 19843 Z= 0.247 Chirality : 0.039 0.174 2235 Planarity : 0.003 0.037 2442 Dihedral : 8.261 91.829 2224 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.29 % Allowed : 12.37 % Favored : 84.34 % 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: -0.74 (0.20), residues: 1701 helix: 0.34 (0.18), residues: 831 sheet: -1.40 (0.36), residues: 168 loop : -1.19 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 445 HIS 0.003 0.001 HIS B 59 PHE 0.008 0.001 PHE A 566 TYR 0.020 0.001 TYR A 969 ARG 0.003 0.000 ARG A1163 *********************** 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 277 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 228 time to evaluate : 1.543 Fit side-chains REVERT: A 101 TYR cc_start: 0.8264 (m-80) cc_final: 0.7938 (m-80) REVERT: A 114 ASN cc_start: 0.7614 (t0) cc_final: 0.7063 (p0) REVERT: A 240 ASP cc_start: 0.7471 (t0) cc_final: 0.7071 (t0) REVERT: A 249 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8894 (pp) REVERT: A 382 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8751 (mtpp) REVERT: A 403 GLU cc_start: 0.7865 (tp30) cc_final: 0.7622 (tp30) REVERT: A 483 ASP cc_start: 0.7533 (t0) cc_final: 0.6591 (t0) REVERT: A 623 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 768 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8398 (tt) REVERT: A 812 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.5882 (pmt) REVERT: A 899 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6608 (mm-30) REVERT: A 1080 ARG cc_start: 0.7915 (ttt180) cc_final: 0.7623 (ttt-90) REVERT: A 1130 TYR cc_start: 0.8086 (t80) cc_final: 0.7779 (t80) REVERT: B 201 TYR cc_start: 0.8686 (m-10) cc_final: 0.8411 (m-10) REVERT: B 427 ILE cc_start: 0.8935 (mm) cc_final: 0.8618 (mt) REVERT: B 550 MET cc_start: 0.8852 (mtp) cc_final: 0.8567 (mtm) outliers start: 49 outliers final: 35 residues processed: 258 average time/residue: 0.3029 time to fit residues: 110.8111 Evaluate side-chains 247 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 209 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1028 ASP Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 76 optimal weight: 0.0050 overall best weight: 3.1600 ------------------------------------------------------------------------------- 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: 0.8428 moved from start: 0.3105 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= 0.185 Angle : 0.495 11.081 19843 Z= 0.249 Chirality : 0.039 0.160 2235 Planarity : 0.003 0.039 2442 Dihedral : 8.187 92.627 2224 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.29 % Allowed : 12.70 % Favored : 84.01 % 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: -0.56 (0.20), residues: 1701 helix: 0.49 (0.19), residues: 825 sheet: -1.33 (0.36), residues: 168 loop : -1.08 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 445 HIS 0.003 0.001 HIS A1036 PHE 0.010 0.001 PHE A1086 TYR 0.020 0.001 TYR A 969 ARG 0.004 0.000 ARG A1163 *********************** 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 268 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 219 time to evaluate : 1.572 Fit side-chains REVERT: A 101 TYR cc_start: 0.8254 (m-80) cc_final: 0.7932 (m-80) REVERT: A 114 ASN cc_start: 0.7608 (t0) cc_final: 0.7072 (p0) REVERT: A 240 ASP cc_start: 0.7614 (t0) cc_final: 0.7168 (t0) REVERT: A 249 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8889 (pp) REVERT: A 382 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8756 (mtpp) REVERT: A 403 GLU cc_start: 0.7868 (tp30) cc_final: 0.7620 (tp30) REVERT: A 623 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7312 (tm-30) REVERT: A 768 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8411 (tt) REVERT: A 812 MET cc_start: 0.6532 (OUTLIER) cc_final: 0.5896 (pmt) REVERT: A 828 MET cc_start: 0.6873 (ppp) cc_final: 0.6243 (ptm) REVERT: A 899 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6644 (mm-30) REVERT: A 1080 ARG cc_start: 0.7914 (ttt180) cc_final: 0.7662 (ttt-90) REVERT: A 1136 ASN cc_start: 0.7686 (p0) cc_final: 0.7470 (p0) REVERT: B 212 ASN cc_start: 0.7894 (t0) cc_final: 0.7497 (t0) REVERT: B 427 ILE cc_start: 0.8939 (mm) cc_final: 0.8626 (mt) REVERT: B 550 MET cc_start: 0.8848 (mtp) cc_final: 0.8569 (mtm) outliers start: 49 outliers final: 41 residues processed: 251 average time/residue: 0.2976 time to fit residues: 105.7872 Evaluate side-chains 251 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 207 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1028 ASP Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 112 optimal weight: 0.4980 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14567 Z= 0.225 Angle : 0.519 11.572 19843 Z= 0.260 Chirality : 0.040 0.152 2235 Planarity : 0.003 0.040 2442 Dihedral : 8.166 94.399 2224 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.56 % Allowed : 13.17 % Favored : 83.27 % 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: -0.54 (0.20), residues: 1701 helix: 0.52 (0.19), residues: 823 sheet: -1.28 (0.36), residues: 168 loop : -1.09 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 445 HIS 0.003 0.001 HIS A1036 PHE 0.010 0.001 PHE A 566 TYR 0.019 0.001 TYR A 969 ARG 0.004 0.000 ARG A1163 *********************** 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 260 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 207 time to evaluate : 1.614 Fit side-chains REVERT: A 114 ASN cc_start: 0.7596 (t0) cc_final: 0.7066 (p0) REVERT: A 249 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8906 (pp) REVERT: A 250 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8114 (ttmm) REVERT: A 382 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8764 (mtpp) REVERT: A 403 GLU cc_start: 0.7883 (tp30) cc_final: 0.7630 (tp30) REVERT: A 623 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7289 (tm-30) REVERT: A 768 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8452 (tt) REVERT: A 812 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6078 (pmt) REVERT: A 828 MET cc_start: 0.6913 (ppp) cc_final: 0.6384 (ptm) REVERT: A 899 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6657 (mm-30) REVERT: A 911 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6587 (tp) REVERT: A 1080 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7746 (ttt-90) REVERT: A 1130 TYR cc_start: 0.7927 (t80) cc_final: 0.7582 (t80) REVERT: A 1136 ASN cc_start: 0.7665 (p0) cc_final: 0.7429 (p0) REVERT: B 212 ASN cc_start: 0.7954 (t0) cc_final: 0.7535 (t0) REVERT: B 427 ILE cc_start: 0.8946 (mm) cc_final: 0.8638 (mt) REVERT: B 550 MET cc_start: 0.8889 (mtp) cc_final: 0.8559 (mtm) outliers start: 53 outliers final: 44 residues processed: 244 average time/residue: 0.3072 time to fit residues: 106.3006 Evaluate side-chains 251 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 202 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1028 ASP Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 20.0000 chunk 157 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- 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: 0.8472 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14567 Z= 0.326 Angle : 0.567 11.877 19843 Z= 0.286 Chirality : 0.042 0.175 2235 Planarity : 0.004 0.042 2442 Dihedral : 8.263 97.321 2224 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.49 % Allowed : 13.24 % Favored : 83.27 % 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: -0.67 (0.20), residues: 1701 helix: 0.38 (0.18), residues: 824 sheet: -1.38 (0.36), residues: 170 loop : -1.10 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 445 HIS 0.005 0.001 HIS A1036 PHE 0.013 0.001 PHE A 566 TYR 0.020 0.002 TYR A 969 ARG 0.004 0.000 ARG A1163 *********************** 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 258 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 206 time to evaluate : 1.743 Fit side-chains REVERT: A 101 TYR cc_start: 0.8345 (m-80) cc_final: 0.8095 (m-80) REVERT: A 114 ASN cc_start: 0.7895 (t0) cc_final: 0.7317 (p0) REVERT: A 240 ASP cc_start: 0.7495 (t0) cc_final: 0.7185 (t0) REVERT: A 249 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8912 (pp) REVERT: A 250 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8023 (ttmm) REVERT: A 382 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8708 (mtpp) REVERT: A 483 ASP cc_start: 0.7582 (t0) cc_final: 0.6284 (t0) REVERT: A 623 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7300 (tm-30) REVERT: A 768 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8535 (tp) REVERT: A 812 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6235 (pmt) REVERT: A 828 MET cc_start: 0.6975 (ppp) cc_final: 0.6445 (ptm) REVERT: A 899 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6635 (mm-30) REVERT: A 1080 ARG cc_start: 0.8123 (ttt180) cc_final: 0.7808 (ttt-90) REVERT: B 212 ASN cc_start: 0.7983 (t0) cc_final: 0.7601 (t0) REVERT: B 427 ILE cc_start: 0.8971 (mm) cc_final: 0.8662 (mt) REVERT: B 550 MET cc_start: 0.8932 (mtp) cc_final: 0.8699 (mtm) outliers start: 52 outliers final: 45 residues processed: 241 average time/residue: 0.2987 time to fit residues: 101.9353 Evaluate side-chains 252 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 203 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1028 ASP Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 170 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 135 optimal weight: 0.0000 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14567 Z= 0.213 Angle : 0.528 13.355 19843 Z= 0.265 Chirality : 0.040 0.152 2235 Planarity : 0.003 0.042 2442 Dihedral : 8.144 96.482 2224 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.43 % Allowed : 13.51 % Favored : 83.06 % 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: 820 sheet: -1.31 (0.36), residues: 168 loop : -1.01 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 445 HIS 0.003 0.001 HIS A1036 PHE 0.009 0.001 PHE A 566 TYR 0.025 0.001 TYR A 969 ARG 0.004 0.000 ARG A1163 ********************** 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 260 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 209 time to evaluate : 1.723 Fit side-chains REVERT: A 101 TYR cc_start: 0.8272 (m-80) cc_final: 0.8004 (m-10) REVERT: A 114 ASN cc_start: 0.7715 (t0) cc_final: 0.7169 (p0) REVERT: A 240 ASP cc_start: 0.7542 (t0) cc_final: 0.7310 (t0) REVERT: A 249 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8867 (pp) REVERT: A 250 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8171 (ttmm) REVERT: A 382 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8722 (mtpp) REVERT: A 403 GLU cc_start: 0.7877 (tp30) cc_final: 0.7630 (tp30) REVERT: A 623 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7284 (tm-30) REVERT: A 768 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8501 (tp) REVERT: A 812 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6089 (pmt) REVERT: A 828 MET cc_start: 0.6977 (ppp) cc_final: 0.6377 (ptm) REVERT: A 899 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6645 (mm-30) REVERT: A 911 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6571 (tp) REVERT: A 1080 ARG cc_start: 0.8114 (ttt180) cc_final: 0.7798 (ttt-90) REVERT: B 212 ASN cc_start: 0.7933 (t0) cc_final: 0.7523 (t0) REVERT: B 321 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8277 (ttp) REVERT: B 427 ILE cc_start: 0.8959 (mm) cc_final: 0.8645 (mt) REVERT: B 550 MET cc_start: 0.8856 (mtp) cc_final: 0.8623 (mtm) outliers start: 51 outliers final: 40 residues processed: 245 average time/residue: 0.2993 time to fit residues: 103.8886 Evaluate side-chains 254 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 208 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1028 ASP Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 135 optimal weight: 0.2980 chunk 56 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- 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 = 0.3190 r_free = 0.3190 target = 0.113174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.094992 restraints weight = 20814.999| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.55 r_work: 0.2830 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14567 Z= 0.242 Angle : 0.537 13.332 19843 Z= 0.270 Chirality : 0.040 0.157 2235 Planarity : 0.003 0.042 2442 Dihedral : 8.131 97.566 2224 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.09 % Allowed : 13.91 % Favored : 83.00 % 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: -0.46 (0.20), residues: 1701 helix: 0.56 (0.19), residues: 820 sheet: -1.33 (0.36), residues: 170 loop : -0.98 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 445 HIS 0.004 0.001 HIS A1036 PHE 0.011 0.001 PHE A 566 TYR 0.024 0.001 TYR A 969 ARG 0.005 0.000 ARG A 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3124.62 seconds wall clock time: 59 minutes 2.61 seconds (3542.61 seconds total)